3rz5 - Revision history

OCA at 09:46, 1 March 2024

2024-03-01T09:46:22Z

←Older revision		Revision as of 09:46, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3rz5' size='340' side='right'caption='[[3rz5]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='3rz5' size='340' side='right'caption='[[3rz5]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rz5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RZ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RZ5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rz5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RZ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RZ5 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=RZ5:N~~-~~PENTYL-4-SULFAMOYLBENZAMIDE'>RZ5</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.65Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3ryv\|3ryv]], [[3ryx\|3ryx]], [[3ryy\|3ryy]], [[3ryz\|3ryz]], [[3rz0\|3rz0]], [[3rz1\|3rz1]], [[3ryj\|3ryj]], [[3rz7\|3rz7]], [[3rz8\|3rz8]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=RZ5:N-PENTYL-4-SULFAMOYLBENZAMIDE'>RZ5</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~CA2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN])</td~~></tr>	+
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1]~~ </~~span~~></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3rz5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rz5 OCA], [https://pdbe.org/3rz5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rz5 RCSB], [https://www.ebi.ac.uk/pdbsum/3rz5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rz5 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3rz5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rz5 OCA], [https://pdbe.org/3rz5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rz5 RCSB], [https://www.ebi.ac.uk/pdbsum/3rz5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rz5 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[https://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Defects in CA2 are the cause of osteopetrosis autosomal recessive type 3 (OPTB3) [MIM:[https://omim.org/entry/259730 259730]]; also known as osteopetrosis with renal tubular acidosis, carbonic anhydrase II deficiency syndrome, Guibaud-Vainsel syndrome or marble brain disease. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. The disorder occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Autosomal recessive osteopetrosis is usually associated with normal or elevated amount of non-functional osteoclasts. OPTB3 is associated with renal tubular acidosis, cerebral calcification (marble brain disease) and in some cases with mental retardation.<ref>PMID:1928091</ref> <ref>PMID:1542674</ref> <ref>PMID:8834238</ref> <ref>PMID:9143915</ref> <ref>PMID:15300855</ref>	+	[https://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN] Defects in CA2 are the cause of osteopetrosis autosomal recessive type 3 (OPTB3) [MIM:[https://omim.org/entry/259730 259730]; also known as osteopetrosis with renal tubular acidosis, carbonic anhydrase II deficiency syndrome, Guibaud-Vainsel syndrome or marble brain disease. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. The disorder occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Autosomal recessive osteopetrosis is usually associated with normal or elevated amount of non-functional osteoclasts. OPTB3 is associated with renal tubular acidosis, cerebral calcification (marble brain disease) and in some cases with mental retardation.<ref>PMID:1928091</ref> <ref>PMID:1542674</ref> <ref>PMID:8834238</ref> <ref>PMID:9143915</ref> <ref>PMID:15300855</ref>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Essential for bone resorption and osteoclast differentiation (By similarity). Reversible hydration of carbon dioxide. Can hydrate cyanamide to urea. Involved in the regulation of fluid secretion into the anterior chamber of the eye.<ref>PMID:10550681</ref> <ref>PMID:11831900</ref>	+	[https://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN] Essential for bone resorption and osteoclast differentiation (By similarity). Reversible hydration of carbon dioxide. Can hydrate cyanamide to urea. Involved in the regulation of fluid secretion into the anterior chamber of the eye.<ref>PMID:10550681</ref> <ref>PMID:11831900</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The hydrophobic effect-the free-energetically favorable association of non-polar solutes in water- makes a dominant contribution to binding of many systems of ligands and proteins. The objective of this study was to examine the hydrophobic effect in biomolecular recognition using two chemically different, but structurally similar hydrophobic groups-aliphatic hydrocarbons and aliphatic fluorocarbons-and to determine whether the hydrophobicity of the two groups could be distinguished by thermodynamic and biostructural analysis. This paper uses isothermal titration calorimetry (ITC) to examine the thermodynamics of binding of benzenesulfonamides substituted in the para position with alkyl and fluoroalkyl chains (H2NSO2C6H4-CONHCH2(CX2)nCX3, n = 0-4, X = H, F) to human carbonic anhydrase II (HCA II). Both alkyl and fluoroalkyl substituents contribute favorably to the enthalpy and the entropy of binding; these contributions increase as the length of chain of the hydrophobic substituent increases. Crystallography of the protein-ligand complexes indicates that the benzenesulfonamide groups of all ligands examined bind with similar geometry, that the tail groups associate with the hydrophobic wall of HCA II (which is made up of the side chains of residues Phe131, Val135, Pro202, and Leu204), and that the structure of the protein is indistinguishable for all but one of the complexes (the longest member of the fluoroalkyl series). Analysis of the thermodynamics of binding as a function of structure is compatible with the hypothesis that hydrophobic binding of both alkyl and fluoroalkyl chains to hydrophobic surface of carbonic anhydrase is due primarily to the release of non-optimally hydrogen-bonded water molecules that hydrate the binding cavity (including the hydrophobic wall) of HCA II and to the release of water molecules that surround the hydrophobic chain of the ligands. This study defines the balance of enthalpic and entropic contributions to the hydrophobic effect in this representative system of protein and ligand: hydrophobic interactions, here, seem to comprise approximately equal contributions from enthalpy (plausibly from strengthening networks among molecules of water hydrogen bonds) and entropy (from release of water from configurationally restricted positions).	+
-		+
-	Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the ''Hydrophobic Wall'' of Carbonic Anhydrase.,Mecinovic J, Snyder PW, Mirica KA, Bai S, Mack ET, Kwant RL, Moustakas DT, Heroux A, Whitesides GM J Am Chem Soc. 2011 Jul 26. PMID:21790183<ref>PMID:21790183</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3rz5" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 30:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Carbonate dehydratase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bai, S]]	+	[[Category: Bai S]]
-	[[Category: Heroux, A]]	+	[[Category: Heroux A]]
-	[[Category: Snyder~~, P W~~]]	+	[[Category: Snyder PW]]
-	[[Category: Whitesides~~, G W]]~~	+	[[Category: Whitesides GW]]
-	~~[[Category: Alpha beta]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 10:31, 22 June 2022

2022-06-22T10:31:05Z

←Older revision		Revision as of 10:31, 22 June 2022
Line 1:		Line 1:

	==Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase==		==Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase==
-	<StructureSection load='3rz5' size='340' side='right' caption='[[3rz5]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='3rz5' size='340' side='right'caption='[[3rz5]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rz5]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RZ5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3RZ5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rz5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RZ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RZ5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=RZ5:N-PENTYL-4-SULFAMOYLBENZAMIDE'>RZ5</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=RZ5:N-PENTYL-4-SULFAMOYLBENZAMIDE'>RZ5</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ryv\|3ryv]], [[3ryx\|3ryx]], [[3ryy\|3ryy]], [[3ryz\|3ryz]], [[3rz0\|3rz0]], [[3rz1\|3rz1]], [[3ryj\|3ryj]], [[3rz7\|3rz7]], [[3rz8\|3rz8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ryv\|3ryv]], [[3ryx\|3ryx]], [[3ryy\|3ryy]], [[3ryz\|3ryz]], [[3rz0\|3rz0]], [[3rz1\|3rz1]], [[3ryj\|3ryj]], [[3rz7\|3rz7]], [[3rz8\|3rz8]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CA2 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CA2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3rz5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rz5 OCA], [~~http~~://pdbe.org/3rz5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3rz5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3rz5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3rz5 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3rz5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rz5 OCA], [https://pdbe.org/3rz5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rz5 RCSB], [https://www.ebi.ac.uk/pdbsum/3rz5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rz5 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Defects in CA2 are the cause of osteopetrosis autosomal recessive type 3 (OPTB3) [MIM:[~~http~~://omim.org/entry/259730 259730]]; also known as osteopetrosis with renal tubular acidosis, carbonic anhydrase II deficiency syndrome, Guibaud-Vainsel syndrome or marble brain disease. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. The disorder occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Autosomal recessive osteopetrosis is usually associated with normal or elevated amount of non-functional osteoclasts. OPTB3 is associated with renal tubular acidosis, cerebral calcification (marble brain disease) and in some cases with mental retardation.<ref>PMID:1928091</ref> <ref>PMID:1542674</ref> <ref>PMID:8834238</ref> <ref>PMID:9143915</ref> <ref>PMID:15300855</ref>	+	[[https://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Defects in CA2 are the cause of osteopetrosis autosomal recessive type 3 (OPTB3) [MIM:[https://omim.org/entry/259730 259730]]; also known as osteopetrosis with renal tubular acidosis, carbonic anhydrase II deficiency syndrome, Guibaud-Vainsel syndrome or marble brain disease. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. The disorder occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Autosomal recessive osteopetrosis is usually associated with normal or elevated amount of non-functional osteoclasts. OPTB3 is associated with renal tubular acidosis, cerebral calcification (marble brain disease) and in some cases with mental retardation.<ref>PMID:1928091</ref> <ref>PMID:1542674</ref> <ref>PMID:8834238</ref> <ref>PMID:9143915</ref> <ref>PMID:15300855</ref>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Essential for bone resorption and osteoclast differentiation (By similarity). Reversible hydration of carbon dioxide. Can hydrate cyanamide to urea. Involved in the regulation of fluid secretion into the anterior chamber of the eye.<ref>PMID:10550681</ref> <ref>PMID:11831900</ref>	+	[[https://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Essential for bone resorption and osteoclast differentiation (By similarity). Reversible hydration of carbon dioxide. Can hydrate cyanamide to urea. Involved in the regulation of fluid secretion into the anterior chamber of the eye.<ref>PMID:10550681</ref> <ref>PMID:11831900</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:

	==See Also==		==See Also==
-	*[[Carbonic anhydrase\|Carbonic anhydrase]]	+	*[[Carbonic anhydrase 3D structures\|Carbonic anhydrase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 32:		Line 32:
	[[Category: Carbonate dehydratase]]		[[Category: Carbonate dehydratase]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Bai, S]]		[[Category: Bai, S]]
	[[Category: Heroux, A]]		[[Category: Heroux, A]]

OCA at 07:40, 5 August 2016

2016-08-05T07:40:00Z

←Older revision		Revision as of 07:40, 5 August 2016
Line 1:		Line 1:
		+
	==Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase==		==Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase==
	<StructureSection load='3rz5' size='340' side='right' caption='[[3rz5]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='3rz5' size='340' side='right' caption='[[3rz5]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rz5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RZ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RZ5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rz5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RZ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RZ5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=RZ5:N-PENTYL-4-SULFAMOYLBENZAMIDE'>RZ5</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=RZ5:N-PENTYL-4-SULFAMOYLBENZAMIDE'>RZ5</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ryv\|3ryv]], [[3ryx\|3ryx]], [[3ryy\|3ryy]], [[3ryz\|3ryz]], [[3rz0\|3rz0]], [[3rz1\|3rz1]], [[3ryj\|3ryj]], [[3rz7\|3rz7]], [[3rz8\|3rz8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ryv\|3ryv]], [[3ryx\|3ryx]], [[3ryy\|3ryy]], [[3ryz\|3ryz]], [[3rz0\|3rz0]], [[3rz1\|3rz1]], [[3ryj\|3ryj]], [[3rz7\|3rz7]], [[3rz8\|3rz8]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CA2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CA2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rz5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rz5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rz5 RCSB], [http://www.ebi.ac.uk/pdbsum/3rz5 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rz5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rz5 OCA], [http://pdbe.org/3rz5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rz5 RCSB], [http://www.ebi.ac.uk/pdbsum/3rz5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rz5 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 21:		Line 22:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3rz5" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 29:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Carbonate dehydratase]]		[[Category: Carbonate dehydratase]]
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Bai, S]]		[[Category: Bai, S]]
	[[Category: Heroux, A]]		[[Category: Heroux, A]]

OCA at 11:00, 19 December 2014

2014-12-19T11:00:16Z

←Older revision		Revision as of 11:00, 19 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3rz5\| PDB=3rz5 \| SCENE= }}~~	+	==Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase==
-	===Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase===	+	<StructureSection load='3rz5' size='340' side='right' caption='[[3rz5]], [[Resolution\|resolution]] 1.65Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21790183}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3rz5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RZ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RZ5 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=RZ5:N-PENTYL-4-SULFAMOYLBENZAMIDE'>RZ5</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ryv\|3ryv]], [[3ryx\|3ryx]], [[3ryy\|3ryy]], [[3ryz\|3ryz]], [[3rz0\|3rz0]], [[3rz1\|3rz1]], [[3ryj\|3ryj]], [[3rz7\|3rz7]], [[3rz8\|3rz8]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CA2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rz5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rz5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rz5 RCSB], [http://www.ebi.ac.uk/pdbsum/3rz5 PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Defects in CA2 are the cause of osteopetrosis autosomal recessive type 3 (OPTB3) [MIM:[http://omim.org/entry/259730 259730]]; also known as osteopetrosis with renal tubular acidosis, carbonic anhydrase II deficiency syndrome, Guibaud-Vainsel syndrome or marble brain disease. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. The disorder occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Autosomal recessive osteopetrosis is usually associated with normal or elevated amount of non-functional osteoclasts. OPTB3 is associated with renal tubular acidosis, cerebral calcification (marble brain disease) and in some cases with mental retardation.<ref>PMID:1928091</ref> <ref>PMID:1542674</ref> <ref>PMID:8834238</ref> <ref>PMID:9143915</ref> <ref>PMID:15300855</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Essential for bone resorption and osteoclast differentiation (By similarity). Reversible hydration of carbon dioxide. Can hydrate cyanamide to urea. Involved in the regulation of fluid secretion into the anterior chamber of the eye.<ref>PMID:10550681</ref> <ref>PMID:11831900</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The hydrophobic effect-the free-energetically favorable association of non-polar solutes in water- makes a dominant contribution to binding of many systems of ligands and proteins. The objective of this study was to examine the hydrophobic effect in biomolecular recognition using two chemically different, but structurally similar hydrophobic groups-aliphatic hydrocarbons and aliphatic fluorocarbons-and to determine whether the hydrophobicity of the two groups could be distinguished by thermodynamic and biostructural analysis. This paper uses isothermal titration calorimetry (ITC) to examine the thermodynamics of binding of benzenesulfonamides substituted in the para position with alkyl and fluoroalkyl chains (H2NSO2C6H4-CONHCH2(CX2)nCX3, n = 0-4, X = H, F) to human carbonic anhydrase II (HCA II). Both alkyl and fluoroalkyl substituents contribute favorably to the enthalpy and the entropy of binding; these contributions increase as the length of chain of the hydrophobic substituent increases. Crystallography of the protein-ligand complexes indicates that the benzenesulfonamide groups of all ligands examined bind with similar geometry, that the tail groups associate with the hydrophobic wall of HCA II (which is made up of the side chains of residues Phe131, Val135, Pro202, and Leu204), and that the structure of the protein is indistinguishable for all but one of the complexes (the longest member of the fluoroalkyl series). Analysis of the thermodynamics of binding as a function of structure is compatible with the hypothesis that hydrophobic binding of both alkyl and fluoroalkyl chains to hydrophobic surface of carbonic anhydrase is due primarily to the release of non-optimally hydrogen-bonded water molecules that hydrate the binding cavity (including the hydrophobic wall) of HCA II and to the release of water molecules that surround the hydrophobic chain of the ligands. This study defines the balance of enthalpic and entropic contributions to the hydrophobic effect in this representative system of protein and ligand: hydrophobic interactions, here, seem to comprise approximately equal contributions from enthalpy (plausibly from strengthening networks among molecules of water hydrogen bonds) and entropy (from release of water from configurationally restricted positions).

-	~~==Disease==~~	+	Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the ''Hydrophobic Wall'' of Carbonic Anhydrase.,Mecinovic J, Snyder PW, Mirica KA, Bai S, Mack ET, Kwant RL, Moustakas DT, Heroux A, Whitesides GM J Am Chem Soc. 2011 Jul 26. PMID:21790183<ref>PMID:21790183</ref>
-	~~[[http://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Defects~~ in ~~CA2 are~~ the ~~cause~~ of ~~osteopetrosis autosomal recessive type 3 (OPTB3) [MIM:[http://omim~~.~~org/entry/259730 259730]]; also known as osteopetrosis with renal tubular acidosis~~, ~~carbonic anhydrase II deficiency syndrome~~, ~~Guibaud-Vainsel syndrome or marble brain disease. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone~~, ~~due to defective resorption of immature bone. The disorder occurs in two forms: a severe autosomal recessive form occurring in utero~~, ~~infancy~~, ~~or childhood~~, ~~and a benign autosomal dominant form occurring in adolescence or adulthood~~. ~~Autosomal recessive osteopetrosis is usually associated with normal or elevated amount of non-functional osteoclasts~~. ~~OPTB3 is associated with renal tubular acidosis, cerebral calcification (marble brain disease) and in some cases with mental retardation.<ref>~~PMID:~~1928091</ref><ref>PMID:1542674</ref><ref>PMID:8834238</ref><ref>PMID:9143915</ref>~~<ref>PMID:~~15300855~~</ref>	+

-	~~==Function==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[http:~~/~~/www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Essential for bone resorption and osteoclast differentiation (By similarity). Reversible hydration~~ of ~~carbon dioxide~~. ~~Can hydrate cyanamide to urea~~. ~~Involved in the regulation~~ of ~~fluid secretion into the anterior chamber of the eye~~.<~~ref~~>~~PMID:10550681~~</~~ref~~>~~<ref>PMID:11831900</ref>~~	+	</div>
-		+
-	~~==About this Structure==~~	+
-	[[3rz5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RZ5 OCA].	+

	==See Also==		==See Also==
	*[[Carbonic anhydrase\|Carbonic anhydrase]]		*[[Carbonic anhydrase\|Carbonic anhydrase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:021790183</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Carbonate dehydratase]]		[[Category: Carbonate dehydratase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Bai, S.]]	+	[[Category: Bai, S]]
-	[[Category: Heroux, A.]]	+	[[Category: Heroux, A]]
-	[[Category: Snyder, P W.]]	+	[[Category: Snyder, P W]]
-	[[Category: Whitesides, G W.]]	+	[[Category: Whitesides, G W]]
	[[Category: Alpha beta]]		[[Category: Alpha beta]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 17:52, 24 March 2013

2013-03-24T17:52:08Z

←Older revision		Revision as of 17:52, 24 March 2013
Line 1:		Line 1:
-	[[Image:3rz5.png\|left\|200px]]
-
	{{STRUCTURE_3rz5\| PDB=3rz5 \| SCENE= }}		{{STRUCTURE_3rz5\| PDB=3rz5 \| SCENE= }}
-
	===Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase===		===Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase===
		+	{{ABSTRACT_PUBMED_21790183}}

-	~~{{ABSTRACT_PUBMED_21790183}}~~	+	==Disease==
		+	[[http://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Defects in CA2 are the cause of osteopetrosis autosomal recessive type 3 (OPTB3) [MIM:[http://omim.org/entry/259730 259730]]; also known as osteopetrosis with renal tubular acidosis, carbonic anhydrase II deficiency syndrome, Guibaud-Vainsel syndrome or marble brain disease. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. The disorder occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Autosomal recessive osteopetrosis is usually associated with normal or elevated amount of non-functional osteoclasts. OPTB3 is associated with renal tubular acidosis, cerebral calcification (marble brain disease) and in some cases with mental retardation.<ref>PMID:1928091</ref><ref>PMID:1542674</ref><ref>PMID:8834238</ref><ref>PMID:9143915</ref><ref>PMID:15300855</ref>
		+
		+	==Function==
		+	[[http://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Essential for bone resorption and osteoclast differentiation (By similarity). Reversible hydration of carbon dioxide. Can hydrate cyanamide to urea. Involved in the regulation of fluid secretion into the anterior chamber of the eye.<ref>PMID:10550681</ref><ref>PMID:11831900</ref>

	==About this Structure==		==About this Structure==
Line 14:		Line 16:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:021790183</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021790183</ref><references group="xtra"/><references/>
	[[Category: Carbonate dehydratase]]		[[Category: Carbonate dehydratase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]

OCA at 10:37, 20 October 2012

2012-10-20T10:37:00Z

←Older revision		Revision as of 10:37, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3rz5]] is a 1 chain structure ~~of [[Carbonic anhydrase]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RZ5 OCA].	+	[[3rz5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RZ5 OCA].

	==See Also==		==See Also==

OCA at 02:42, 26 July 2012

2012-07-26T02:42:24Z

←Older revision		Revision as of 02:42, 26 July 2012
Line 1:		Line 1:
	[[Image:3rz5.png\|left\|200px]]		[[Image:3rz5.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3rz5", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3rz5\| PDB=3rz5 \| SCENE= }}		{{STRUCTURE_3rz5\| PDB=3rz5 \| SCENE= }}

	===Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase===		===Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21790183}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21790183 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_21790183}}		{{ABSTRACT_PUBMED_21790183}}

Line 22:		Line 11:

	==See Also==		==See Also==
-	*[[Carbonic anhydrase]]	+	*[[Carbonic anhydrase\|Carbonic anhydrase]]

	==Reference==		==Reference==

OCA at 11:12, 16 November 2011

2011-11-16T11:12:44Z

←Older revision		Revision as of 11:12, 16 November 2011
Line 1:		Line 1:
-	[[Image:3rz5.~~jpg~~\|left\|200px]]	+	[[Image:3rz5.png\|left\|200px]]

	<!--		<!--
Line 19:		Line 19:

	==About this Structure==		==About this Structure==
-	[[3rz5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RZ5 OCA].	+	[[3rz5]] is a 1 chain structure of [[Carbonic anhydrase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RZ5 OCA].
		+
		+	==See Also==
		+	*[[Carbonic anhydrase]]

	==Reference==		==Reference==

OCA at 05:58, 10 August 2011

2011-08-10T05:58:24Z

←Older revision		Revision as of 05:58, 10 August 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3rz5.jpg\|left\|200px]]

-	The ~~entry 3rz5~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3rz5", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3rz5\| PDB=3rz5 \| SCENE= }}

-	~~Authors: Snyder, P.W., Bai, S., Heroux, A., Whitesides, G.W.~~	+	===Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase===

-	~~Description: Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding~~ to the ~~Hydrophobic Wall of Carbonic Anhydrase~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21790183}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21790183 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21790183}}
		+
		+	==About this Structure==
		+	[[3rz5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RZ5 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021790183</ref><references group="xtra"/>
		+	[[Category: Carbonate dehydratase]]
		+	[[Category: Homo sapiens]]
		+	[[Category: Bai, S.]]
		+	[[Category: Heroux, A.]]
		+	[[Category: Snyder, P W.]]
		+	[[Category: Whitesides, G W.]]
		+	[[Category: Alpha beta]]
		+	[[Category: Lyase]]

OCA at 05:53, 15 June 2011

2011-06-15T05:53:10Z

←Older revision		Revision as of 05:53, 15 June 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3rz5 is ON HOLD	+	The entry 3rz5 is ON HOLD until Paper Publication

	Authors: Snyder, P.W., Bai, S., Heroux, A., Whitesides, G.W.		Authors: Snyder, P.W., Bai, S., Heroux, A., Whitesides, G.W.

	Description: Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase		Description: Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase