2hsk - Revision history

OCA at 06:41, 1 May 2024

OCA — Wed, 01 May 2024 06:41:04 GMT

←Older revision		Revision as of 06:41, 1 May 2024
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsk OCA], [https://pdbe.org/2hsk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hsk RCSB], [https://www.ebi.ac.uk/pdbsum/2hsk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hsk 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=2hsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsk OCA], [https://pdbe.org/2hsk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hsk RCSB], [https://www.ebi.ac.uk/pdbsum/2hsk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hsk ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A 4'-oxidized abasic site (X) has been synthesized in a defined duplex DNA sequence, 5'-d(CCAAAGXACCGGG)-3'/3'-d(GGTTTCATGGCCC)-5' (1). Its structure has been determined by two-dimensional NMR methods, molecular modeling, and molecular dynamics simulations. 1 is globally B-form with the base (A) opposite X intrahelical and well-stacked. Only the alpha anomer of X is observed, and the abasic site deoxyribose is largely intrahelical. These results are compared with a normal abasic site (Y) in the same sequence context (2). Y is composed of a 60:40 mixture of alpha and beta anomers (2alpha and 2beta). In both 2alpha and 2beta, the base (A) opposite Y is intrahelical and well-stacked and the abasic site deoxyribose is predominantly extrahelical, consistent with the reported structures of the normal abasic site in a similar sequence context [Hoehn, S. T., Turner, C. J., and Stubbe, J. (2001) Nucleic Acids Res. 29, 3413-3423]. Molecular dynamics simulations reveal that the normal abasic site appears to be conformationally more flexible than the 4'-oxidized abasic site. The importance of the structure and flexibility of the abasic site in the recognition by the DNA repair enzyme Ape1 is discussed.
-
-	Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sites.,Chen J, Dupradeau FY, Case DA, Turner CJ, Stubbe J Biochemistry. 2007 Mar 20;46(11):3096-107. Epub 2007 Feb 27. PMID:17323932<ref>PMID:17323932</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2hsk" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:50, 22 November 2023

OCA — Wed, 22 Nov 2023 11:50:03 GMT

←Older revision		Revision as of 11:50, 22 November 2023
Line 1:		Line 1:

	==NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)==		==NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)==
-	<StructureSection load='2hsk' size='340' side='right'caption='[[2hsk~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>	+	<StructureSection load='2hsk' size='340' side='right'caption='[[2hsk]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hsk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HSK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hsk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HSK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2hou\|2hou]], [[2hpx\|2hpx]], [[2hss\|2hss]], [[2hsl\|2hsl]], [[2hsr\|2hsr]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></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=2hsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsk OCA], [https://pdbe.org/2hsk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hsk RCSB], [https://www.ebi.ac.uk/pdbsum/2hsk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hsk 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=2hsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsk OCA], [https://pdbe.org/2hsk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hsk RCSB], [https://www.ebi.ac.uk/pdbsum/2hsk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hsk ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Case, D A~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Chen, J~~]]	+	[[Category: Case DA]]
-	[[Category: ~~Dupradeau, F Y~~]]	+	[[Category: Chen J]]
-	[[Category: ~~Stubbe, J~~]]	+	[[Category: Dupradeau FY]]
-	[[Category: ~~Turner, C~~ J]]	+	[[Category: Stubbe J]]
-	[[Category: ~~Abasic site]]~~	+	[[Category: Turner CJ]]
-	~~[[Category: Ape1]]~~	+
-	~~[[Category: Base excision repair]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Dna lesion~~]]	+

OCA at 11:29, 16 February 2022

OCA — Wed, 16 Feb 2022 11:29:09 GMT

←Older revision		Revision as of 11:29, 16 February 2022
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	<StructureSection load='2hsk' size='340' side='right'caption='[[2hsk]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2hsk' size='340' side='right'caption='[[2hsk]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hsk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2HSK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hsk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HSK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hou\|2hou]], [[2hpx\|2hpx]], [[2hss\|2hss]], [[2hsl\|2hsl]], [[2hsr\|2hsr]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2hou\|2hou]], [[2hpx\|2hpx]], [[2hss\|2hss]], [[2hsl\|2hsl]], [[2hsr\|2hsr]]</div></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2hsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsk OCA], [~~http~~://pdbe.org/2hsk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2hsk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2hsk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2hsk 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=2hsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsk OCA], [https://pdbe.org/2hsk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hsk RCSB], [https://www.ebi.ac.uk/pdbsum/2hsk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hsk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:14, 13 May 2020

OCA — Wed, 13 May 2020 06:14:54 GMT

←Older revision		Revision as of 06:14, 13 May 2020
Line 1:		Line 1:

	==NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)==		==NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)==
-	<StructureSection load='2hsk' size='340' side='right' caption='[[2hsk]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>	+	<StructureSection load='2hsk' size='340' side='right'caption='[[2hsk]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hsk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2HSK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hsk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2HSK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hou\|2hou]], [[2hpx\|2hpx]], [[2hss\|2hss]], [[2hsl\|2hsl]], [[2hsr\|2hsr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hou\|2hou]], [[2hpx\|2hpx]], [[2hss\|2hss]], [[2hsl\|2hsl]], [[2hsr\|2hsr]]</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=2hsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsk OCA], [http://pdbe.org/2hsk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hsk RCSB], [http://www.ebi.ac.uk/pdbsum/2hsk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hsk ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2hsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsk OCA], [http://pdbe.org/2hsk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hsk RCSB], [http://www.ebi.ac.uk/pdbsum/2hsk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hsk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Case, D A]]		[[Category: Case, D A]]
	[[Category: Chen, J]]		[[Category: Chen, J]]

OCA at 06:11, 27 June 2018

OCA — Wed, 27 Jun 2018 06:11:20 GMT

←Older revision		Revision as of 06:11, 27 June 2018
Line 1:		Line 1:
		+
	==NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)==		==NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)==
	<StructureSection load='2hsk' size='340' side='right' caption='[[2hsk]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2hsk' size='340' side='right' caption='[[2hsk]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hou\|2hou]], [[2hpx\|2hpx]], [[2hss\|2hss]], [[2hsl\|2hsl]], [[2hsr\|2hsr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hou\|2hou]], [[2hpx\|2hpx]], [[2hss\|2hss]], [[2hsl\|2hsl]], [[2hsr\|2hsr]]</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=2hsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsk OCA], [http://pdbe.org/2hsk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hsk RCSB], [http://www.ebi.ac.uk/pdbsum/2hsk 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=2hsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsk OCA], [http://pdbe.org/2hsk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hsk RCSB], [http://www.ebi.ac.uk/pdbsum/2hsk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hsk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 12:41, 11 September 2015

OCA — Fri, 11 Sep 2015 12:41:26 GMT

←Older revision		Revision as of 12:41, 11 September 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hou\|2hou]], [[2hpx\|2hpx]], [[2hss\|2hss]], [[2hsl\|2hsl]], [[2hsr\|2hsr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hou\|2hou]], [[2hpx\|2hpx]], [[2hss\|2hss]], [[2hsl\|2hsl]], [[2hsr\|2hsr]]</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=2hsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hsk RCSB], [http://www.ebi.ac.uk/pdbsum/2hsk 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=2hsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsk OCA], [http://pdbe.org/2hsk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hsk RCSB], [http://www.ebi.ac.uk/pdbsum/2hsk PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 15:
	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 2hsk" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:49, 16 January 2015

OCA — Fri, 16 Jan 2015 08:49:24 GMT

←Older revision		Revision as of 08:49, 16 January 2015
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Case, D A.]]	+	[[Category: Case, D A]]
-	[[Category: Chen, J.]]	+	[[Category: Chen, J]]
-	[[Category: Dupradeau, F Y.]]	+	[[Category: Dupradeau, F Y]]
-	[[Category: Stubbe, J.]]	+	[[Category: Stubbe, J]]
-	[[Category: Turner, C J.]]	+	[[Category: Turner, C J]]
	[[Category: Abasic site]]		[[Category: Abasic site]]
	[[Category: Ape1]]		[[Category: Ape1]]

OCA at 15:27, 12 October 2014

OCA — Sun, 12 Oct 2014 15:27:52 GMT

←Older revision		Revision as of 15:27, 12 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2hsk.~~png~~\|~~left~~\|~~200px~~]]	+	==NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)==
		+	<StructureSection load='2hsk' size='340' side='right' caption='[[2hsk]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2hsk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HSK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hou\|2hou]], [[2hpx\|2hpx]], [[2hss\|2hss]], [[2hsl\|2hsl]], [[2hsr\|2hsr]]</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=2hsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hsk RCSB], [http://www.ebi.ac.uk/pdbsum/2hsk PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A 4'-oxidized abasic site (X) has been synthesized in a defined duplex DNA sequence, 5'-d(CCAAAGXACCGGG)-3'/3'-d(GGTTTCATGGCCC)-5' (1). Its structure has been determined by two-dimensional NMR methods, molecular modeling, and molecular dynamics simulations. 1 is globally B-form with the base (A) opposite X intrahelical and well-stacked. Only the alpha anomer of X is observed, and the abasic site deoxyribose is largely intrahelical. These results are compared with a normal abasic site (Y) in the same sequence context (2). Y is composed of a 60:40 mixture of alpha and beta anomers (2alpha and 2beta). In both 2alpha and 2beta, the base (A) opposite Y is intrahelical and well-stacked and the abasic site deoxyribose is predominantly extrahelical, consistent with the reported structures of the normal abasic site in a similar sequence context [Hoehn, S. T., Turner, C. J., and Stubbe, J. (2001) Nucleic Acids Res. 29, 3413-3423]. Molecular dynamics simulations reveal that the normal abasic site appears to be conformationally more flexible than the 4'-oxidized abasic site. The importance of the structure and flexibility of the abasic site in the recognition by the DNA repair enzyme Ape1 is discussed.

-	~~{{STRUCTURE_2hsk\| PDB=2hsk \| SCENE= }}~~	+	Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sites.,Chen J, Dupradeau FY, Case DA, Turner CJ, Stubbe J Biochemistry. 2007 Mar 20;46(11):3096-107. Epub 2007 Feb 27. PMID:17323932<ref>PMID:17323932</ref>

-	~~===NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures~~, ~~alpha anomer)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17323932}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2hsk]] is~~ a ~~2 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=2HSK OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017323932<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Case, D A.]]		[[Category: Case, D A.]]
	[[Category: Chen, J.]]		[[Category: Chen, J.]]

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

OCA — Mon, 07 Jan 2013 12:13:12 GMT

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

←Older revision

Revision as of 12:13, 7 January 2013

OCA at 12:13, 7 January 2013

OCA — Mon, 07 Jan 2013 12:13:09 GMT

←Older revision		Revision as of 12:13, 7 January 2013
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-	{{Seed}}
	[[Image:2hsk.png\|left\|200px]]		[[Image:2hsk.png\|left\|200px]]

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	{{STRUCTURE_2hsk\| PDB=2hsk \| SCENE= }}		{{STRUCTURE_2hsk\| PDB=2hsk \| SCENE= }}

	===NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)===		===NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)===

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-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17323932}}, adds the Publication Abstract to the page
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	{{ABSTRACT_PUBMED_17323932}}		{{ABSTRACT_PUBMED_17323932}}

	==About this Structure==		==About this Structure==
-	~~2HSK~~ is a 2 ~~chains~~ structure. Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSK OCA].	+	[[2hsk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSK OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17323932~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017323932</ref><references group="xtra"/>
	[[Category: Case, D A.]]		[[Category: Case, D A.]]
	[[Category: Chen, J.]]		[[Category: Chen, J.]]
Line 32:		Line 20:
	[[Category: Ape1]]		[[Category: Ape1]]
	[[Category: Base excision repair]]		[[Category: Base excision repair]]
		+	[[Category: Dna]]
	[[Category: Dna lesion]]		[[Category: Dna lesion]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Apr 19 08:20:58 2009''