3lk9 - Revision history

OCA at 08:38, 6 September 2023

OCA — Wed, 06 Sep 2023 08:38:58 GMT

←Older revision		Revision as of 08:38, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3lk9' size='340' side='right'caption='[[3lk9]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3lk9' size='340' side='right'caption='[[3lk9]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lk9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LK9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LK9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lk9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LK9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LK9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TFF:5-O-[(R)-{[(R)-[DIFLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL](DIFLUORO)METHYL}(HYDROXY)PHOSPHORYL]THYMIDINE'>TFF</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]] 2.5Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gdx\|3gdx]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TFF:5-O-[(R)-{[(R)-[DIFLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL](DIFLUORO)METHYL}(HYDROXY)PHOSPHORYL]THYMIDINE'>TFF</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=3lk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lk9 OCA], [https://pdbe.org/3lk9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lk9 RCSB], [https://www.ebi.ac.uk/pdbsum/3lk9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lk9 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=3lk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lk9 OCA], [https://pdbe.org/3lk9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lk9 RCSB], [https://www.ebi.ac.uk/pdbsum/3lk9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lk9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>	+	[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 3lk9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3lk9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Batra~~, V K~~]]	+	[[Category: Batra VK]]
-	[[Category: Beard~~, W A~~]]	+	[[Category: Beard WA]]
-	[[Category: Goodman~~, M F~~]]	+	[[Category: Goodman MF]]
-	[[Category: Kashemirov~~, B A~~]]	+	[[Category: Kashemirov BA]]
-	[[Category: McKenna~~, C E~~]]	+	[[Category: McKenna CE]]
-	[[Category: Oertell, K]]	+	[[Category: Oertell K]]
-	[[Category: Pedersen~~, L C~~]]	+	[[Category: Pedersen LC]]
-	[[Category: Prakash~~, G K.Surya~~]]	+	[[Category: Surya Prakash GK]]
-	[[Category: Upton~~, T G~~]]	+	[[Category: Upton TG]]
-	[[Category: Wilson~~, S H~~]]	+	[[Category: Wilson SH]]
-	[[Category: Zibinsky, M]]	+	[[Category: Zibinsky M]]
-	~~[[Category: Dna damage]]~~	+
-	~~[[Category: Dna polyemrase]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Dna replication]]~~	+
-	~~[[Category: Dna synthesis]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Dna-directed dna polymerase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Magnesium]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Methylation]]~~	+
-	~~[[Category: Nucleotidyl transferase]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 13:40, 4 May 2022

OCA — Wed, 04 May 2022 13:40:57 GMT

←Older revision		Revision as of 13:40, 4 May 2022
Line 1:		Line 1:

	==DNA polymerase beta with a gapped DNA substrate and dTMP(CF2)P(CF2)P==		==DNA polymerase beta with a gapped DNA substrate and dTMP(CF2)P(CF2)P==
-	<StructureSection load='3lk9' size='340' side='right' caption='[[3lk9]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='3lk9' size='340' side='right'caption='[[3lk9]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lk9]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LK9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3LK9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lk9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LK9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LK9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TFF:5-O-[(R)-{[(R)-[DIFLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL](DIFLUORO)METHYL}(HYDROXY)PHOSPHORYL]THYMIDINE'>TFF</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TFF:5-O-[(R)-{[(R)-[DIFLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL](DIFLUORO)METHYL}(HYDROXY)PHOSPHORYL]THYMIDINE'>TFF</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gdx\|3gdx]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gdx\|3gdx]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3lk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lk9 OCA], [~~http~~://pdbe.org/3lk9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3lk9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3lk9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3lk9 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=3lk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lk9 OCA], [https://pdbe.org/3lk9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lk9 RCSB], [https://www.ebi.ac.uk/pdbsum/3lk9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lk9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>	+	[[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 3lk9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3lk9" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Batra, V K]]		[[Category: Batra, V K]]
	[[Category: Beard, W A]]		[[Category: Beard, W A]]

OCA at 12:02, 4 August 2016

OCA — Thu, 04 Aug 2016 12:02:19 GMT

←Older revision		Revision as of 12:02, 4 August 2016
Line 1:		Line 1:
		+
	==DNA polymerase beta with a gapped DNA substrate and dTMP(CF2)P(CF2)P==		==DNA polymerase beta with a gapped DNA substrate and dTMP(CF2)P(CF2)P==
	<StructureSection load='3lk9' size='340' side='right' caption='[[3lk9]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3lk9' size='340' side='right' caption='[[3lk9]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lk9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LK9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LK9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lk9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LK9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LK9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TFF:5-O-[(R)-{[(R)-[DIFLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL](DIFLUORO)METHYL}(HYDROXY)PHOSPHORYL]THYMIDINE'>TFF</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TFF:5-O-[(R)-{[(R)-[DIFLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL](DIFLUORO)METHYL}(HYDROXY)PHOSPHORYL]THYMIDINE'>TFF</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gdx\|3gdx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gdx\|3gdx]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3lk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lk9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lk9 RCSB], [http://www.ebi.ac.uk/pdbsum/3lk9 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=3lk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lk9 OCA], [http://pdbe.org/3lk9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lk9 RCSB], [http://www.ebi.ac.uk/pdbsum/3lk9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lk9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 3lk9" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Batra, V K]]		[[Category: Batra, V K]]
	[[Category: Beard, W A]]		[[Category: Beard, W A]]

OCA at 14:15, 24 December 2014

OCA — Wed, 24 Dec 2014 14:15:53 GMT

←Older revision		Revision as of 14:15, 24 December 2014
Line 8:		Line 8:
	<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=3lk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lk9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lk9 RCSB], [http://www.ebi.ac.uk/pdbsum/3lk9 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=3lk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lk9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lk9 RCSB], [http://www.ebi.ac.uk/pdbsum/3lk9 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 10:07, 9 December 2014

OCA — Tue, 09 Dec 2014 10:07:11 GMT

←Older revision		Revision as of 10:07, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3lk9.~~png~~\|~~left~~\|~~200px~~]]	+	==DNA polymerase beta with a gapped DNA substrate and dTMP(CF2)P(CF2)P==
		+	<StructureSection load='3lk9' size='340' side='right' caption='[[3lk9]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3lk9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LK9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LK9 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TFF:5-O-[(R)-{[(R)-[DIFLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL](DIFLUORO)METHYL}(HYDROXY)PHOSPHORYL]THYMIDINE'>TFF</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gdx\|3gdx]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3lk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lk9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lk9 RCSB], [http://www.ebi.ac.uk/pdbsum/3lk9 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	It is difficult to overestimate the importance of nucleoside triphosphates in cellular chemistry: They are the building blocks for DNA and RNA and important sources of energy. Modifications of biologically important organic molecules with fluorine are of great interest to chemists and biologists because the size and electronegativity of the fluorine atom can be used to make defined structural alterations to biologically important molecules. Although the concept of nonhydrolyzable nucleotides has been around for some time, the progress in the area of modified triphosphates was limited by the lack of synthetic methods allowing to access bisCF(2)-substituted nucleotide analogs-one of the most interesting classes of nonhydrolyzable nucleotides. These compounds have "correct" polarity and the smallest possible steric perturbation compared to natural nucleotides. No other known nucleotides have these advantages, making bisCF(2)-substituted analogs unique. Herein, we report a concise route for the preparation of hitherto unknown highly acidic and polybasic bis(difluoromethylene)triphosphoric acid 1 using a phosphorous(III)/phosphorous(V) interconversion approach. The analog 1 compared to triphosphoric acid is enzymatically nonhydrolyzable due to substitution of two bridging oxygen atoms with CF(2) groups, maintaining minimal perturbations in steric bulkiness and overall polarity of the triphosphate polyanion. The fluorinated triphosphoric acid 1 was used for the preparation of the corresponding fluorinated deoxynucleotides (dNTPs). One of these dNTP analogs (dT) was demonstrated to fit into DNA polymerase beta (DNA pol beta) binding pocket by obtaining a 2.5 A resolution crystal structure of a ternary complex with the enzyme. Unexpected dominating effect of triphosphate/Mg(2+) interaction over Watson-Crick hydrogen bonding was found and discussed.

-	~~{{STRUCTURE_3lk9\| PDB=3lk9 \| SCENE= }}~~	+	Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid.,Surya Prakash GK, Zibinsky M, Upton TG, Kashemirov BA, McKenna CE, Oertell K, Goodman MF, Batra VK, Pedersen LC, Beard WA, Shock DD, Wilson SH, Olah GA Proc Natl Acad Sci U S A. 2010 Sep 7;107(36):15693-8. Epub 2010 Aug 19. PMID:20724659<ref>PMID:20724659</ref>

-	~~===DNA polymerase beta with~~ a ~~gapped DNA substrate and dTMP(CF2)P(CF2)P===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20724659}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3lk9]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3LK9 OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:020724659<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Batra, V K.]]	+	[[Category: Batra, V K]]
-	[[Category: Beard, W A.]]	+	[[Category: Beard, W A]]
-	[[Category: Goodman, M F.]]	+	[[Category: Goodman, M F]]
-	[[Category: Kashemirov, B A.]]	+	[[Category: Kashemirov, B A]]
-	[[Category: McKenna, C E.]]	+	[[Category: McKenna, C E]]
-	[[Category: Oertell, K.]]	+	[[Category: Oertell, K]]
-	[[Category: Pedersen, L C.]]	+	[[Category: Pedersen, L C]]
-	[[Category: Prakash, G K.Surya.]]	+	[[Category: Prakash, G K.Surya]]
-	[[Category: Upton, T G.]]	+	[[Category: Upton, T G]]
-	[[Category: Wilson, S H.]]	+	[[Category: Wilson, S H]]
-	[[Category: Zibinsky, M.]]	+	[[Category: Zibinsky, M]]
	[[Category: Dna damage]]		[[Category: Dna damage]]
	[[Category: Dna polyemrase]]		[[Category: Dna polyemrase]]

OCA at 06:18, 20 October 2012

OCA — Sat, 20 Oct 2012 06:18:45 GMT

←Older revision		Revision as of 06:18, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3lk9]] is a 4 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LK9 OCA].	+	[[3lk9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LK9 OCA].

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

OCA at 12:46, 25 July 2012

OCA — Wed, 25 Jul 2012 12:46:59 GMT

←Older revision		Revision as of 12:46, 25 July 2012
Line 1:		Line 1:
-	[[Image:3lk9.~~jpg~~\|left\|200px]]	+	[[Image:3lk9.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3lk9", 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_3lk9\| PDB=3lk9 \| SCENE= }}		{{STRUCTURE_3lk9\| PDB=3lk9 \| SCENE= }}

	===DNA polymerase beta with a gapped DNA substrate and dTMP(CF2)P(CF2)P===		===DNA polymerase beta with a gapped DNA substrate and dTMP(CF2)P(CF2)P===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20724659}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20724659 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20724659}}		{{ABSTRACT_PUBMED_20724659}}

	==About this Structure==		==About this Structure==
-	[[3lk9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LK9 OCA].	+	[[3lk9]] is a 4 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LK9 OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20724659~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020724659</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Batra, V K.]]		[[Category: Batra, V K.]]
Line 35:		Line 27:
	[[Category: Wilson, S H.]]		[[Category: Wilson, S H.]]
	[[Category: Zibinsky, M.]]		[[Category: Zibinsky, M.]]
		+	[[Category: Dna damage]]
		+	[[Category: Dna polyemrase]]
		+	[[Category: Dna repair]]
		+	[[Category: Dna replication]]
		+	[[Category: Dna synthesis]]
		+	[[Category: Dna-binding]]
		+	[[Category: Dna-directed dna polymerase]]
		+	[[Category: Lyase]]
		+	[[Category: Magnesium]]
		+	[[Category: Metal-binding]]
		+	[[Category: Methylation]]
		+	[[Category: Nucleotidyl transferase]]
		+	[[Category: Nucleotidyltransferase]]
		+	[[Category: Nucleus]]
		+	[[Category: Transferase]]
		+	[[Category: Transferase-dna complex]]

OCA: Protected "3lk9" [edit=sysop:move=sysop]

OCA — Wed, 12 Jan 2011 05:14:04 GMT

Protected "3lk9" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:14, 12 January 2011

OCA at 05:14, 12 January 2011

OCA — Wed, 12 Jan 2011 05:14:00 GMT

←Older revision		Revision as of 05:14, 12 January 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3lk9.jpg\|left\|200px]]

-	The ~~entry 3lk9~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3lk9", 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_3lk9\| PDB=3lk9 \| SCENE= }}

-	~~Authors: Zibinsky, M., Surya Prakash, G.K., Upton, T.G., Kashemirov, B.A., McKenna, C.E., Oertell, K., Goodman, M.F., Batra, V.K., Pedersen, L.C., Beard, W.A., Wilson, S.H.~~	+	===DNA polymerase beta with a gapped DNA substrate and dTMP(CF2)P(CF2)P===

-	Description: DNA polymerase beta with a gapped DNA substrate and dTMP(CF2)P(CF2)P

-	~~''Page seeded by~~ [http://oca.weizmann.ac.il/oca OCA ] ~~on Wed Jul 28 12~~:22:~~06 2010''~~	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20724659}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20724659 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20724659}}
		+
		+	==About this Structure==
		+	[[3lk9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LK9 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20724659</ref><references group="xtra"/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Batra, V K.]]
		+	[[Category: Beard, W A.]]
		+	[[Category: Goodman, M F.]]
		+	[[Category: Kashemirov, B A.]]
		+	[[Category: McKenna, C E.]]
		+	[[Category: Oertell, K.]]
		+	[[Category: Pedersen, L C.]]
		+	[[Category: Prakash, G K.Surya.]]
		+	[[Category: Upton, T G.]]
		+	[[Category: Wilson, S H.]]
		+	[[Category: Zibinsky, M.]]

OCA at 08:15, 28 July 2010

OCA — Wed, 28 Jul 2010 08:15:23 GMT

←Older revision		Revision as of 08:15, 28 July 2010
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3lk9 is ON HOLD	+	The entry 3lk9 is ON HOLD until Paper Publication

	Authors: Zibinsky, M., Surya Prakash, G.K., Upton, T.G., Kashemirov, B.A., McKenna, C.E., Oertell, K., Goodman, M.F., Batra, V.K., Pedersen, L.C., Beard, W.A., Wilson, S.H.		Authors: Zibinsky, M., Surya Prakash, G.K., Upton, T.G., Kashemirov, B.A., McKenna, C.E., Oertell, K., Goodman, M.F., Batra, V.K., Pedersen, L.C., Beard, W.A., Wilson, S.H.
Line 7:		Line 7:
	Description: DNA polymerase beta with a gapped DNA substrate and dTMP(CF2)P(CF2)P		Description: DNA polymerase beta with a gapped DNA substrate and dTMP(CF2)P(CF2)P

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Feb 10 16~~:58:55 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 28 12:22:06 2010''