5oxj - Revision history

OCA at 01:27, 28 December 2023

OCA — Thu, 28 Dec 2023 01:27:42 GMT

←Older revision		Revision as of 01:27, 28 December 2023
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	==Crystal structure of KlenTaq mutant M747K in a closed ternary complex with a O6-MeG:BenziTP base pair==		==Crystal structure of KlenTaq mutant M747K in a closed ternary complex with a O6-MeG:BenziTP base pair==
-	<StructureSection load='5oxj' size='340' side='right' caption='[[5oxj]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5oxj' size='340' side='right'caption='[[5oxj]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5oxj]] 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=5OXJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OXJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5oxj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OXJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OXJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NZI:[(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)oxolan-2-yl]methyl+[oxidanyl(phosphonooxy)phosphoryl]+hydrogen+phosphate'>NZI</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]] 2Å</td></tr>
-	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6OG:6-O-METHYL+GUANOSINE-5-MONOPHOSPHATE'>6OG</scene>, <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=6OG:6-O-METHYL+GUANOSINE-5-MONOPHOSPHATE'>6OG</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NZI:[(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)oxolan-2-yl]methyl+[oxidanyl(phosphonooxy)phosphoryl]+hydrogen+phosphate'>NZI</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA, pol1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</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=5oxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oxj OCA], [https://pdbe.org/5oxj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5oxj RCSB], [https://www.ebi.ac.uk/pdbsum/5oxj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5oxj ProSAT]</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=5oxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oxj OCA], [~~http~~://pdbe.org/5oxj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5oxj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5oxj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5oxj ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5oxj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5oxj" 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 25104~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~DNA-directed DNA polymerase~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Betz, K~~]]	+	[[Category: Thermus aquaticus]]
-	[[Category: ~~Diederichs,~~ K]]	+	[[Category: Betz K]]
-	[[Category: ~~Marx, A~~]]	+	[[Category: Diederichs K]]
-	[[Category: ~~Dna polymerase]]~~	+	[[Category: Marx A]]
-	~~[[Category: Transferase~~]]	+

OCA at 07:46, 6 December 2017

OCA — Wed, 06 Dec 2017 07:46:16 GMT

←Older revision		Revision as of 07:46, 6 December 2017
Line 3:		Line 3:
	<StructureSection load='5oxj' size='340' side='right' caption='[[5oxj]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5oxj' size='340' side='right' caption='[[5oxj]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5oxj]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OXJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OXJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5oxj]] 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=5OXJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OXJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NZI:[(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)oxolan-2-yl]methyl+[oxidanyl(phosphonooxy)phosphoryl]+hydrogen+phosphate'>NZI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NZI:[(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)oxolan-2-yl]methyl+[oxidanyl(phosphonooxy)phosphoryl]+hydrogen+phosphate'>NZI</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6OG:6-O-METHYL+GUANOSINE-5-MONOPHOSPHATE'>6OG</scene>, <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=6OG:6-O-METHYL+GUANOSINE-5-MONOPHOSPHATE'>6OG</scene>, <scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA, pol1 ([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=5oxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oxj OCA], [http://pdbe.org/5oxj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oxj RCSB], [http://www.ebi.ac.uk/pdbsum/5oxj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oxj ProSAT]</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=5oxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oxj OCA], [http://pdbe.org/5oxj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oxj RCSB], [http://www.ebi.ac.uk/pdbsum/5oxj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oxj ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 25104]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Betz, K]]		[[Category: Betz, K]]

OCA at 06:10, 29 November 2017

OCA — Wed, 29 Nov 2017 06:10:58 GMT

←Older revision		Revision as of 06:10, 29 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5oxj is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of KlenTaq mutant M747K in a closed ternary complex with a O6-MeG:BenziTP base pair==
		+	<StructureSection load='5oxj' size='340' side='right' caption='[[5oxj]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5oxj]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OXJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OXJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NZI:[(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)oxolan-2-yl]methyl+[oxidanyl(phosphonooxy)phosphoryl]+hydrogen+phosphate'>NZI</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6OG:6-O-METHYL+GUANOSINE-5-MONOPHOSPHATE'>6OG</scene>, <scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></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=5oxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oxj OCA], [http://pdbe.org/5oxj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oxj RCSB], [http://www.ebi.ac.uk/pdbsum/5oxj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oxj ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The possibility to sequence cytotoxic O(6)-alkylG DNA adducts would greatly benefit research. Recently we reported a benzimidazole-derived nucleotide that is selectively incorporated opposite the damaged site by a mutated DNA polymerase. Here we provide the structural basis for this reaction which may spur future developments in DNA damage sequencing.

-	~~Authors: Betz~~, K., ~~Diederichs~~, K., ~~Marx~~, A.	+	Structural basis for the selective incorporation of an artificial nucleotide opposite a DNA adduct by a DNA polymerase.,Betz K, Nilforoushan A, Wyss LA, Diederichs K, Sturla SJ, Marx A Chem Commun (Camb). 2017 Nov 23;53(94):12704-12707. doi: 10.1039/c7cc07173f. PMID:29136072<ref>PMID:29136072</ref>

-	~~Description: Crystal structure of KlenTaq mutant M747K in~~ a ~~closed ternary complex with a O6~~-~~MeG~~:~~BenziTP base pair~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Diederichs, K~~]]	+	<div class="pdbe-citations 5oxj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed DNA polymerase]]
	[[Category: Betz, K]]		[[Category: Betz, K]]
		+	[[Category: Diederichs, K]]
	[[Category: Marx, A]]		[[Category: Marx, A]]
		+	[[Category: Dna polymerase]]
		+	[[Category: Transferase]]

OCA at 05:19, 11 October 2017

OCA — Wed, 11 Oct 2017 05:19:21 GMT

←Older revision		Revision as of 05:19, 11 October 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5oxj is ON HOLD	+	The entry 5oxj is ON HOLD until Paper Publication

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

OCA: Protected "5oxj" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:58:14 GMT

Protected "5oxj" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:58, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5oxj is ON HOLD Authors: Betz, K., Diederichs, K., Marx, A. Description: Crystal structure of KlenTaq mutant M747K in a closed ternary complex with...

OCA — Wed, 27 Sep 2017 12:58:13 GMT

New page: '''Unreleased structure''' The entry 5oxj is ON HOLD Authors: Betz, K., Diederichs, K., Marx, A. Description: Crystal structure of KlenTaq mutant M747K in a closed ternary complex with...

New page

'''Unreleased structure'''

The entry 5oxj is ON HOLD

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

Description: Crystal structure of KlenTaq mutant M747K in a closed ternary complex with a O6-MeG:BenziTP base pair
[[Category: Unreleased Structures]]
[[Category: Diederichs, K]]
[[Category: Betz, K]]
[[Category: Marx, A]]