Sandbox Reserved 782 - Revision history

http://52.214.119.220/wiki/index.php?action=history&feed=atom&title=Sandbox_Reserved_782 Sandbox Reserved 782 - Revision history 2026-04-14T20:11:46Z Revision history for this page on the wiki MediaWiki 1.11.2 http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_782&diff=1852210&oldid=prev Student at 18:52, 15 October 2013 2013-10-15T18:52:33Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 18:52, 15 October 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 16:</td> <td colspan="2" class="diff-lineno">Line 16:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Looking at this phosphofructokinase you can see that the <scene name='56/563194/Best_interactions/5'>residues involved in ligand binding</scene> are located around both the ATP and the glycerol. The residues around the glycerol, represented in yellow, are lysine, arginine, histidine, and aspartic acid. These particular residues would be expected because they are all charged and polar, which would be ideal for interacting with glycerol (green) which is a polar molecule. The residues around ATP, in teal, are serine, lysine, and glutamic acid. These residues would also be expected because they are polar and would interact well with the polar ATP (which is in pink). In addition, the catalytic residues are represented in orange.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Looking at this phosphofructokinase you can see that the <scene name='56/563194/Best_interactions/5'>residues involved in ligand binding</scene> are located around both the ATP and the glycerol. The residues around the glycerol, represented in yellow, are lysine, arginine, histidine, and aspartic acid. These particular residues would be expected because they are all charged and polar, which would be ideal for interacting with glycerol (green) which is a polar molecule. The residues around ATP, in teal, are serine, lysine, and glutamic acid. These residues would also be expected because they are polar and would interact well with the polar ATP (which is in pink). In addition, the catalytic residues are represented in orange.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Taking a further look into the active site of the protein, one can see that phosphofructokinase contains <scene name='56/563194/Interactions_with_catalyst/2'>four catalytic residues</scene> (represented in pink), two glycines, one aspartic acid, and one alanine. This particular placement of catalytic residues is to be expected because it allows the catalytic residues to have direct contact with the ligand (the green ATP), thus enabling the reaction to proceed at a faster rate via a catalytic mechanism.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Taking a further look into the active site of the protein, one can see that phosphofructokinase contains <scene name='56/563194/Interactions_with_catalyst/2'>four catalytic residues</scene> (represented in pink), two glycines, one aspartic acid, and one alanine<ins style="color: red; font-weight: bold; text-decoration: none;">. The rest of the ligand binding residues are represented in yellow</ins>. This particular placement of catalytic residues is to be expected because it allows the catalytic residues to have direct contact with the ligand (the green ATP), thus enabling the reaction to proceed at a faster rate via a catalytic mechanism.</div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_782&diff=1852209&oldid=prev Student at 18:49, 15 October 2013 2013-10-15T18:49:51Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 18:49, 15 October 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 14:</td> <td colspan="2" class="diff-lineno">Line 14:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As previously mentioned, the hydrophobic interactions are critical in determining the protein structure. Here, the <scene name='56/563194/Solvent/1'>interactions with water</scene> show that the water molecules predominantly gather around the outside of the protein, which is where most of the hydrophilic residues lie.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As previously mentioned, the hydrophobic interactions are critical in determining the protein structure. Here, the <scene name='56/563194/Solvent/1'>interactions with water</scene> show that the water molecules predominantly gather around the outside of the protein, which is where most of the hydrophilic residues lie.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Looking at this phosphofructokinase you can see that the <scene name='56/563194/Best_interactions/<del style="color: red; font-weight: bold; text-decoration: none;">3</del>'>residues involved <del style="color: red; font-weight: bold; text-decoration: none;">with </del>ligand binding</scene><del style="color: red; font-weight: bold; text-decoration: none;">(</del>represented in yellow<del style="color: red; font-weight: bold; text-decoration: none;">) </del>are lysine, arginine, histidine, and aspartic acid. These particular residues would be expected because they are all charged and polar, which would be ideal for interacting with glycerol (green) which is a polar molecule. <del style="color: red; font-weight: bold; text-decoration: none;">In addition</del>, <del style="color: red; font-weight: bold; text-decoration: none;">the program did not specify any </del>residues <del style="color: red; font-weight: bold; text-decoration: none;">that </del>interact with the ATP <del style="color: red; font-weight: bold; text-decoration: none;">molecule </del>(in pink).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Looking at this phosphofructokinase you can see that the <scene name='56/563194/Best_interactions/<ins style="color: red; font-weight: bold; text-decoration: none;">5</ins>'>residues involved <ins style="color: red; font-weight: bold; text-decoration: none;">in </ins>ligand binding</scene> <ins style="color: red; font-weight: bold; text-decoration: none;">are located around both the ATP and the glycerol. The residues around the glycerol, </ins>represented in yellow<ins style="color: red; font-weight: bold; text-decoration: none;">, </ins>are lysine, arginine, histidine, and aspartic acid. These particular residues would be expected because they are all charged and polar, which would be ideal for interacting with glycerol (green) which is a polar molecule. <ins style="color: red; font-weight: bold; text-decoration: none;">The residues around ATP</ins>, <ins style="color: red; font-weight: bold; text-decoration: none;">in teal, are serine, lysine, and glutamic acid. These </ins>residues <ins style="color: red; font-weight: bold; text-decoration: none;">would also be expected because they are polar and would </ins>interact <ins style="color: red; font-weight: bold; text-decoration: none;">well </ins>with the <ins style="color: red; font-weight: bold; text-decoration: none;">polar </ins>ATP (<ins style="color: red; font-weight: bold; text-decoration: none;">which is </ins>in pink)<ins style="color: red; font-weight: bold; text-decoration: none;">. In addition, the catalytic residues are represented in orange</ins>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Taking a further look into the active site of the protein, one can see that phosphofructokinase contains <scene name='56/563194/Interactions_with_catalyst/2'>four catalytic residues</scene> (represented in pink), two glycines, one aspartic acid, and one alanine. This particular placement of catalytic residues is to be expected because it allows the catalytic residues to have direct contact with the ligand (the green ATP), thus enabling the reaction to proceed at a faster rate via a catalytic mechanism.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Taking a further look into the active site of the protein, one can see that phosphofructokinase contains <scene name='56/563194/Interactions_with_catalyst/2'>four catalytic residues</scene> (represented in pink), two glycines, one aspartic acid, and one alanine. This particular placement of catalytic residues is to be expected because it allows the catalytic residues to have direct contact with the ligand (the green ATP), thus enabling the reaction to proceed at a faster rate via a catalytic mechanism.</div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_782&diff=1852196&oldid=prev Student at 18:22, 15 October 2013 2013-10-15T18:22:43Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 18:22, 15 October 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 4:</td> <td colspan="2" class="diff-lineno">Line 4:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><Structure load='3ie7' size='500' frame='true' align='right' caption='Phosphofructokinase from Listeria' scene='Scene 1' /></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><Structure load='3ie7' size='500' frame='true' align='right' caption='Phosphofructokinase from Listeria' scene='Scene 1' /></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Phosphofructokinase==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Phosphofructokinase==</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><scene name='56/563194/Phosphofructokinase_scene_1/1'>Phosphofructokinase</scene> is <del style="color: red; font-weight: bold; text-decoration: none;">an </del>enzyme that is involved in <del style="color: red; font-weight: bold; text-decoration: none;">the process of </del>glycolysis. The particular reaction that it carries out is the catalysis of fructose-6-phosphate to fructose-1,6- bisphosphate via phosphorylation. The phosphofructokinase that is discussed on this page comes from the microbe ''Listeria innocua''. At the center you can see that the phosphofructokinase is bound to a molecule of ATP. In addition, the three green balls represent the three Mg atoms, and the small grey and red group off to the side is the glycerol.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><scene name='56/563194/Phosphofructokinase_scene_1/1'>Phosphofructokinase</scene> is <ins style="color: red; font-weight: bold; text-decoration: none;">a regulatory </ins>enzyme that is involved in glycolysis. The particular reaction that it carries out is the catalysis of fructose-6-phosphate to fructose-1,6- bisphosphate via phosphorylation. The phosphofructokinase that is discussed on this page comes from the microbe ''Listeria innocua''. At the center you can see that the phosphofructokinase is bound to a molecule of ATP. In addition, the three green balls represent the three Mg atoms, and the small grey and red group off to the side is the glycerol.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The secondary structure is comprised of <scene name='56/563194/Alpha_helices_and_beta_sheets/1'>10 alpha-helices and 14 beta-sheets</scene>. The alpha helices are in yellow and the beta sheets are in grey.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The secondary structure is comprised of <scene name='56/563194/Alpha_helices_and_beta_sheets/1'>10 alpha-helices and 14 beta-sheets</scene>. The alpha helices are in yellow and the beta sheets are in grey.</div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_782&diff=1852195&oldid=prev Student at 18:20, 15 October 2013 2013-10-15T18:20:37Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 18:20, 15 October 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 4:</td> <td colspan="2" class="diff-lineno">Line 4:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><Structure load='3ie7' size='500' frame='true' align='right' caption='Phosphofructokinase from Listeria' scene='Scene 1' /></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><Structure load='3ie7' size='500' frame='true' align='right' caption='Phosphofructokinase from Listeria' scene='Scene 1' /></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Phosphofructokinase==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Phosphofructokinase==</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">This is the enzyme </del><scene name='56/563194/Phosphofructokinase_scene_1/1'>Phosphofructokinase</scene>. <del style="color: red; font-weight: bold; text-decoration: none;">This </del>particular phosphofructokinase <del style="color: red; font-weight: bold; text-decoration: none;"> </del>comes from the microbe Listeria innocua. At the center you can see that the phosphofructokinase is bound to a molecule of ATP. In addition, the three green balls represent the three Mg atoms, and the small grey and red group off to the side is the glycerol.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><scene name='56/563194/Phosphofructokinase_scene_1/1'>Phosphofructokinase</scene> <ins style="color: red; font-weight: bold; text-decoration: none;">is an enzyme that is involved in the process of glycolysis</ins>. <ins style="color: red; font-weight: bold; text-decoration: none;">The </ins>particular <ins style="color: red; font-weight: bold; text-decoration: none;">reaction that it carries out is the catalysis of fructose-6-phosphate to fructose-1,6- bisphosphate via phosphorylation. The </ins>phosphofructokinase <ins style="color: red; font-weight: bold; text-decoration: none;">that is discussed on this page </ins>comes from the microbe <ins style="color: red; font-weight: bold; text-decoration: none;">''</ins>Listeria innocua<ins style="color: red; font-weight: bold; text-decoration: none;">''</ins>. At the center you can see that the phosphofructokinase is bound to a molecule of ATP. In addition, the three green balls represent the three Mg atoms, and the small grey and red group off to the side is the glycerol.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The secondary structure is comprised of <scene name='56/563194/Alpha_helices_and_beta_sheets/1'>10 alpha-helices and 14 beta-sheets</scene>. The alpha helices are in yellow and the beta sheets are in grey.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The secondary structure is comprised of <scene name='56/563194/Alpha_helices_and_beta_sheets/1'>10 alpha-helices and 14 beta-sheets</scene>. The alpha helices are in yellow and the beta sheets are in grey.</div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_782&diff=1852096&oldid=prev Student at 00:10, 14 October 2013 2013-10-14T00:10:55Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 00:10, 14 October 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 14:</td> <td colspan="2" class="diff-lineno">Line 14:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As previously mentioned, the hydrophobic interactions are critical in determining the protein structure. Here, the <scene name='56/563194/Solvent/1'>interactions with water</scene> show that the water molecules predominantly gather around the outside of the protein, which is where most of the hydrophilic residues lie.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As previously mentioned, the hydrophobic interactions are critical in determining the protein structure. Here, the <scene name='56/563194/Solvent/1'>interactions with water</scene> show that the water molecules predominantly gather around the outside of the protein, which is where most of the hydrophilic residues lie.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Looking at this phosphofructokinase you can see that the <scene name='56/563194/Best_interactions/<del style="color: red; font-weight: bold; text-decoration: none;">2</del>'>residues involved with ligand binding</scene> (represented in yellow) are lysine, arginine, histidine, and aspartic acid. These particular residues would be expected because they are all charged and polar, which would be ideal for interacting with glycerol (green) which is a polar molecule. In addition, the program did not specify any residues that interact with the ATP molecule (in pink).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Looking at this phosphofructokinase you can see that the <scene name='56/563194/Best_interactions/<ins style="color: red; font-weight: bold; text-decoration: none;">3</ins>'>residues involved with ligand binding</scene>(represented in yellow) are lysine, arginine, histidine, and aspartic acid. These particular residues would be expected because they are all charged and polar, which would be ideal for interacting with glycerol (green) which is a polar molecule. In addition, the program did not specify any residues that interact with the ATP molecule (in pink).</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Taking a further look into the active site of the protein, one can see that phosphofructokinase contains <scene name='56/563194/Interactions_with_catalyst/<del style="color: red; font-weight: bold; text-decoration: none;">1</del>'> four catalytic residues</scene> (represented in pink), two glycines, one aspartic acid, and one alanine. This particular placement of catalytic residues is to be expected because it allows the catalytic residues to have direct contact with the ligand, thus enabling the reaction to proceed at a faster rate via a catalytic mechanism.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Taking a further look into the active site of the protein, one can see that phosphofructokinase contains <scene name='56/563194/Interactions_with_catalyst/<ins style="color: red; font-weight: bold; text-decoration: none;">2</ins>'>four catalytic residues</scene> (represented in pink), two glycines, one aspartic acid, and one alanine. This particular placement of catalytic residues is to be expected because it allows the catalytic residues to have direct contact with the ligand <ins style="color: red; font-weight: bold; text-decoration: none;">(the green ATP)</ins>, thus enabling the reaction to proceed at a faster rate via a catalytic mechanism.</div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_782&diff=1852095&oldid=prev Student at 00:04, 14 October 2013 2013-10-14T00:04:38Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 00:04, 14 October 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 6:</td> <td colspan="2" class="diff-lineno">Line 6:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This is the enzyme <scene name='56/563194/Phosphofructokinase_scene_1/1'>Phosphofructokinase</scene>. This particular phosphofructokinase comes from the microbe Listeria innocua. At the center you can see that the phosphofructokinase is bound to a molecule of ATP. In addition, the three green balls represent the three Mg atoms, and the small grey and red group off to the side is the glycerol.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This is the enzyme <scene name='56/563194/Phosphofructokinase_scene_1/1'>Phosphofructokinase</scene>. This particular phosphofructokinase comes from the microbe Listeria innocua. At the center you can see that the phosphofructokinase is bound to a molecule of ATP. In addition, the three green balls represent the three Mg atoms, and the small grey and red group off to the side is the glycerol.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The secondary structure is comprised of <scene name='56/563194/Alpha_helices_and_beta_sheets/1'>alpha helices and beta sheets</scene>. The alpha helices are in yellow and the beta sheets are in grey.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The secondary structure is comprised of <scene name='56/563194/Alpha_helices_and_beta_sheets/1'><ins style="color: red; font-weight: bold; text-decoration: none;">10 </ins>alpha<ins style="color: red; font-weight: bold; text-decoration: none;">-</ins>helices and <ins style="color: red; font-weight: bold; text-decoration: none;">14 </ins>beta<ins style="color: red; font-weight: bold; text-decoration: none;">-</ins>sheets</scene>. <ins style="color: red; font-weight: bold; text-decoration: none;"> </ins>The alpha helices are in yellow and the beta sheets are in grey.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><scene name='56/563194/Phosphofructokinase_hbonds/1'>Hydrogen bonding</scene> is a very important part of a proteins structure and stability. The hydrogen bonds of phosphofructokinase are designated by the orange dotted lines throughout the structure. Phosphofructokinase contains both anti-parallel and parallel sheets, which are identified by parallel hydrogen bonds and angled hydrogen bonds respectively.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><scene name='56/563194/Phosphofructokinase_hbonds/1'>Hydrogen bonding</scene> is a very important part of a proteins structure and stability. The hydrogen bonds of phosphofructokinase are designated by the orange dotted lines throughout the structure. Phosphofructokinase contains both anti-parallel and parallel sheets, which are identified by parallel hydrogen bonds and angled hydrogen bonds respectively.</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 14:</td> <td colspan="2" class="diff-lineno">Line 14:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As previously mentioned, the hydrophobic interactions are critical in determining the protein structure. Here, the <scene name='56/563194/Solvent/1'>interactions with water</scene> show that the water molecules predominantly gather around the outside of the protein, which is where most of the hydrophilic residues lie.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As previously mentioned, the hydrophobic interactions are critical in determining the protein structure. Here, the <scene name='56/563194/Solvent/1'>interactions with water</scene> show that the water molecules predominantly gather around the outside of the protein, which is where most of the hydrophilic residues lie.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">The active site of a protein is the part that binds with substrates to catalyze a given reaction. </del>Looking at phosphofructokinase you can see that the <scene name='56/563194/<del style="color: red; font-weight: bold; text-decoration: none;">Alternate_interactions</del>/<del style="color: red; font-weight: bold; text-decoration: none;">1</del>'><del style="color: red; font-weight: bold; text-decoration: none;">proteins </del>involved with ligand <del style="color: red; font-weight: bold; text-decoration: none;">interactions</del></scene> are <del style="color: red; font-weight: bold; text-decoration: none;">mostly polar </del>residues<del style="color: red; font-weight: bold; text-decoration: none;">. This </del>would be expected because.<del style="color: red; font-weight: bold; text-decoration: none;">.</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Looking at <ins style="color: red; font-weight: bold; text-decoration: none;">this </ins>phosphofructokinase you can see that the <scene name='56/563194/<ins style="color: red; font-weight: bold; text-decoration: none;">Best_interactions</ins>/<ins style="color: red; font-weight: bold; text-decoration: none;">2</ins>'><ins style="color: red; font-weight: bold; text-decoration: none;">residues </ins>involved with ligand <ins style="color: red; font-weight: bold; text-decoration: none;">binding</ins></scene> <ins style="color: red; font-weight: bold; text-decoration: none;">(represented in yellow) </ins>are <ins style="color: red; font-weight: bold; text-decoration: none;">lysine, arginine, histidine, and aspartic acid. These particular </ins>residues would be expected because <ins style="color: red; font-weight: bold; text-decoration: none;">they are all charged and polar, which would be ideal for interacting with glycerol (green) which is a polar molecule</ins>. <ins style="color: red; font-weight: bold; text-decoration: none;">In addition, the program did not specify any residues that interact with the ATP molecule (in pink)</ins>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Taking a further look into the active site, <del style="color: red; font-weight: bold; text-decoration: none;">One </del>can see that phosphofructokinase contains <scene name='56/563194/Interactions_with_catalyst/1'>catalytic residues</scene><del style="color: red; font-weight: bold; text-decoration: none;">, </del>represented in pink, <del style="color: red; font-weight: bold; text-decoration: none;">in the heart of the active site</del>. This particular placement of catalytic residues is to be expected because it allows the catalytic residues to have direct contact with the ligand, thus enabling the reaction to proceed at a faster rate via a catalytic mechanism.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Taking a further look into the active site <ins style="color: red; font-weight: bold; text-decoration: none;">of the protein</ins>, <ins style="color: red; font-weight: bold; text-decoration: none;">one </ins>can see that phosphofructokinase contains <scene name='56/563194/Interactions_with_catalyst/1'> <ins style="color: red; font-weight: bold; text-decoration: none;">four </ins>catalytic residues</scene> <ins style="color: red; font-weight: bold; text-decoration: none;">(</ins>represented in pink<ins style="color: red; font-weight: bold; text-decoration: none;">)</ins>, <ins style="color: red; font-weight: bold; text-decoration: none;">two glycines, one aspartic acid, and one alanine</ins>. This particular placement of catalytic residues is to be expected because it allows the catalytic residues to have direct contact with the ligand, thus enabling the reaction to proceed at a faster rate via a catalytic mechanism.</div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_782&diff=1852094&oldid=prev Student at 23:41, 13 October 2013 2013-10-13T23:41:55Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 23:41, 13 October 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><scene name='56/563194/Phosphofructokinase_hbonds/1'>Hydrogen bonding</scene> is a very important part of a proteins structure and stability. The hydrogen bonds of phosphofructokinase are designated by the orange dotted lines throughout the structure. Phosphofructokinase contains both anti-parallel and parallel sheets, which are identified by parallel hydrogen bonds and angled hydrogen bonds respectively.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><scene name='56/563194/Phosphofructokinase_hbonds/1'>Hydrogen bonding</scene> is a very important part of a proteins structure and stability. The hydrogen bonds of phosphofructokinase are designated by the orange dotted lines throughout the structure. Phosphofructokinase contains both anti-parallel and parallel sheets, which are identified by parallel hydrogen bonds and angled hydrogen bonds respectively.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>One of the most important determining factors of protein structure lies in <del style="color: red; font-weight: bold; text-decoration: none;">hydrophobic </del>interactions <del style="color: red; font-weight: bold; text-decoration: none;">between </del>the <scene name='56/563194/Phobic_vs_philic/1'>hydrophobic and hydrophilic residues</scene> with the surrounding environment. The hydrophobic residues are designated with light green while the hydrophobic residues are shown in blue. As would be expected the majority of the hydrophobic residues are located at the center of the protein where they are shielded from the hydrophobic environment.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>One of the most important determining factors of protein structure lies in <ins style="color: red; font-weight: bold; text-decoration: none;">the </ins>interactions <ins style="color: red; font-weight: bold; text-decoration: none;">of </ins>the <scene name='56/563194/Phobic_vs_philic/1'>hydrophobic and hydrophilic residues</scene> with the surrounding environment. The hydrophobic residues are designated with light green while the hydrophobic residues are shown in blue. As would be expected the majority of the hydrophobic residues are located at the center of the protein where they are shielded from the hydrophobic environment.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As previously mentioned, the hydrophobic interactions are critical in determining the protein structure. Here, the <scene name='56/563194/Solvent/1'>interactions with water</scene> show that the water molecules predominantly gather around the outside of the protein, which is where most of the hydrophilic residues lie.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As previously mentioned, the hydrophobic interactions are critical in determining the protein structure. Here, the <scene name='56/563194/Solvent/1'>interactions with water</scene> show that the water molecules predominantly gather around the outside of the protein, which is where most of the hydrophilic residues lie.</div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_782&diff=1852093&oldid=prev Student at 23:38, 13 October 2013 2013-10-13T23:38:29Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 23:38, 13 October 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 8:</td> <td colspan="2" class="diff-lineno">Line 8:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The secondary structure is comprised of <scene name='56/563194/Alpha_helices_and_beta_sheets/1'>alpha helices and beta sheets</scene>. The alpha helices are in yellow and the beta sheets are in grey.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The secondary structure is comprised of <scene name='56/563194/Alpha_helices_and_beta_sheets/1'>alpha helices and beta sheets</scene>. The alpha helices are in yellow and the beta sheets are in grey.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><scene name='56/563194/Phosphofructokinase_hbonds/1'>Hydrogen bonding</scene> is a very important part of <del style="color: red; font-weight: bold; text-decoration: none;">protein </del>structure <del style="color: red; font-weight: bold; text-decoration: none;">shape </del>and stability. The hydrogen bonds of phosphofructokinase are designated by the orange dotted lines throughout the structure. Phosphofructokinase contains both anti-parallel and parallel sheets, which are identified by parallel hydrogen bonds and angled hydrogen bonds respectively.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><scene name='56/563194/Phosphofructokinase_hbonds/1'>Hydrogen bonding</scene> is a very important part of <ins style="color: red; font-weight: bold; text-decoration: none;">a proteins </ins>structure and stability. The hydrogen bonds of phosphofructokinase are designated by the orange dotted lines throughout the structure. Phosphofructokinase contains both anti-parallel and parallel sheets, which are identified by parallel hydrogen bonds and angled hydrogen bonds respectively.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>One of the most important determining factors of protein structure lies in hydrophobic interactions between the <scene name='56/563194/Phobic_vs_philic/1'>hydrophobic and hydrophilic residues</scene> with the surrounding environment. The hydrophobic residues are designated with light green while the hydrophobic residues are shown in blue. As would be expected the majority of the hydrophobic residues are located at the center of the protein where they are shielded from the hydrophobic environment.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>One of the most important determining factors of protein structure lies in hydrophobic interactions between the <scene name='56/563194/Phobic_vs_philic/1'>hydrophobic and hydrophilic residues</scene> with the surrounding environment. The hydrophobic residues are designated with light green while the hydrophobic residues are shown in blue. As would be expected the majority of the hydrophobic residues are located at the center of the protein where they are shielded from the hydrophobic environment.</div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_782&diff=1852092&oldid=prev Student at 23:37, 13 October 2013 2013-10-13T23:37:28Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 23:37, 13 October 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 6:</td> <td colspan="2" class="diff-lineno">Line 6:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This is the enzyme <scene name='56/563194/Phosphofructokinase_scene_1/1'>Phosphofructokinase</scene>. This particular phosphofructokinase comes from the microbe Listeria innocua. At the center you can see that the phosphofructokinase is bound to a molecule of ATP. In addition, the three green balls represent the three Mg atoms, and the small grey and red group off to the side is the glycerol.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This is the enzyme <scene name='56/563194/Phosphofructokinase_scene_1/1'>Phosphofructokinase</scene>. This particular phosphofructokinase comes from the microbe Listeria innocua. At the center you can see that the phosphofructokinase is bound to a molecule of ATP. In addition, the three green balls represent the three Mg atoms, and the small grey and red group off to the side is the glycerol.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The <del style="color: red; font-weight: bold; text-decoration: none;">majority of the phosphofructokinase </del>structure is <del style="color: red; font-weight: bold; text-decoration: none;">made up </del>of <scene name='56/563194/Alpha_helices_and_beta_sheets/1'>alpha helices and beta sheets</scene>. The alpha helices are in yellow and the beta sheets are in grey.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The <ins style="color: red; font-weight: bold; text-decoration: none;">secondary </ins>structure is <ins style="color: red; font-weight: bold; text-decoration: none;">comprised </ins>of <scene name='56/563194/Alpha_helices_and_beta_sheets/1'>alpha helices and beta sheets</scene>. The alpha helices are in yellow and the beta sheets are in grey.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><scene name='56/563194/Phosphofructokinase_hbonds/1'>Hydrogen bonding</scene> is a very important part of protein structure shape and stability. The hydrogen bonds of phosphofructokinase are designated by the orange dotted lines throughout the structure. Phosphofructokinase contains both anti-parallel and parallel sheets, which are identified by parallel hydrogen bonds and angled hydrogen bonds respectively.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><scene name='56/563194/Phosphofructokinase_hbonds/1'>Hydrogen bonding</scene> is a very important part of protein structure shape and stability. The hydrogen bonds of phosphofructokinase are designated by the orange dotted lines throughout the structure. Phosphofructokinase contains both anti-parallel and parallel sheets, which are identified by parallel hydrogen bonds and angled hydrogen bonds respectively.</div></td></tr> </table>

Student http://52.214.119.220/wiki/index.php?title=Sandbox_Reserved_782&diff=1852091&oldid=prev Student at 23:35, 13 October 2013 2013-10-13T23:35:49Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 23:35, 13 October 2013</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 4:</td> <td colspan="2" class="diff-lineno">Line 4:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><Structure load='3ie7' size='500' frame='true' align='right' caption='Phosphofructokinase from Listeria' scene='Scene 1' /></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><Structure load='3ie7' size='500' frame='true' align='right' caption='Phosphofructokinase from Listeria' scene='Scene 1' /></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Phosphofructokinase==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Phosphofructokinase==</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>This is the <scene name='56/563194/Phosphofructokinase_scene_1/1'><del style="color: red; font-weight: bold; text-decoration: none;">Secondary Structure</del></scene> <del style="color: red; font-weight: bold; text-decoration: none;">of Phosphofructokinase</del>. <del style="color: red; font-weight: bold; text-decoration: none;">The Purple designates </del>the <del style="color: red; font-weight: bold; text-decoration: none;">alpha helices</del>...<del style="color: red; font-weight: bold; text-decoration: none;">finish description</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>This is the <ins style="color: red; font-weight: bold; text-decoration: none;">enzyme </ins><scene name='56/563194/Phosphofructokinase_scene_1/1'><ins style="color: red; font-weight: bold; text-decoration: none;">Phosphofructokinase</ins></scene>. <ins style="color: red; font-weight: bold; text-decoration: none;">This particular phosphofructokinase comes from </ins>the <ins style="color: red; font-weight: bold; text-decoration: none;">microbe Listeria innocua</ins>. <ins style="color: red; font-weight: bold; text-decoration: none;">At the center you can see that the phosphofructokinase is bound to a molecule of ATP</ins>. <ins style="color: red; font-weight: bold; text-decoration: none;">In addition, the three green balls represent the three Mg atoms, and the small grey and red group off to the side is the glycerol</ins>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The <del style="color: red; font-weight: bold; text-decoration: none;">bulk </del>of <del style="color: red; font-weight: bold; text-decoration: none;">this proteins </del>structure is made up of <scene name='56/563194/Alpha_helices_and_beta_sheets/1'>alpha helices and beta sheets</scene> <del style="color: red; font-weight: bold; text-decoration: none;">the </del>alpha helices are in yellow and the beta sheets are in grey<del style="color: red; font-weight: bold; text-decoration: none;">. In addition the three green balls represent the three Mg atoms, the internal compound is ATP and the small grey and red group off to the side is the glycerol</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The <ins style="color: red; font-weight: bold; text-decoration: none;">majority </ins>of <ins style="color: red; font-weight: bold; text-decoration: none;">the phosphofructokinase </ins>structure is made up of <scene name='56/563194/Alpha_helices_and_beta_sheets/1'>alpha helices and beta sheets</scene><ins style="color: red; font-weight: bold; text-decoration: none;">. The </ins>alpha helices are in yellow and the beta sheets are in grey.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><scene name='56/563194/Phosphofructokinase_hbonds/1'>Hydrogen bonding</scene> is a very important part of protein structure shape and stability. The hydrogen bonds of phosphofructokinase are designated by the orange dotted lines throughout the structure. Phosphofructokinase contains both anti-parallel and parallel sheets, which are identified by parallel hydrogen bonds and angled hydrogen bonds respectively.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><scene name='56/563194/Phosphofructokinase_hbonds/1'>Hydrogen bonding</scene> is a very important part of protein structure shape and stability. The hydrogen bonds of phosphofructokinase are designated by the orange dotted lines throughout the structure. Phosphofructokinase contains both anti-parallel and parallel sheets, which are identified by parallel hydrogen bonds and angled hydrogen bonds respectively.</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 14:</td> <td colspan="2" class="diff-lineno">Line 14:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As previously mentioned, the hydrophobic interactions are critical in determining the protein structure. Here, the <scene name='56/563194/Solvent/1'>interactions with water</scene> show that the water molecules predominantly gather around the outside of the protein, which is where most of the hydrophilic residues lie.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As previously mentioned, the hydrophobic interactions are critical in determining the protein structure. Here, the <scene name='56/563194/Solvent/1'>interactions with water</scene> show that the water molecules predominantly gather around the outside of the protein, which is where most of the hydrophilic residues lie.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><scene name='56/563194/<del style="color: red; font-weight: bold; text-decoration: none;">Interactions</del>/1'><del style="color: red; font-weight: bold; text-decoration: none;">interactions </del>with <del style="color: red; font-weight: bold; text-decoration: none;">ligands</del></scene> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">The active site of a protein is the part that binds with substrates to catalyze a given reaction. Looking at phosphofructokinase you can see that the </ins><scene name='56/563194/<ins style="color: red; font-weight: bold; text-decoration: none;">Alternate_interactions</ins>/1'><ins style="color: red; font-weight: bold; text-decoration: none;">proteins involved </ins>with <ins style="color: red; font-weight: bold; text-decoration: none;">ligand interactions</ins></scene> <ins style="color: red; font-weight: bold; text-decoration: none;">are mostly polar residues. This would be expected because...</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">Or alternate interactions showing the ATP molecule in green, with the ligands in yellow? <scene name='56/563194/Alternate_interactions/1'>Alternate interaction</scene></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Taking a further look into the active site, One can see that phosphofructokinase contains <scene name='56/563194/Interactions_with_catalyst/1'>catalytic residues</scene>, represented in pink, in the heart of the active site. This <ins style="color: red; font-weight: bold; text-decoration: none;">particular </ins>placement <ins style="color: red; font-weight: bold; text-decoration: none;">of catalytic residues </ins>is to be expected because it allows the catalytic residues to have direct contact with the ligand, thus enabling the reaction to proceed at a faster rate via a catalytic mechanism.</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Taking a further look into the active site, One can see that phosphofructokinase contains <scene name='56/563194/Interactions_with_catalyst/1'>catalytic residues</scene>, represented in pink, in the heart of the active site. This placement <del style="color: red; font-weight: bold; text-decoration: none;">is to be expected </del>is to be expected because it allows the catalytic residues to have direct contact with the ligand, thus enabling the reaction to proceed at a faster rate via a catalytic mechanism.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> </table>

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