2lsz - Revision history

OCA at 06:57, 1 May 2024

OCA — Wed, 01 May 2024 06:57:10 GMT

←Older revision		Revision as of 06:57, 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=2lsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lsz OCA], [https://pdbe.org/2lsz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lsz RCSB], [https://www.ebi.ac.uk/pdbsum/2lsz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lsz 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=2lsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lsz OCA], [https://pdbe.org/2lsz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lsz RCSB], [https://www.ebi.ac.uk/pdbsum/2lsz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lsz ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Acrolein, a cell metabolic product and main component of cigarette smoke, reacts with DNA generating alpha-OH-PdG lesions, which have the ability to pair with dATP during replication thereby causing G to T transversions. We describe the solution structure of an 11-mer DNA duplex containing the mutagenic alpha-OH-PdG.dA base pair intermediate, as determined by solution nuclear magnetic resonance (NMR) spectroscopy and retrained molecular dynamics (MD) simulations. The NMR data support a mostly regular right-handed helix that is only perturbed at its center by the presence of the lesion. Undamaged residues of the duplex are in anti orientation, forming standard Watson-Crick base pairs alignments. Duplication of proton signals at and near the damaged base pair reveals the presence of two enantiomeric duplexes, thus establishing the exocyclic nature of the lesion. The alpha-OH-PdG adduct assumes a syn conformation pairing to its partner dA base that is protonated at pH 6.6. The three-dimensional structure obtained by restrained molecular dynamics simulations show hydrogen bond interactions that stabilize alpha-OH-PdG in a syn conformation and across the lesion containing base pair. We discuss the implications of the structures for the mutagenic bypass of acrolein lesions.
-
-	NMR structure of duplex DNA containing the alpha-OH-PdG.dA base pair: a mutagenic intermediate of acrolein.,Zaliznyak T, Lukin M, El-khateeb M, Bonala R, Johnson F, de los Santos C Biopolymers. 2010 Apr;93(4):391-401. PMID:20049919<ref>PMID:20049919</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2lsz" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:18, 15 November 2023

OCA — Wed, 15 Nov 2023 12:18:20 GMT

←Older revision		Revision as of 12:18, 15 November 2023
Line 1:		Line 1:

	==NMR structure of duplex DNA containing the alpha-OH-PdG dA base pair: A mutagenic intermediate of acrolein==		==NMR structure of duplex DNA containing the alpha-OH-PdG dA base pair: A mutagenic intermediate of acrolein==
-	<StructureSection load='2lsz' size='340' side='right'caption='[[2lsz~~]], [[NMR_Ensembles_of_Models \| 26 NMR models~~]]' scene=''>	+	<StructureSection load='2lsz' size='340' side='right'caption='[[2lsz]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2lsz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LSZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LSZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lsz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LSZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LSZ FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=63H:(6R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-HYDROXY-5,6,7,8-TETRAHYDROPYRIMIDO[1,2-A]PURIN-10(3H)-ONE'>63H</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;'>[[2lt0\|2lt0]]</div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=63H:(6R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-HYDROXY-5,6,7,8-TETRAHYDROPYRIMIDO[1,2-A]PURIN-10(3H)-ONE'>63H</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=2lsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lsz OCA], [https://pdbe.org/2lsz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lsz RCSB], [https://www.ebi.ac.uk/pdbsum/2lsz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lsz 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=2lsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lsz OCA], [https://pdbe.org/2lsz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lsz RCSB], [https://www.ebi.ac.uk/pdbsum/2lsz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lsz ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bonala, R]]	+	[[Category: Bonala R]]
-	[[Category: El-khateeb, M]]	+	[[Category: El-khateeb M]]
-	[[Category: Johnson, F]]	+	[[Category: Johnson F]]
-	[[Category: Lukin, M]]	+	[[Category: Lukin M]]
-	~~[[Category: Santos, C de los~~]]	+	[[Category: Zaliznyak T]]
-	[[Category: Zaliznyak, T]]	+	[[Category: De los Santos C]]
-	[[Category: ~~Acrolein adduct]]~~	+
-	~~[[Category: Damaged dna structure]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Dna lesion~~]]	+

OCA at 07:54, 9 February 2022

OCA — Wed, 09 Feb 2022 07:54:17 GMT

←Older revision		Revision as of 07:54, 9 February 2022
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	<StructureSection load='2lsz' size='340' side='right'caption='[[2lsz]], [[NMR_Ensembles_of_Models \| 26 NMR models]]' scene=''>		<StructureSection load='2lsz' size='340' side='right'caption='[[2lsz]], [[NMR_Ensembles_of_Models \| 26 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2lsz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LSZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2LSZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2lsz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LSZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LSZ FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=63H:(6R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-HYDROXY-5,6,7,8-TETRAHYDROPYRIMIDO[1,2-A]PURIN-10(3H)-ONE'>63H</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=63H:(6R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-HYDROXY-5,6,7,8-TETRAHYDROPYRIMIDO[1,2-A]PURIN-10(3H)-ONE'>63H</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2lt0\|2lt0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2lt0\|2lt0]]</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=2lsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lsz OCA], [~~http~~://pdbe.org/2lsz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2lsz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2lsz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2lsz 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=2lsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lsz OCA], [https://pdbe.org/2lsz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lsz RCSB], [https://www.ebi.ac.uk/pdbsum/2lsz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lsz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:08, 6 May 2020

OCA — Wed, 06 May 2020 07:08:00 GMT

←Older revision		Revision as of 07:08, 6 May 2020
Line 1:		Line 1:

	==NMR structure of duplex DNA containing the alpha-OH-PdG dA base pair: A mutagenic intermediate of acrolein==		==NMR structure of duplex DNA containing the alpha-OH-PdG dA base pair: A mutagenic intermediate of acrolein==
-	<StructureSection load='2lsz' size='340' side='right' caption='[[2lsz]], [[NMR_Ensembles_of_Models \| 26 NMR models]]' scene=''>	+	<StructureSection load='2lsz' size='340' side='right'caption='[[2lsz]], [[NMR_Ensembles_of_Models \| 26 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2lsz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LSZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2LSZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2lsz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LSZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2LSZ FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=63H:(6R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-HYDROXY-5,6,7,8-TETRAHYDROPYRIMIDO[1,2-A]PURIN-10(3H)-ONE'>63H</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=63H:(6R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-HYDROXY-5,6,7,8-TETRAHYDROPYRIMIDO[1,2-A]PURIN-10(3H)-ONE'>63H</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2lt0\|2lt0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2lt0\|2lt0]]</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=2lsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lsz OCA], [http://pdbe.org/2lsz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lsz RCSB], [http://www.ebi.ac.uk/pdbsum/2lsz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2lsz 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=2lsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lsz OCA], [http://pdbe.org/2lsz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lsz RCSB], [http://www.ebi.ac.uk/pdbsum/2lsz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2lsz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Bonala, R]]		[[Category: Bonala, R]]
	[[Category: El-khateeb, M]]		[[Category: El-khateeb, M]]

OCA at 19:46, 1 August 2018

OCA — Wed, 01 Aug 2018 19:46:30 GMT

←Older revision		Revision as of 19:46, 1 August 2018
Line 1:		Line 1:
		+
	==NMR structure of duplex DNA containing the alpha-OH-PdG dA base pair: A mutagenic intermediate of acrolein==		==NMR structure of duplex DNA containing the alpha-OH-PdG dA base pair: A mutagenic intermediate of acrolein==
	<StructureSection load='2lsz' size='340' side='right' caption='[[2lsz]], [[NMR_Ensembles_of_Models \| 26 NMR models]]' scene=''>		<StructureSection load='2lsz' size='340' side='right' caption='[[2lsz]], [[NMR_Ensembles_of_Models \| 26 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=63H:(6R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-HYDROXY-5,6,7,8-TETRAHYDROPYRIMIDO[1,2-A]PURIN-10(3H)-ONE'>63H</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=63H:(6R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-HYDROXY-5,6,7,8-TETRAHYDROPYRIMIDO[1,2-A]PURIN-10(3H)-ONE'>63H</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2lt0\|2lt0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2lt0\|2lt0]]</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=2lsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lsz OCA], [http://pdbe.org/2lsz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lsz RCSB], [http://www.ebi.ac.uk/pdbsum/2lsz 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=2lsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lsz OCA], [http://pdbe.org/2lsz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lsz RCSB], [http://www.ebi.ac.uk/pdbsum/2lsz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2lsz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:21, 11 September 2015

OCA — Fri, 11 Sep 2015 03:21:19 GMT

←Older revision		Revision as of 03:21, 11 September 2015
Line 5:		Line 5:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=63H:(6R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-HYDROXY-5,6,7,8-TETRAHYDROPYRIMIDO[1,2-A]PURIN-10(3H)-ONE'>63H</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=63H:(6R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-HYDROXY-5,6,7,8-TETRAHYDROPYRIMIDO[1,2-A]PURIN-10(3H)-ONE'>63H</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2lt0\|2lt0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2lt0\|2lt0]]</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=2lsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lsz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lsz RCSB], [http://www.ebi.ac.uk/pdbsum/2lsz 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=2lsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lsz OCA], [http://pdbe.org/2lsz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lsz RCSB], [http://www.ebi.ac.uk/pdbsum/2lsz 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 2lsz" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:35, 22 December 2014

OCA — Mon, 22 Dec 2014 05:35:09 GMT

←Older revision		Revision as of 05:35, 22 December 2014
Line 2:		Line 2:
	<StructureSection load='2lsz' size='340' side='right' caption='[[2lsz]], [[NMR_Ensembles_of_Models \| 26 NMR models]]' scene=''>		<StructureSection load='2lsz' size='340' side='right' caption='[[2lsz]], [[NMR_Ensembles_of_Models \| 26 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2lsz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LSZ OCA]. <br>	+	<table><tr><td colspan='2'>[[2lsz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LSZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LSZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=63H:(6R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-HYDROXY-5,6,7,8-TETRAHYDROPYRIMIDO[1,2-A]PURIN-10(3H)-ONE'>63H</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=63H:(6R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-HYDROXY-5,6,7,8-TETRAHYDROPYRIMIDO[1,2-A]PURIN-10(3H)-ONE'>63H</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2lt0\|2lt0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2lt0\|2lt0]]</td></tr>
-	<tr~~><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class~~='~~plainlinks~~'~~>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2lsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lsz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lsz RCSB], [http://www.ebi.ac.uk/pdbsum/2lsz PDBsum]</span></td></tr>
-	~~<tr~~><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lsz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lsz RCSB], [http://www.ebi.ac.uk/pdbsum/2lsz PDBsum]</span></td></tr>	+	</table>
-	<table>	+
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 13:
	NMR structure of duplex DNA containing the alpha-OH-PdG.dA base pair: a mutagenic intermediate of acrolein.,Zaliznyak T, Lukin M, El-khateeb M, Bonala R, Johnson F, de los Santos C Biopolymers. 2010 Apr;93(4):391-401. PMID:20049919<ref>PMID:20049919</ref>		NMR structure of duplex DNA containing the alpha-OH-PdG.dA base pair: a mutagenic intermediate of acrolein.,Zaliznyak T, Lukin M, El-khateeb M, Bonala R, Johnson F, de los Santos C Biopolymers. 2010 Apr;93(4):391-401. PMID:20049919<ref>PMID:20049919</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 20:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bonala, R.]]	+	[[Category: Bonala, R]]
-	[[Category: El-khateeb, M.]]	+	[[Category: El-khateeb, M]]
-	[[Category: Johnson, F.]]	+	[[Category: Johnson, F]]
-	[[Category: Lukin, M.]]	+	[[Category: Lukin, M]]
-	[[Category: Santos, C de los.]]	+	[[Category: Santos, C de los]]
-	[[Category: Zaliznyak, T.]]	+	[[Category: Zaliznyak, T]]
	[[Category: Acrolein adduct]]		[[Category: Acrolein adduct]]
	[[Category: Damaged dna structure]]		[[Category: Damaged dna structure]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Dna lesion]]		[[Category: Dna lesion]]

OCA at 08:32, 7 May 2014

OCA — Wed, 07 May 2014 08:32:17 GMT

←Older revision		Revision as of 08:32, 7 May 2014
Line 1:		Line 1:
-	[[~~Image:~~2lsz.~~jpg~~\|~~left~~\|~~200px~~]]	+	==NMR structure of duplex DNA containing the alpha-OH-PdG dA base pair: A mutagenic intermediate of acrolein==
		+	<StructureSection load='2lsz' size='340' side='right' caption='[[2lsz]], [[NMR_Ensembles_of_Models \| 26 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2lsz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LSZ OCA]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=63H:(6R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-HYDROXY-5,6,7,8-TETRAHYDROPYRIMIDO[1,2-A]PURIN-10(3H)-ONE'>63H</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2lt0\|2lt0]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lsz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lsz RCSB], [http://www.ebi.ac.uk/pdbsum/2lsz PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Acrolein, a cell metabolic product and main component of cigarette smoke, reacts with DNA generating alpha-OH-PdG lesions, which have the ability to pair with dATP during replication thereby causing G to T transversions. We describe the solution structure of an 11-mer DNA duplex containing the mutagenic alpha-OH-PdG.dA base pair intermediate, as determined by solution nuclear magnetic resonance (NMR) spectroscopy and retrained molecular dynamics (MD) simulations. The NMR data support a mostly regular right-handed helix that is only perturbed at its center by the presence of the lesion. Undamaged residues of the duplex are in anti orientation, forming standard Watson-Crick base pairs alignments. Duplication of proton signals at and near the damaged base pair reveals the presence of two enantiomeric duplexes, thus establishing the exocyclic nature of the lesion. The alpha-OH-PdG adduct assumes a syn conformation pairing to its partner dA base that is protonated at pH 6.6. The three-dimensional structure obtained by restrained molecular dynamics simulations show hydrogen bond interactions that stabilize alpha-OH-PdG in a syn conformation and across the lesion containing base pair. We discuss the implications of the structures for the mutagenic bypass of acrolein lesions.

-	<!--	+	NMR structure of duplex DNA containing the alpha-OH-PdG.dA base pair: a mutagenic intermediate of acrolein.,Zaliznyak T, Lukin M, El-khateeb M, Bonala R, Johnson F, de los Santos C Biopolymers. 2010 Apr;93(4):391-401. PMID:20049919<ref>PMID:20049919</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_2lsz"~~, ~~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_2lsz\| PDB=2lsz \| SCENE= }}~~	+

-	~~===NMR structure~~ of ~~duplex DNA containing~~ the ~~alpha-OH-PdG dA base pair: A mutagenic intermediate of acrolein===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_20049919}}, adds the Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 20049919 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_20049919}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2lsz]] is a 2 chain structure. Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2LSZ OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:020049919<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Bonala, R.]]		[[Category: Bonala, R.]]
	[[Category: El-khateeb, M.]]		[[Category: El-khateeb, M.]]

OCA at 06:09, 13 June 2012

OCA — Wed, 13 Jun 2012 06:09:43 GMT

←Older revision		Revision as of 06:09, 13 June 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:2lsz.jpg\|left\|200px]]

-	The ~~entry 2lsz~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_2lsz", 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_2lsz\| PDB=2lsz \| SCENE= }}

-	~~Authors: Zaliznyak, T., de los Santos, C., Lukin, M., El~~-~~khateeb, M., Bonala, R., Johnson, F.~~	+	===NMR structure of duplex DNA containing the alpha-OH-PdG dA base pair: A mutagenic intermediate of acrolein===

-	~~Description~~: ~~NMR structure of duplex DNA containing~~ the ~~alpha~~-OH-~~PdG dA base pair~~: ~~A mutagenic intermediate of acrolein~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20049919}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20049919 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20049919}}
		+
		+	==About this Structure==
		+	[[2lsz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LSZ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:020049919</ref><references group="xtra"/>
		+	[[Category: Bonala, R.]]
		+	[[Category: El-khateeb, M.]]
		+	[[Category: Johnson, F.]]
		+	[[Category: Lukin, M.]]
		+	[[Category: Santos, C de los.]]
		+	[[Category: Zaliznyak, T.]]
		+	[[Category: Acrolein adduct]]
		+	[[Category: Damaged dna structure]]
		+	[[Category: Dna]]
		+	[[Category: Dna lesion]]

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

OCA — Wed, 16 May 2012 08:32:56 GMT

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

←Older revision

Revision as of 08:32, 16 May 2012