2xhb - Revision history

OCA at 10:31, 20 December 2023

OCA — Wed, 20 Dec 2023 10:31:37 GMT

←Older revision		Revision as of 10:31, 20 December 2023
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	<StructureSection load='2xhb' size='340' side='right'caption='[[2xhb]], [[Resolution\|resolution]] 2.72Å' scene=''>		<StructureSection load='2xhb' size='340' side='right'caption='[[2xhb]], [[Resolution\|resolution]] 2.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2xhb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_700654 Atcc 700654~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XHB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2xhb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_gorgonarius Thermococcus gorgonarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XHB FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.72Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>~~[[~~Non-Standard_Residue~~\|~~NonStd Res:~~]]~~</b></td><td class="sblockDat"><scene name='pdbligand=DI:~~2~~-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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;'>[[1wn7\|1wn7]], [[2vwk\|2vwk]], [[2vwj\|2vwj]], [[1tgo\|1tgo]]</div></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=2xhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xhb OCA], [https://pdbe.org/2xhb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xhb RCSB], [https://www.ebi.ac.uk/pdbsum/2xhb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xhb 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=2xhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xhb OCA], [https://pdbe.org/2xhb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xhb RCSB], [https://www.ebi.ac.uk/pdbsum/2xhb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xhb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DPOL_THEGO DPOL_THEGO]] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.	+	[https://www.uniprot.org/uniprot/DPOL_THEGO DPOL_THEGO] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2xhb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2xhb" 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 700654]]
-	[[Category: DNA-directed DNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Connolly~~, B A~~]]	+	[[Category: Thermococcus gorgonarius]]
-	[[Category: Firbank~~, S J~~]]	+	[[Category: Connolly BA]]
-	[[Category: Ghosh, S]]	+	[[Category: Firbank SJ]]
-	[[Category: Heslop, P]]	+	[[Category: Ghosh S]]
-	[[Category: Killelea, T]]	+	[[Category: Heslop P]]
-	[[Category: Kool~~, E T~~]]	+	[[Category: Killelea T]]
-	[[Category: Tan~~, S S]]~~	+	[[Category: Kool ET]]
-	~~[[Category: Dna damage]]~~	+	[[Category: Tan SS]]
-	~~[[Category: Exo minus]]~~	+
-	~~[[Category: Exonuclease]]~~	+
-	~~[[Category: Replication]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 10:52, 13 April 2022

OCA — Wed, 13 Apr 2022 10:52:54 GMT

←Older revision		Revision as of 10:52, 13 April 2022
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	<StructureSection load='2xhb' size='340' side='right'caption='[[2xhb]], [[Resolution\|resolution]] 2.72Å' scene=''>		<StructureSection load='2xhb' size='340' side='right'caption='[[2xhb]], [[Resolution\|resolution]] 2.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2xhb]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_700654 Atcc 700654]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2XHB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2xhb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_700654 Atcc 700654]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XHB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wn7\|1wn7]], [[2vwk\|2vwk]], [[2vwj\|2vwj]], [[1tgo\|1tgo]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wn7\|1wn7]], [[2vwk\|2vwk]], [[2vwj\|2vwj]], [[1tgo\|1tgo]]</div></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~~://proteopedia.org/fgij/fg.htm?mol=2xhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xhb OCA], [~~http~~://pdbe.org/2xhb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2xhb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2xhb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2xhb 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=2xhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xhb OCA], [https://pdbe.org/2xhb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xhb RCSB], [https://www.ebi.ac.uk/pdbsum/2xhb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xhb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DPOL_THEGO DPOL_THEGO]] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.	+	[[https://www.uniprot.org/uniprot/DPOL_THEGO DPOL_THEGO]] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 2xhb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2xhb" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:14, 8 July 2020

OCA — Wed, 08 Jul 2020 15:14:33 GMT

←Older revision		Revision as of 15:14, 8 July 2020
Line 1:		Line 1:

	==Crystal structure of DNA polymerase from Thermococcus gorgonarius in complex with hypoxanthine-containing DNA==		==Crystal structure of DNA polymerase from Thermococcus gorgonarius in complex with hypoxanthine-containing DNA==
-	<StructureSection load='2xhb' size='340' side='right' caption='[[2xhb]], [[Resolution\|resolution]] 2.72Å' scene=''>	+	<StructureSection load='2xhb' size='340' side='right'caption='[[2xhb]], [[Resolution\|resolution]] 2.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2xhb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_700654 Atcc 700654]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHB OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2XHB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2xhb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_700654 Atcc 700654]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2XHB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wn7\|1wn7]], [[2vwk\|2vwk]], [[2vwj\|2vwj]], [[1tgo\|1tgo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wn7\|1wn7]], [[2vwk\|2vwk]], [[2vwj\|2vwj]], [[1tgo\|1tgo]]</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=2xhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xhb OCA], [http://pdbe.org/2xhb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xhb RCSB], [http://www.ebi.ac.uk/pdbsum/2xhb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xhb ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2xhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xhb OCA], [http://pdbe.org/2xhb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xhb RCSB], [http://www.ebi.ac.uk/pdbsum/2xhb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xhb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[DNA polymerase\|DNA polymerase]]	+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 40:		Line 40:
	[[Category: Atcc 700654]]		[[Category: Atcc 700654]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Connolly, B A]]		[[Category: Connolly, B A]]
	[[Category: Firbank, S J]]		[[Category: Firbank, S J]]

OCA at 09:26, 3 October 2018

OCA — Wed, 03 Oct 2018 09:26:10 GMT

←Older revision		Revision as of 09:26, 3 October 2018
Line 1:		Line 1:

-	==~~CRYSTAL STRUCTURE OF~~ DNA ~~POLYMERASE FROM THERMOCOCCUS GORGONARIUS IN COMPLEX WITH HYPOXANTHINE~~-~~CONTAINING~~ DNA==	+	==Crystal structure of DNA polymerase from Thermococcus gorgonarius in complex with hypoxanthine-containing DNA==
	<StructureSection load='2xhb' size='340' side='right' caption='[[2xhb]], [[Resolution\|resolution]] 2.72Å' scene=''>		<StructureSection load='2xhb' size='340' side='right' caption='[[2xhb]], [[Resolution\|resolution]] 2.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 16:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xh/2xhb_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xh/2xhb_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>

OCA at 21:48, 4 August 2016

OCA — Thu, 04 Aug 2016 21:48:40 GMT

←Older revision		Revision as of 21:48, 4 August 2016
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF DNA POLYMERASE FROM THERMOCOCCUS GORGONARIUS IN COMPLEX WITH HYPOXANTHINE-CONTAINING DNA==		==CRYSTAL STRUCTURE OF DNA POLYMERASE FROM THERMOCOCCUS GORGONARIUS IN COMPLEX WITH HYPOXANTHINE-CONTAINING DNA==
	<StructureSection load='2xhb' size='340' side='right' caption='[[2xhb]], [[Resolution\|resolution]] 2.72Å' scene=''>		<StructureSection load='2xhb' size='340' side='right' caption='[[2xhb]], [[Resolution\|resolution]] 2.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2xhb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermococcus_gorgonarius Thermococcus gorgonarius~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XHB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2xhb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_700654 Atcc 700654]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XHB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wn7\|1wn7]], [[2vwk\|2vwk]], [[2vwj\|2vwj]], [[1tgo\|1tgo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wn7\|1wn7]], [[2vwk\|2vwk]], [[2vwj\|2vwj]], [[1tgo\|1tgo]]</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=2xhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xhb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xhb RCSB], [http://www.ebi.ac.uk/pdbsum/2xhb 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=2xhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xhb OCA], [http://pdbe.org/2xhb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xhb RCSB], [http://www.ebi.ac.uk/pdbsum/2xhb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xhb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<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=2xhb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	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 2xhb" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 700654]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Thermococcus gorgonarius]]
	[[Category: Connolly, B A]]		[[Category: Connolly, B A]]
	[[Category: Firbank, S J]]		[[Category: Firbank, S J]]

OCA at 13:25, 25 December 2014

OCA — Thu, 25 Dec 2014 13:25:23 GMT

←Older revision		Revision as of 13:25, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2xhb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermococcus_gorgonarius Thermococcus gorgonarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XHB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2xhb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermococcus_gorgonarius Thermococcus gorgonarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XHB FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wn7\|1wn7]], [[2vwk\|2vwk]], [[2vwj\|2vwj]], [[1tgo\|1tgo]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wn7\|1wn7]], [[2vwk\|2vwk]], [[2vwj\|2vwj]], [[1tgo\|1tgo]]</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=2xhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xhb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xhb RCSB], [http://www.ebi.ac.uk/pdbsum/2xhb 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=2xhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xhb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xhb RCSB], [http://www.ebi.ac.uk/pdbsum/2xhb PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPOL_THEGO DPOL_THEGO]] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Thermococcus gorgonarius]]		[[Category: Thermococcus gorgonarius]]
-	[[Category: Connolly, B A.]]	+	[[Category: Connolly, B A]]
-	[[Category: Firbank, S J.]]	+	[[Category: Firbank, S J]]
-	[[Category: Ghosh, S.]]	+	[[Category: Ghosh, S]]
-	[[Category: Heslop, P.]]	+	[[Category: Heslop, P]]
-	[[Category: Killelea, T.]]	+	[[Category: Killelea, T]]
-	[[Category: Kool, E T.]]	+	[[Category: Kool, E T]]
-	[[Category: Tan, S S.]]	+	[[Category: Tan, S S]]
	[[Category: Dna damage]]		[[Category: Dna damage]]
	[[Category: Exo minus]]		[[Category: Exo minus]]

OCA at 01:05, 2 October 2014

OCA — Thu, 02 Oct 2014 01:05:07 GMT

←Older revision		Revision as of 01:05, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2xhb.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF DNA POLYMERASE FROM THERMOCOCCUS GORGONARIUS IN COMPLEX WITH HYPOXANTHINE-CONTAINING DNA==
		+	<StructureSection load='2xhb' size='340' side='right' caption='[[2xhb]], [[Resolution\|resolution]] 2.72Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2xhb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermococcus_gorgonarius Thermococcus gorgonarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XHB FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wn7\|1wn7]], [[2vwk\|2vwk]], [[2vwj\|2vwj]], [[1tgo\|1tgo]]</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=2xhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xhb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xhb RCSB], [http://www.ebi.ac.uk/pdbsum/2xhb 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/xh/2xhb_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 ==
		+	Archaeal family-B DNA polymerases stall replication on encountering the pro-mutagenic bases uracil and hypoxanthine. This publication describes an X-ray crystal structure of Thermococcus gorgonarius polymerase in complex with a DNA containing hypoxanthine in the single-stranded region of the template, two bases ahead of the primer-template junction. Full details of the specific recognition of hypoxanthine are revealed, allowing a comparison with published data that describe uracil binding. The two bases are recognized by the same pocket, in the N-terminal domain, and make very similar protein-DNA interactions. Specificity for hypoxanthine (and uracil) arises from a combination of polymerase-base hydrogen bonds and shape fit between the deaminated bases and the pocket. The structure with hypoxanthine at position 2 explains the stimulation of the polymerase 3'-5' proofreading exonuclease, observed with deaminated bases at this location. A beta-hairpin element, involved in partitioning the primer strand between the polymerase and exonuclease active sites, inserts between the two template bases at the extreme end of the double-stranded DNA. This denatures the two complementary primer bases and directs the resulting 3' single-stranded extension toward the exonuclease active site. Finally, the relative importance of hydrogen bonding and shape fit in determining selectivity for deaminated bases has been examined using nonpolar isosteres. Affinity for both 2,4-difluorobenzene and fluorobenzimidazole, non-hydrogen bonding shape mimics of uracil and hypoxanthine, respectively, is strongly diminished, suggesting polar protein-base contacts are important. However, residual interaction with 2,4-difluorobenzene is seen, confirming a role for shape recognition.

-	~~{{STRUCTURE_2xhb\| PDB=2xhb \| SCENE= }}~~	+	Probing the interaction of archaeal DNA polymerases with deaminated bases using X-ray crystallography and non-hydrogen bonding isosteric base analogues.,Killelea T, Ghosh S, Tan SS, Heslop P, Firbank SJ, Kool ET, Connolly BA Biochemistry. 2010 Jul 13;49(27):5772-81. PMID:20527806<ref>PMID:20527806</ref>

-	~~===CRYSTAL STRUCTURE OF DNA POLYMERASE FROM THERMOCOCCUS GORGONARIUS IN COMPLEX WITH HYPOXANTHINE-CONTAINING DNA===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20527806}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2xhb]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermococcus_gorgonarius Thermococcus gorgonarius]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2XHB OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:020527806<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Thermococcus gorgonarius]]		[[Category: Thermococcus gorgonarius]]

OCA at 17:12, 20 October 2012

OCA — Sat, 20 Oct 2012 17:12:54 GMT

←Older revision		Revision as of 17:12, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2xhb]] is a 3 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermococcus_gorgonarius Thermococcus gorgonarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHB OCA].	+	[[2xhb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermococcus_gorgonarius Thermococcus gorgonarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHB OCA].

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

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

OCA — Fri, 27 Jul 2012 00:12:01 GMT

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

←Older revision

Revision as of 00:12, 27 July 2012

OCA at 00:11, 27 July 2012

OCA — Fri, 27 Jul 2012 00:11:58 GMT

←Older revision		Revision as of 00:11, 27 July 2012
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:2xhb.png\|left\|200px]]
-	[[Image:2xhb.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2xhb", 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_2xhb\| PDB=2xhb \| SCENE= }}		{{STRUCTURE_2xhb\| PDB=2xhb \| SCENE= }}

	===CRYSTAL STRUCTURE OF DNA POLYMERASE FROM THERMOCOCCUS GORGONARIUS IN COMPLEX WITH HYPOXANTHINE-CONTAINING DNA===		===CRYSTAL STRUCTURE OF DNA POLYMERASE FROM THERMOCOCCUS GORGONARIUS IN COMPLEX WITH HYPOXANTHINE-CONTAINING DNA===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20527806}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20527806 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20527806}}		{{ABSTRACT_PUBMED_20527806}}

	==About this Structure==		==About this Structure==
-	~~2XHB~~ is a 3 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Thermococcus_gorgonarius Thermococcus gorgonarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHB OCA].	+	[[2xhb]] is a 3 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Thermococcus_gorgonarius Thermococcus gorgonarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XHB OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20527806~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020527806</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Thermococcus gorgonarius]]		[[Category: Thermococcus gorgonarius]]
Line 38:		Line 29:
	[[Category: Replication]]		[[Category: Replication]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 21 10:14:55 2010''