2hvi - Revision history

OCA at 10:02, 30 August 2023

OCA — Wed, 30 Aug 2023 10:02:13 GMT

←Older revision		Revision as of 10:02, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2hvi' size='340' side='right'caption='[[2hvi]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='2hvi' size='340' side='right'caption='[[2hvi]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hvi]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_12980 Atcc 12980~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HVI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hvi]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HVI FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DCT:2,3~~-~~DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>~~, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</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]] 1.98Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class~~=~~"sblockDat"><div style~~=~~'overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1lv5\|1lv5]], [[2hhw\|2hhw]], [[2hhv\|2hhv]], [[2hhu\|2hhu]], [[2hht\|2hht]], [[2hhs\|2hhs]], [[2hhx\|2hhx]], [[2hhy\|2hhy]], [[2hhq\|2hhq]], [[2hvh\|2hvh]], [[2hw3\|2hw3]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class~~=~~"sblockDat">polA ([https~~:~~//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td~~></tr>	+
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7]~~ </~~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=2hvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hvi OCA], [https://pdbe.org/2hvi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hvi RCSB], [https://www.ebi.ac.uk/pdbsum/2hvi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hvi 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=2hvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hvi OCA], [https://pdbe.org/2hvi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hvi RCSB], [https://www.ebi.ac.uk/pdbsum/2hvi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hvi ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5KWC1_GEOKA Q5KWC1_GEOKA]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</div>		</div>
	<div class="pdbe-citations 2hvi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2hvi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 12980]]~~	+	[[Category: Geobacillus stearothermophilus]]
-	~~[[Category: DNA-directed DNA polymerase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Beese~~, L S~~]]	+	[[Category: Beese LS]]
-	[[Category: Forsberg~~, L J~~]]	+	[[Category: Forsberg LJ]]
-	[[Category: Warren~~, J J]]~~	+	[[Category: Warren JJ]]
-	~~[[Category: Closed conformation]]~~	+
-	~~[[Category: Dna polymerase i]]~~	+
-	~~[[Category: Dna replication]]~~	+
-	~~[[Category: Klenow fragment]]~~	+
-	~~[[Category: Protein-dna complex]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 10:03, 12 May 2021

OCA — Wed, 12 May 2021 10:03:49 GMT

←Older revision		Revision as of 10:03, 12 May 2021
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	<StructureSection load='2hvi' size='340' side='right'caption='[[2hvi]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='2hvi' size='340' side='right'caption='[[2hvi]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hvi]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2HVI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hvi]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HVI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=~~SUC~~:~~SUCROSE~~'>~~SUC~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lv5\|1lv5]], [[2hhw\|2hhw]], [[2hhv\|2hhv]], [[2hhu\|2hhu]], [[2hht\|2hht]], [[2hhs\|2hhs]], [[2hhx\|2hhx]], [[2hhy\|2hhy]], [[2hhq\|2hhq]], [[2hvh\|2hvh]], [[2hw3\|2hw3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1lv5\|1lv5]], [[2hhw\|2hhw]], [[2hhv\|2hhv]], [[2hhu\|2hhu]], [[2hht\|2hht]], [[2hhs\|2hhs]], [[2hhx\|2hhx]], [[2hhy\|2hhy]], [[2hhq\|2hhq]], [[2hvh\|2hvh]], [[2hw3\|2hw3]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=2hvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hvi OCA], [~~http~~://pdbe.org/2hvi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2hvi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2hvi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2hvi 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=2hvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hvi OCA], [https://pdbe.org/2hvi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hvi RCSB], [https://www.ebi.ac.uk/pdbsum/2hvi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hvi ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</div>		</div>
	<div class="pdbe-citations 2hvi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2hvi" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:20, 24 July 2019

OCA — Wed, 24 Jul 2019 07:20:18 GMT

←Older revision		Revision as of 07:20, 24 July 2019
Line 1:		Line 1:

	==ddCTP:G pair in the polymerase active site (0 position)==		==ddCTP:G pair in the polymerase active site (0 position)==
-	<StructureSection load='2hvi' size='340' side='right' caption='[[2hvi]], [[Resolution\|resolution]] 1.98Å' scene=''>	+	<StructureSection load='2hvi' size='340' side='right'caption='[[2hvi]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2hvi]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HVI FirstGlance]. <br>		<table><tr><td colspan='2'>[[2hvi]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HVI FirstGlance]. <br>
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hv/2hvi_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hv/2hvi_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 2hvi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2hvi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 39:
	[[Category: Atcc 12980]]		[[Category: Atcc 12980]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Beese, L S]]		[[Category: Beese, L S]]
	[[Category: Forsberg, L J]]		[[Category: Forsberg, L J]]

OCA at 08:17, 18 October 2017

OCA — Wed, 18 Oct 2017 08:17:39 GMT

←Older revision		Revision as of 08:17, 18 October 2017
Line 1:		Line 1:
		+
	==ddCTP:G pair in the polymerase active site (0 position)==		==ddCTP:G pair in the polymerase active site (0 position)==
	<StructureSection load='2hvi' size='340' side='right' caption='[[2hvi]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='2hvi' size='340' side='right' caption='[[2hvi]], [[Resolution\|resolution]] 1.98Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=2hvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hvi OCA], [http://pdbe.org/2hvi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hvi RCSB], [http://www.ebi.ac.uk/pdbsum/2hvi 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=2hvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hvi OCA], [http://pdbe.org/2hvi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hvi RCSB], [http://www.ebi.ac.uk/pdbsum/2hvi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hvi ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 2hvi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2hvi" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:03, 9 February 2016

OCA — Tue, 09 Feb 2016 06:03:15 GMT

←Older revision		Revision as of 06:03, 9 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2hvi ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:20, 10 September 2015

OCA — Thu, 10 Sep 2015 19:20:13 GMT

←Older revision		Revision as of 19:20, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2hvi' size='340' side='right' caption='[[2hvi]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='2hvi' size='340' side='right' caption='[[2hvi]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hvi]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Geobacillus_stearothermophilus Geobacillus stearothermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HVI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hvi]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HVI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lv5\|1lv5]], [[2hhw\|2hhw]], [[2hhv\|2hhv]], [[2hhu\|2hhu]], [[2hht\|2hht]], [[2hhs\|2hhs]], [[2hhx\|2hhx]], [[2hhy\|2hhy]], [[2hhq\|2hhq]], [[2hvh\|2hvh]], [[2hw3\|2hw3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lv5\|1lv5]], [[2hhw\|2hhw]], [[2hhv\|2hhv]], [[2hhu\|2hhu]], [[2hht\|2hht]], [[2hhs\|2hhs]], [[2hhx\|2hhx]], [[2hhy\|2hhy]], [[2hhq\|2hhq]], [[2hvh\|2hvh]], [[2hw3\|2hw3]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ~~Geobacillus stearothermophilus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=2hvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hvi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hvi RCSB], [http://www.ebi.ac.uk/pdbsum/2hvi 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=2hvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hvi OCA], [http://pdbe.org/2hvi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hvi RCSB], [http://www.ebi.ac.uk/pdbsum/2hvi PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 28:		Line 28:
	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 2hvi" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 12980]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Geobacillus stearothermophilus]]
	[[Category: Beese, L S]]		[[Category: Beese, L S]]
	[[Category: Forsberg, L J]]		[[Category: Forsberg, L J]]

OCA at 08:15, 16 January 2015

OCA — Fri, 16 Jan 2015 08:15:45 GMT

OCA at 04:36, 29 September 2014

OCA — Mon, 29 Sep 2014 04:36:48 GMT

←Older revision		Revision as of 04:36, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2hvi.~~png~~\|~~left~~\|200px]]	+	==ddCTP:G pair in the polymerase active site (0 position)==
		+	<StructureSection load='2hvi' size='340' side='right' caption='[[2hvi]], [[Resolution\|resolution]] 1.98Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2hvi]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HVI FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lv5\|1lv5]], [[2hhw\|2hhw]], [[2hhv\|2hhv]], [[2hhu\|2hhu]], [[2hht\|2hht]], [[2hhs\|2hhs]], [[2hhx\|2hhx]], [[2hhy\|2hhy]], [[2hhq\|2hhq]], [[2hvh\|2hvh]], [[2hw3\|2hw3]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hvi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hvi RCSB], [http://www.ebi.ac.uk/pdbsum/2hvi PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hv/2hvi_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Methylating agents are widespread environmental carcinogens that generate a broad spectrum of DNA damage. Methylation at the guanine O(6) position confers the greatest mutagenic and carcinogenic potential. DNA polymerases insert cytosine and thymine with similar efficiency opposite O(6)-methyl-guanine (O6MeG). We combined pre-steady-state kinetic analysis and a series of nine x-ray crystal structures to contrast the reaction pathways of accurate and mutagenic replication of O6MeG in a high-fidelity DNA polymerase from Bacillus stearothermophilus. Polymerases achieve substrate specificity by selecting for nucleotides with shape and hydrogen-bonding patterns that complement a canonical DNA template. Our structures reveal that both thymine and cytosine O6MeG base pairs evade proofreading by mimicking the essential molecular features of canonical substrates. The steric mimicry depends on stabilization of a rare cytosine tautomer in C.O6MeG-polymerase complexes. An unusual electrostatic interaction between O-methyl protons and a thymine carbonyl oxygen helps stabilize T.O6MeG pairs bound to DNA polymerase. Because DNA methylators constitute an important class of chemotherapeutic agents, the molecular mechanisms of replication of these DNA lesions are important for our understanding of both the genesis and treatment of cancer.

-	~~{{STRUCTURE_2hvi\| PDB=2hvi \| SCENE= }}~~	+	The structural basis for the mutagenicity of O(6)-methyl-guanine lesions.,Warren JJ, Forsberg LJ, Beese LS Proc Natl Acad Sci U S A. 2006 Dec 26;103(52):19701-6. Epub 2006 Dec 18. PMID:17179038<ref>PMID:17179038</ref>

-	~~===ddCTP:G pair in~~ the ~~polymerase active site (0 position)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17179038}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2hvi]] is a 6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2HVI OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017179038<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]

OCA at 12:53, 20 October 2012

OCA — Sat, 20 Oct 2012 12:53:44 GMT

←Older revision		Revision as of 12:53, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2hvi]] is a 6 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVI OCA].	+	[[2hvi]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVI OCA].

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

OCA: Protected "2hvi" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 10:14:39 GMT

Protected "2hvi" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:14, 26 July 2012

←Older revision		Revision as of 08:15, 16 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2hvi]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HVI FirstGlance]. <br>		<table><tr><td colspan='2'>[[2hvi]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HVI FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lv5\|1lv5]], [[2hhw\|2hhw]], [[2hhv\|2hhv]], [[2hhu\|2hhu]], [[2hht\|2hht]], [[2hhs\|2hhs]], [[2hhx\|2hhx]], [[2hhy\|2hhy]], [[2hhq\|2hhq]], [[2hvh\|2hvh]], [[2hw3\|2hw3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lv5\|1lv5]], [[2hhw\|2hhw]], [[2hhv\|2hhv]], [[2hhu\|2hhu]], [[2hht\|2hht]], [[2hhs\|2hhs]], [[2hhx\|2hhx]], [[2hhy\|2hhy]], [[2hhq\|2hhq]], [[2hvh\|2hvh]], [[2hw3\|2hw3]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hvi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hvi RCSB], [http://www.ebi.ac.uk/pdbsum/2hvi 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=2hvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hvi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hvi RCSB], [http://www.ebi.ac.uk/pdbsum/2hvi PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 37:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
-	[[Category: Beese, L S.]]	+	[[Category: Beese, L S]]
-	[[Category: Forsberg, L J.]]	+	[[Category: Forsberg, L J]]
-	[[Category: Warren, J J.]]	+	[[Category: Warren, J J]]
	[[Category: Closed conformation]]		[[Category: Closed conformation]]
	[[Category: Dna polymerase i]]		[[Category: Dna polymerase i]]