3syz - Revision history

OCA at 13:12, 14 March 2024

OCA — Thu, 14 Mar 2024 13:12:35 GMT

←Older revision		Revision as of 13:12, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3syz' size='340' side='right'caption='[[3syz]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3syz' size='340' side='right'caption='[[3syz]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3syz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_25104 Atcc 25104~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SYZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SYZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3syz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SYZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SYZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.952Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMN:(1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>BMN</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMN:(1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>BMN</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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;'>[[3sv4\|3sv4]]~~, ~~[[3sv3\|3sv3]], [[3svn\|3svn]], [[3svo\|3svo]], [[3sz2\|3sz2]]~~<~~/div></td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></~~td><td class="sblockDat"~~>~~pol I~~, ~~pol1, polA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])~~<~~/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=3syz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3syz OCA], [https://pdbe.org/3syz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3syz RCSB], [https://www.ebi.ac.uk/pdbsum/3syz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3syz 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=3syz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3syz OCA], [https://pdbe.org/3syz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3syz RCSB], [https://www.ebi.ac.uk/pdbsum/3syz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3syz ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ]
-	Many candidate unnatural DNA base pairs have been developed, but some of the best-replicated pairs adopt intercalated structures in free DNA that are difficult to reconcile with known mechanisms of polymerase recognition. Here we present crystal structures of KlenTaq DNA polymerase at different stages of replication for one such pair, dNaM-d5SICS, and show that efficient replication results from the polymerase itself, inducing the required natural-like structure.	+

-	KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.,Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A Nat Chem Biol. 2012 Jun 3. doi: 10.1038/nchembio.966. PMID:22660438<ref>PMID:22660438</ref>	+	==See Also==
-		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 3syz" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 25104]]
-	[[Category: DNA-directed DNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Betz, K~~]]	+	[[Category: Thermus aquaticus]]
-	[[Category: ~~Diederichs,~~ K]]	+	[[Category: Betz K]]
-	[[Category: ~~Marx, A~~]]	+	[[Category: Diederichs K]]
-	[[Category: ~~Artificial base]]~~	+	[[Category: Marx A]]
-	~~[[Category: Dna polymerase]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 08:16, 29 June 2022

OCA — Wed, 29 Jun 2022 08:16:36 GMT

←Older revision		Revision as of 08:16, 29 June 2022
Line 1:		Line 1:

	==Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase==		==Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase==
-	<StructureSection load='3syz' size='340' side='right' caption='[[3syz]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='3syz' size='340' side='right'caption='[[3syz]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3syz]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SYZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3SYZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3syz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SYZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SYZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMN:(1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>BMN</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMN:(1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>BMN</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sv4\|3sv4]], [[3sv3\|3sv3]], [[3svn\|3svn]], [[3svo\|3svo]], [[3sz2\|3sz2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3sv4\|3sv4]], [[3sv3\|3sv3]], [[3svn\|3svn]], [[3svo\|3svo]], [[3sz2\|3sz2]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol I, pol1, polA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol I, pol1, polA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</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=3syz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3syz OCA], [~~http~~://pdbe.org/3syz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3syz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3syz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3syz 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=3syz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3syz OCA], [https://pdbe.org/3syz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3syz RCSB], [https://www.ebi.ac.uk/pdbsum/3syz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3syz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 3syz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3syz" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
Line 29:		Line 26:
	[[Category: Atcc 25104]]		[[Category: Atcc 25104]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Betz, K]]		[[Category: Betz, K]]
	[[Category: Diederichs, K]]		[[Category: Diederichs, K]]

OCA at 09:43, 11 August 2016

OCA — Thu, 11 Aug 2016 09:43:31 GMT

←Older revision		Revision as of 09:43, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase==		==Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase==
	<StructureSection load='3syz' size='340' side='right' caption='[[3syz]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3syz' size='340' side='right' caption='[[3syz]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3syz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_aquaticus Thermus aquaticus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SYZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SYZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3syz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SYZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SYZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMN:(1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>BMN</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMN:(1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>BMN</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sv4\|3sv4]], [[3sv3\|3sv3]], [[3svn\|3svn]], [[3svo\|3svo]], [[3sz2\|3sz2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sv4\|3sv4]], [[3sv3\|3sv3]], [[3svn\|3svn]], [[3svo\|3svo]], [[3sz2\|3sz2]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol I, pol1, polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ~~Thermus aquaticus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol I, pol1, polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</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=3syz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3syz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3syz RCSB], [http://www.ebi.ac.uk/pdbsum/3syz 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=3syz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3syz OCA], [http://pdbe.org/3syz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3syz RCSB], [http://www.ebi.ac.uk/pdbsum/3syz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3syz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 19:
	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 3syz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 25104]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Thermus aquaticus]]
	[[Category: Betz, K]]		[[Category: Betz, K]]
	[[Category: Diederichs, K]]		[[Category: Diederichs, K]]

OCA at 10:06, 4 January 2015

OCA — Sun, 04 Jan 2015 10:06:27 GMT

←Older revision		Revision as of 10:06, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3syz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SYZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SYZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[3syz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SYZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SYZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMN:(1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>BMN</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMN:(1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>BMN</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sv4\|3sv4]], [[3sv3\|3sv3]], [[3svn\|3svn]], [[3svo\|3svo]], [[3sz2\|3sz2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sv4\|3sv4]], [[3sv3\|3sv3]], [[3svn\|3svn]], [[3svo\|3svo]], [[3sz2\|3sz2]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol I, pol1, polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol I, pol1, polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</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=3syz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3syz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3syz RCSB], [http://www.ebi.ac.uk/pdbsum/3syz 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=3syz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3syz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3syz RCSB], [http://www.ebi.ac.uk/pdbsum/3syz PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 16:		Line 16:
	KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.,Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A Nat Chem Biol. 2012 Jun 3. doi: 10.1038/nchembio.966. PMID:22660438<ref>PMID:22660438</ref>		KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.,Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A Nat Chem Biol. 2012 Jun 3. doi: 10.1038/nchembio.966. PMID:22660438<ref>PMID:22660438</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>

Line 27:		Line 27:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
-	[[Category: Betz, K.]]	+	[[Category: Betz, K]]
-	[[Category: Diederichs, K.]]	+	[[Category: Diederichs, K]]
-	[[Category: Marx, A.]]	+	[[Category: Marx, A]]
	[[Category: Artificial base]]		[[Category: Artificial base]]
	[[Category: Dna polymerase]]		[[Category: Dna polymerase]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 05:28, 5 June 2014

OCA — Thu, 05 Jun 2014 05:28:08 GMT

←Older revision		Revision as of 05:28, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3syz.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase==
		+	<StructureSection load='3syz' size='340' side='right' caption='[[3syz]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3syz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SYZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SYZ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMN:(1R)-1,4-ANHYDRO-2-DEOXY-1-(3-METHOXYNAPHTHALEN-2-YL)-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>BMN</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sv4\|3sv4]], [[3sv3\|3sv3]], [[3svn\|3svn]], [[3svo\|3svo]], [[3sz2\|3sz2]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol I, pol1, polA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</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=3syz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3syz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3syz RCSB], [http://www.ebi.ac.uk/pdbsum/3syz PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many candidate unnatural DNA base pairs have been developed, but some of the best-replicated pairs adopt intercalated structures in free DNA that are difficult to reconcile with known mechanisms of polymerase recognition. Here we present crystal structures of KlenTaq DNA polymerase at different stages of replication for one such pair, dNaM-d5SICS, and show that efficient replication results from the polymerase itself, inducing the required natural-like structure.

-	~~{{STRUCTURE_3syz\| PDB=3syz \| SCENE= }}~~	+	KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.,Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A Nat Chem Biol. 2012 Jun 3. doi: 10.1038/nchembio.966. PMID:22660438<ref>PMID:22660438</ref>

-	~~===Crystal structure~~ of the ~~large fragment~~ of ~~DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_22660438}}~~	+	==See Also==
-		+	*[[DNA polymerase\|DNA polymerase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~3syz~~]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SYZ OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:022660438<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]

OCA at 06:53, 4 July 2012

OCA — Wed, 04 Jul 2012 06:53:42 GMT

←Older revision		Revision as of 06:53, 4 July 2012
Line 1:		Line 1:
-	[[Image:3syz.~~jpg~~\|left\|200px]]	+	[[Image:3syz.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3syz", 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_3syz\| PDB=3syz \| SCENE= }}		{{STRUCTURE_3syz\| PDB=3syz \| SCENE= }}

	===Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase===		===Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase===

		+	{{ABSTRACT_PUBMED_22660438}}

	==About this Structure==		==About this Structure==
	[[3syz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SYZ OCA].		[[3syz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SYZ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022660438</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]

OCA at 07:51, 6 June 2012

OCA — Wed, 06 Jun 2012 07:51:06 GMT

←Older revision		Revision as of 07:51, 6 June 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3syz.jpg\|left\|200px]]

-	The ~~entry 3syz~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3syz", 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_3syz\| PDB=3syz \| SCENE= }}

-	~~Authors: Betz, K., Diederichs, K., Marx, A.~~	+	===Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase===

-	~~Description: Crystal~~ structure ~~of the large fragment of~~ DNA polymerase ~~I from~~ Thermus ~~Aquaticus in an open binary~~ complex ~~with dNaM as templating nucleobase~~	+
		+	==About this Structure==
		+	[[3syz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SYZ OCA].
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Thermus aquaticus]]
		+	[[Category: Betz, K.]]
		+	[[Category: Diederichs, K.]]
		+	[[Category: Marx, A.]]
		+	[[Category: Artificial base]]
		+	[[Category: Dna polymerase]]
		+	[[Category: Transferase-dna complex]]

OCA at 07:07, 24 August 2011

OCA — Wed, 24 Aug 2011 07:07:30 GMT

←Older revision		Revision as of 07:07, 24 August 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Betz, K., Diederichs, K., Marx, A.		Authors: Betz, K., Diederichs, K., Marx, A.

	Description: Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase		Description: Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase

OCA: Protected "3syz" [edit=sysop:move=sysop]

OCA — Wed, 27 Jul 2011 05:45:12 GMT

Protected "3syz" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:45, 27 July 2011

OCA: New page: '''Unreleased structure''' The entry 3syz is ON HOLD Authors: Betz, K., Diederichs, K., Marx, A. Description: Crystal structure of the large fragment of DNA polymerase I from Thermus A...

OCA — Wed, 27 Jul 2011 05:45:11 GMT

New page: '''Unreleased structure''' The entry 3syz is ON HOLD Authors: Betz, K., Diederichs, K., Marx, A. Description: Crystal structure of the large fragment of DNA polymerase I from Thermus A...

New page

'''Unreleased structure'''

The entry 3syz is ON HOLD

Authors: Betz, K., Diederichs, K., Marx, A.

Description: Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase