7ict - Revision history

OCA at 11:07, 2 August 2023

OCA — Wed, 02 Aug 2023 11:07:37 GMT

←Older revision		Revision as of 11:07, 2 August 2023
Line 1:		Line 1:
		+
	==DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 AND MGCL2==		==DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 AND MGCL2==
-	<StructureSection load='7ict' size='340' side='right' caption='[[7ict]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='7ict' size='340' side='right'caption='[[7ict]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7ict]] is a 3 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=7ICT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=7ICT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ict]] is a 3 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=7ICT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ICT 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~~>, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[7ice\|7ice]]~~, [[7icf\|7icf]], [[7icg\|7icg]], [[7ich\|7ich]], [[7ici\|7ici]], [[7icj\|7icj]], [[7ick\|7ick]], [[7icl\|7icl]], [[7icm\|7icm]], [[7icn\|7icn]], [[7ico\|7ico]], [[7icp\|7icp]], [[7icq\|7icq]], [[7icr\|7icr]], [[7ics\|7ics]], [[7icu\|7icu]], [[7icv\|7icv]], [[8ica\|8ica]], [[8icb\|8icb]], [[8icc\|8icc]], [[8ice\|8ice]], [[8icf\|8icf]], [[8icg\|8icg]], [[8ich\|8ich]], [[8ici\|8ici]], [[8icj\|8icj]], [[8ick\|8ick]], [[8icl\|8icl]], [[8icm\|8icm]], [[8icn\|8icn]], [[8ico\|8ico]], [[8icp\|8icp]], [[8icq\|8icq]], [[8icr\|8icr]], [[8ics\|8ics]], [[8ict\|8ict]], [[8icu\|8icu]], [[8icv\|8icv]], [[8icw\|8icw]], [[8icx\|8icx]], [[8icy\|8icy]], [[8icz\|8icz]], [[9ica\|9ica]], [[9icb\|9icb]], [[9icc\|9icc]], [[9ice\|9ice]], [[9icf\|9icf]], [[9icg\|9icg]], [[9ich\|9ich]], [[9ici\|9ici]], [[9icj\|9icj]], [[9ick\|9ick]], [[9icl\|9icl]], [[9icm\|9icm]], [[9icn\|9icn]], [[9ico\|9ico]], [[9icp\|9icp]], [[9icq\|9icq]], [[9icr\|9icr]], [[9ics\|9ics]], [[9ict\|9ict]], [[9icu\|9icu]], [[9icv\|9icv]], [[9icw\|9icw]], [[9icx\|9icx]], [[9icy\|9icy]], [[1zqa\|1zqa]], [[1zqb\|1zqb]], [[1zqc\|1zqc]], [[1zqd\|1zqd]], [[1zqe\|1zqe]], [[1zqf\|1zqf]], [[1zqg\|1zqg]], [[1zqh\|1zqh]], [[1zqi\|1zqi]], [[1zqj\|1zqj]], [[1zqk\|1zqk]], [[1zql\|1zql]], [[1zqm\|1zqm]], [[1zqn\|1zqn]], [[1zqo\|1zqo]], [[1zqp\|1zqp]], [[1zqq\|1zqq]], [[1zqr\|1zqr]], [[1zqs\|1zqs]], [[1zqt\|1zqt]]</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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=7ict FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ict OCA], [~~http~~://pdbe.org/7ict PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7ict RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7ict PDBsum]</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=7ict FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ict OCA], [https://pdbe.org/7ict PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ict RCSB], [https://www.ebi.ac.uk/pdbsum/7ict PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ict 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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ic/7ict_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ic/7ict_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>
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	==See Also==		==See Also==
-	*[[DNA polymerase\|DNA polymerase]]	+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Pelletier, H~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Sawaya, M R~~]]	+	[[Category: Pelletier H]]
-	[[Category: ~~Dna repair]]~~	+	[[Category: Sawaya MR]]
-	~~[[Category: Dna replication]]~~	+
-	~~[[Category: Dna-directed dna polymerase]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 00:00, 8 February 2016

OCA — Mon, 08 Feb 2016 00:00:22 GMT

←Older revision		Revision as of 00:00, 8 February 2016
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	<StructureSection load='7ict' size='340' side='right' caption='[[7ict]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='7ict' size='340' side='right' caption='[[7ict]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7ict]] is a 3 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=7ICT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7ICT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ict]] is a 3 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=7ICT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7ICT 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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[7ice\|7ice]], [[7icf\|7icf]], [[7icg\|7icg]], [[7ich\|7ich]], [[7ici\|7ici]], [[7icj\|7icj]], [[7ick\|7ick]], [[7icl\|7icl]], [[7icm\|7icm]], [[7icn\|7icn]], [[7ico\|7ico]], [[7icp\|7icp]], [[7icq\|7icq]], [[7icr\|7icr]], [[7ics\|7ics]], [[7icu\|7icu]], [[7icv\|7icv]], [[8ica\|8ica]], [[8icb\|8icb]], [[8icc\|8icc]], [[8ice\|8ice]], [[8icf\|8icf]], [[8icg\|8icg]], [[8ich\|8ich]], [[8ici\|8ici]], [[8icj\|8icj]], [[8ick\|8ick]], [[8icl\|8icl]], [[8icm\|8icm]], [[8icn\|8icn]], [[8ico\|8ico]], [[8icp\|8icp]], [[8icq\|8icq]], [[8icr\|8icr]], [[8ics\|8ics]], [[8ict\|8ict]], [[8icu\|8icu]], [[8icv\|8icv]], [[8icw\|8icw]], [[8icx\|8icx]], [[8icy\|8icy]], [[8icz\|8icz]], [[9ica\|9ica]], [[9icb\|9icb]], [[9icc\|9icc]], [[9ice\|9ice]], [[9icf\|9icf]], [[9icg\|9icg]], [[9ich\|9ich]], [[9ici\|9ici]], [[9icj\|9icj]], [[9ick\|9ick]], [[9icl\|9icl]], [[9icm\|9icm]], [[9icn\|9icn]], [[9ico\|9ico]], [[9icp\|9icp]], [[9icq\|9icq]], [[9icr\|9icr]], [[9ics\|9ics]], [[9ict\|9ict]], [[9icu\|9icu]], [[9icv\|9icv]], [[9icw\|9icw]], [[9icx\|9icx]], [[9icy\|9icy]], [[1zqa\|1zqa]], [[1zqb\|1zqb]], [[1zqc\|1zqc]], [[1zqd\|1zqd]], [[1zqe\|1zqe]], [[1zqf\|1zqf]], [[1zqg\|1zqg]], [[1zqh\|1zqh]], [[1zqi\|1zqi]], [[1zqj\|1zqj]], [[1zqk\|1zqk]], [[1zql\|1zql]], [[1zqm\|1zqm]], [[1zqn\|1zqn]], [[1zqo\|1zqo]], [[1zqp\|1zqp]], [[1zqq\|1zqq]], [[1zqr\|1zqr]], [[1zqs\|1zqs]], [[1zqt\|1zqt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[7ice\|7ice]], [[7icf\|7icf]], [[7icg\|7icg]], [[7ich\|7ich]], [[7ici\|7ici]], [[7icj\|7icj]], [[7ick\|7ick]], [[7icl\|7icl]], [[7icm\|7icm]], [[7icn\|7icn]], [[7ico\|7ico]], [[7icp\|7icp]], [[7icq\|7icq]], [[7icr\|7icr]], [[7ics\|7ics]], [[7icu\|7icu]], [[7icv\|7icv]], [[8ica\|8ica]], [[8icb\|8icb]], [[8icc\|8icc]], [[8ice\|8ice]], [[8icf\|8icf]], [[8icg\|8icg]], [[8ich\|8ich]], [[8ici\|8ici]], [[8icj\|8icj]], [[8ick\|8ick]], [[8icl\|8icl]], [[8icm\|8icm]], [[8icn\|8icn]], [[8ico\|8ico]], [[8icp\|8icp]], [[8icq\|8icq]], [[8icr\|8icr]], [[8ics\|8ics]], [[8ict\|8ict]], [[8icu\|8icu]], [[8icv\|8icv]], [[8icw\|8icw]], [[8icx\|8icx]], [[8icy\|8icy]], [[8icz\|8icz]], [[9ica\|9ica]], [[9icb\|9icb]], [[9icc\|9icc]], [[9ice\|9ice]], [[9icf\|9icf]], [[9icg\|9icg]], [[9ich\|9ich]], [[9ici\|9ici]], [[9icj\|9icj]], [[9ick\|9ick]], [[9icl\|9icl]], [[9icm\|9icm]], [[9icn\|9icn]], [[9ico\|9ico]], [[9icp\|9icp]], [[9icq\|9icq]], [[9icr\|9icr]], [[9ics\|9ics]], [[9ict\|9ict]], [[9icu\|9icu]], [[9icv\|9icv]], [[9icw\|9icw]], [[9icx\|9icx]], [[9icy\|9icy]], [[1zqa\|1zqa]], [[1zqb\|1zqb]], [[1zqc\|1zqc]], [[1zqd\|1zqd]], [[1zqe\|1zqe]], [[1zqf\|1zqf]], [[1zqg\|1zqg]], [[1zqh\|1zqh]], [[1zqi\|1zqi]], [[1zqj\|1zqj]], [[1zqk\|1zqk]], [[1zql\|1zql]], [[1zqm\|1zqm]], [[1zqn\|1zqn]], [[1zqo\|1zqo]], [[1zqp\|1zqp]], [[1zqq\|1zqq]], [[1zqr\|1zqr]], [[1zqs\|1zqs]], [[1zqt\|1zqt]]</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=7ict FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ict OCA], [http://www.rcsb.org/pdb/explore.do?structureId=7ict RCSB], [http://www.ebi.ac.uk/pdbsum/7ict 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=7ict FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ict OCA], [http://pdbe.org/7ict PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7ict RCSB], [http://www.ebi.ac.uk/pdbsum/7ict 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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	<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=7ict ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		Line 27:
	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 7ict" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Pelletier, H]]		[[Category: Pelletier, H]]
	[[Category: Sawaya, M R]]		[[Category: Sawaya, M R]]

OCA at 16:46, 10 December 2014

OCA — Wed, 10 Dec 2014 16:46:34 GMT

←Older revision		Revision as of 16:46, 10 December 2014
Line 1:		Line 1:
-	[[~~Image:~~7ict.~~png~~\|~~left~~\|200px]]	+	==DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 AND MGCL2==
		+	<StructureSection load='7ict' size='340' side='right' caption='[[7ict]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7ict]] is a 3 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=7ICT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7ICT 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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[7ice\|7ice]], [[7icf\|7icf]], [[7icg\|7icg]], [[7ich\|7ich]], [[7ici\|7ici]], [[7icj\|7icj]], [[7ick\|7ick]], [[7icl\|7icl]], [[7icm\|7icm]], [[7icn\|7icn]], [[7ico\|7ico]], [[7icp\|7icp]], [[7icq\|7icq]], [[7icr\|7icr]], [[7ics\|7ics]], [[7icu\|7icu]], [[7icv\|7icv]], [[8ica\|8ica]], [[8icb\|8icb]], [[8icc\|8icc]], [[8ice\|8ice]], [[8icf\|8icf]], [[8icg\|8icg]], [[8ich\|8ich]], [[8ici\|8ici]], [[8icj\|8icj]], [[8ick\|8ick]], [[8icl\|8icl]], [[8icm\|8icm]], [[8icn\|8icn]], [[8ico\|8ico]], [[8icp\|8icp]], [[8icq\|8icq]], [[8icr\|8icr]], [[8ics\|8ics]], [[8ict\|8ict]], [[8icu\|8icu]], [[8icv\|8icv]], [[8icw\|8icw]], [[8icx\|8icx]], [[8icy\|8icy]], [[8icz\|8icz]], [[9ica\|9ica]], [[9icb\|9icb]], [[9icc\|9icc]], [[9ice\|9ice]], [[9icf\|9icf]], [[9icg\|9icg]], [[9ich\|9ich]], [[9ici\|9ici]], [[9icj\|9icj]], [[9ick\|9ick]], [[9icl\|9icl]], [[9icm\|9icm]], [[9icn\|9icn]], [[9ico\|9ico]], [[9icp\|9icp]], [[9icq\|9icq]], [[9icr\|9icr]], [[9ics\|9ics]], [[9ict\|9ict]], [[9icu\|9icu]], [[9icv\|9icv]], [[9icw\|9icw]], [[9icx\|9icx]], [[9icy\|9icy]], [[1zqa\|1zqa]], [[1zqb\|1zqb]], [[1zqc\|1zqc]], [[1zqd\|1zqd]], [[1zqe\|1zqe]], [[1zqf\|1zqf]], [[1zqg\|1zqg]], [[1zqh\|1zqh]], [[1zqi\|1zqi]], [[1zqj\|1zqj]], [[1zqk\|1zqk]], [[1zql\|1zql]], [[1zqm\|1zqm]], [[1zqn\|1zqn]], [[1zqo\|1zqo]], [[1zqp\|1zqp]], [[1zqq\|1zqq]], [[1zqr\|1zqr]], [[1zqs\|1zqs]], [[1zqt\|1zqt]]</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=7ict FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ict OCA], [http://www.rcsb.org/pdb/explore.do?structureId=7ict RCSB], [http://www.ebi.ac.uk/pdbsum/7ict 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/ic/7ict_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 ==
		+	When crystals of human DNA polymerase beta (pol beta) complexed with DNA [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996) Biochemistry 35, 12742-12761] are soaked in the presence of dATP and Mn2+, X-ray structural analysis shows that nucleotidyl transfer to the primer 3'-OH takes place directly in the crystals, even though the DNA is blunt-ended at the active site. Under similar crystal-soaking conditions, there is no evidence for a reaction when Mn2+ is replaced by Mg2+, which is thought to be the divalent metal ion utilized by most polymerases in vivo. These results suggest that one way Mn2+ may manifest its mutagenic effect on polymerases is by promoting greater reactivity than Mg2+ at the catalytic site, thereby allowing the nucleotidyl transfer reaction to take place with little or no regard to instructions from a template. Non-template-directed nucleotidyl transfer is also observed when pol beta-DNA cocrystals are soaked in the presence of dATP and Zn2+, but the reaction products differ in that the sugar moiety of the incorporated nucleotide appears distorted or otherwise cleaved, in agreement with reports that Zn2+ may act as a polymerase inhibitor rather than as a mutagen [Sirover, M. A., & Loeb, L. A. (1976) Science 194, 1434-1436]. Although no reaction is observed when crystals are soaked in the presence of dATP and other metal ions such as Ca2+, Co2+, Cr3+, or Ni2+, X-ray structural analyses show that these metal ions coordinate the triphosphate moiety of the nucleotide in a manner that differs from that observed with Mg2+. In addition, all metal ions tested, with the exception of Mg2+, promote a change in the side-chain position of aspartic acid 192, which is one of three highly conserved active-site carboxylate residues. Soaking experiments with nucleotides other than dATP (namely, dCTP, dGTP, dTTP, ATP, ddATP, ddCTP, AZT-TP, and dATP alpha S) reveal a non-base-specific binding site on pol beta for the triphosphate and sugar moieties of a nucleotide, suggesting a possible mechanism for nucleotide selectivity whereby triphosphate-sugar binding precedes a check for correct base pairing with the template.

-	~~{{STRUCTURE_7ict\| PDB=7ict \| SCENE= }}~~	+	A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta.,Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J Biochemistry. 1996 Oct 1;35(39):12762-77. PMID:8841119<ref>PMID:8841119</ref>

-	~~===DNA POLYMERASE BETA (E.C.2.7.7.7)~~/~~DNA COMPLEX~~, ~~SOAKED IN THE PRESENCE OF ZNCL2 AND MGCL2===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_8841119}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[7ict]] is~~ a ~~3 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=7ICT OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:008841119<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Pelletier, H.]]	+	[[Category: Pelletier, H]]
-	[[Category: Sawaya, M R.]]	+	[[Category: Sawaya, M R]]
	[[Category: Dna repair]]		[[Category: Dna repair]]
	[[Category: Dna replication]]		[[Category: Dna replication]]

OCA at 08:13, 20 October 2012

OCA — Sat, 20 Oct 2012 08:13:55 GMT

←Older revision		Revision as of 08:13, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[7ict]] is a 3 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=7ICT OCA].	+	[[7ict]] is a 3 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=7ICT OCA].

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

OCA: Protected "7ict" [edit=sysop:move=sysop]

OCA — Wed, 25 Jul 2012 18:52:23 GMT

Protected "7ict" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:52, 25 July 2012

OCA at 18:52, 25 July 2012

OCA — Wed, 25 Jul 2012 18:52:22 GMT

←Older revision		Revision as of 18:52, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:7ict.png\|left\|200px]]		[[Image:7ict.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_7ict", 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_7ict\| PDB=7ict \| SCENE= }}		{{STRUCTURE_7ict\| PDB=7ict \| SCENE= }}

	===DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 AND MGCL2===		===DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 AND MGCL2===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_8841119}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 8841119 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_8841119}}		{{ABSTRACT_PUBMED_8841119}}

	==About this Structure==		==About this Structure==
-	~~7ICT~~ is a 3 ~~chains~~ structure of ~~sequences~~ 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=7ICT OCA].	+	[[7ict]] is a 3 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=7ICT OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~8841119~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:008841119</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Pelletier, H.]]		[[Category: Pelletier, H.]]
Line 31:		Line 22:
	[[Category: Dna-directed dna polymerase]]		[[Category: Dna-directed dna polymerase]]
	[[Category: Nucleotidyltransferase]]		[[Category: Nucleotidyltransferase]]
-		+	[[Category: Transferase-dna complex]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 17:21:33 2009''~~	+

OCA at 15:21, 16 February 2009

OCA — Mon, 16 Feb 2009 15:21:35 GMT

←Older revision		Revision as of 15:21, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	7ICT is a ~~[[Single protein]]~~ structure of ~~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=7ICT OCA].	+	7ICT is a 3 chains structure of sequences 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=7ICT OCA].

	==Reference==		==Reference==
-	~~A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta., Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J, Biochemistry. 1996 Oct 1;35(39):12762-77.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/8841119 8841119]~~	+	<ref group="xtra">PMID:8841119</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Single protein]]
	[[Category: Pelletier, H.]]		[[Category: Pelletier, H.]]
	[[Category: Sawaya, M R.]]		[[Category: Sawaya, M R.]]
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	[[Category: Nucleotidyltransferase]]		[[Category: Nucleotidyltransferase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 3 14~~:39:~~44 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 17:21:33 2009''

OCA at 11:39, 3 July 2008

OCA — Thu, 03 Jul 2008 11:39:45 GMT

←Older revision		Revision as of 11:39, 3 July 2008
Line 1:		Line 1:
-	[[Image:7ict.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:7ict.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_7ict\| PDB=7ict \| SCENE= }}		{{STRUCTURE_7ict\| PDB=7ict \| SCENE= }}

-	~~'''~~DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 AND MGCL2~~'''~~	+	===DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 AND MGCL2===


-	~~==Overview==~~	+	<!--
-	~~When crystals of human DNA polymerase beta (pol beta) complexed with DNA [Pelletier~~, H., ~~Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996) Biochemistry 35, 12742-12761] are soaked in~~ the ~~presence of dATP and Mn2+, X-ray structural analysis shows that nucleotidyl transfer~~ to the primer 3'-OH takes place directly in the crystals, even though the DNA is blunt-ended at the active site. Under similar crystal-soaking conditions, there is no evidence for a reaction when Mn2+ is replaced by Mg2+, which is thought to be the divalent metal ion utilized by most polymerases in vivo. These results suggest that one way Mn2+ may manifest its mutagenic effect on ~~polymerases is by promoting greater reactivity than Mg2+~~ at ~~the catalytic site, thereby allowing the nucleotidyl transfer reaction to take place with little or no regard to instructions from a template~~. Non-template-directed nucleotidyl transfer is also observed when pol beta-DNA cocrystals are soaked in the presence of dATP and Zn2+, but the reaction products differ in that the sugar moiety of the incorporated nucleotide appears distorted or otherwise cleaved, in agreement with reports that Zn2+ may act as a polymerase inhibitor rather than as a mutagen [Sirover, M. ~~A., & Loeb, L. A. (1976~~) ~~Science 194~~, ~~1434-1436]. Although no reaction~~ is ~~observed when crystals are soaked in~~ the presence of dATP and other metal ions such as Ca2+, Co2+, Cr3+, or Ni2+, X-ray structural analyses show that these metal ions coordinate the triphosphate moiety of the nucleotide in a manner that differs from that observed with Mg2+. ~~In addition, all metal ions tested, with the exception of Mg2+, promote a change in the side~~-~~chain position of aspartic acid 192, which is one of three highly conserved active~~-site carboxylate residues. Soaking experiments with nucleotides other than dATP (namely, dCTP, dGTP, dTTP, ATP, ddATP, ddCTP, AZT-TP, and dATP alpha S) reveal a non-base-specific binding site on pol beta for the triphosphate and sugar moieties of a nucleotide, suggesting a possible mechanism for nucleotide selectivity whereby triphosphate-sugar binding precedes a check for correct base pairing with the template.	+	The line below this paragraph, {{ABSTRACT_PUBMED_8841119}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 8841119 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_8841119}}

	==About this Structure==		==About this Structure==
Line 28:		Line 32:
	[[Category: Dna-directed dna polymerase]]		[[Category: Dna-directed dna polymerase]]
	[[Category: Nucleotidyltransferase]]		[[Category: Nucleotidyltransferase]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:46:12 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 14:39:44 2008''

OCA at 19:46, 4 May 2008

OCA — Sun, 04 May 2008 19:46:13 GMT

←Older revision		Revision as of 19:46, 4 May 2008
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	[[Image:7ict.gif\|left\|200px]]		[[Image:7ict.gif\|left\|200px]]

-	{{Structure	+	<!--
-	\|PDB~~= 7ict \|SIZE=350\|CAPTION= <~~scene ~~name='initialview01'>7ict</scene>~~, ~~resolution 2~~.~~800Å~~	+	The line below this paragraph, containing "STRUCTURE_7ict", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <scene name='pdbligand=DA:2'~~-~~DEOXYADENOSINE~~-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	\|~~ACTIVITY~~=	+	or leave the SCENE parameter empty for the default display.
-	\|~~GENE~~=	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_7ict\| PDB=7ict \| SCENE= }}
-	~~\|RELATEDENTRY=~~	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7ict FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ict OCA], [http://www.ebi.ac.uk/pdbsum/7ict PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=7ict RCSB]</span>	+
-	}}	+

	'''DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 AND MGCL2'''		'''DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 AND MGCL2'''
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	[[Category: Pelletier, H.]]		[[Category: Pelletier, H.]]
	[[Category: Sawaya, M R.]]		[[Category: Sawaya, M R.]]
-	[[Category: ~~complex (nucleotidyltransferase/dna)]]~~	+	[[Category: Dna repair]]
-	~~[[Category: dna~~ repair]]	+	[[Category: Dna replication]]
-	[[Category: ~~dna~~ replication]]	+	[[Category: Dna-directed dna polymerase]]
-	[[Category: ~~dna~~-directed dna polymerase]]	+	[[Category: Nucleotidyltransferase]]
-	[[Category: ~~nucleotidyltransferase~~]]	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:46:12 2008''
-		+
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:44:27 2008''	+

OCA at 02:44, 31 March 2008

OCA — Mon, 31 Mar 2008 02:44:28 GMT

←Older revision		Revision as of 02:44, 31 March 2008
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	\|PDB= 7ict \|SIZE=350\|CAPTION= <scene name='initialview01'>7ict</scene>, resolution 2.800Å		\|PDB= 7ict \|SIZE=350\|CAPTION= <scene name='initialview01'>7ict</scene>, resolution 2.800Å
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> ~~and~~ <scene name='pdbligand=ZN:ZINC ION'>ZN</scene>	+	\|LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE=		\|GENE=
		+	\|DOMAIN=
		+	\|RELATEDENTRY=
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7ict FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ict OCA], [http://www.ebi.ac.uk/pdbsum/7ict PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=7ict RCSB]</span>
	}}		}}

Line 24:		Line 27:
	[[Category: Pelletier, H.]]		[[Category: Pelletier, H.]]
	[[Category: Sawaya, M R.]]		[[Category: Sawaya, M R.]]
-	[[Category: NA]]
-	[[Category: ZN]]
	[[Category: complex (nucleotidyltransferase/dna)]]		[[Category: complex (nucleotidyltransferase/dna)]]
	[[Category: dna repair]]		[[Category: dna repair]]
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	[[Category: nucleotidyltransferase]]		[[Category: nucleotidyltransferase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar ~~20 19:14~~:44 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:44:27 2008''