4o5z - Revision history

OCA at 08:57, 20 March 2024

OCA — Wed, 20 Mar 2024 08:57:34 GMT

←Older revision		Revision as of 08:57, 20 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4o5z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O5Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[4o5z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O5Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=C6G:6-(CARBOXYMETHOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE'>C6G</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.75Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=C6G:6-(CARBOXYMETHOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE'>C6G</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=4o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5z OCA], [https://pdbe.org/4o5z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o5z RCSB], [https://www.ebi.ac.uk/pdbsum/4o5z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o5z 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=4o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5z OCA], [https://pdbe.org/4o5z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o5z RCSB], [https://www.ebi.ac.uk/pdbsum/4o5z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o5z ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	N-Nitrosation of glycine and its derivatives generates potent alkylating agents that can lead to the formation of O(6)-carboxymethylguanine (O(6)-CMG) in DNA. O(6)-CMG has been identified in DNA derived from human colon tissue and its occurrence has been linked to diets high in red and processed meats, implying an association with the induction of colorectal cancer. By analogy to O(6)-methylguanine, O(6)-CMG is expected to be mutagenic, inducing G-to-A mutations that may be the molecular basis of increased cancer risk. Previously, the crystal structure of the DNA dodecamer d(CGCG[O(6)-CMG]ATTCGCG) has been reported, in which O(6)-CMG forms a Watson-Crick-type pair with thymine similar to the canonical A:T pair. In order to further investigate the versatility of O(6)-CMG in base-pair formation, the structure of the DNA dodecamer d(CGC[O(6)-CMG]AATTTGCG) containing O(6)-CMG at a different position has been determined by X-ray crystallography using four crystal forms obtained under conditions containing different solvent ions (Sr(2+), Ba(2+), Mg(2+), K(+) or Na(+)) with and without Hoechst 33258. The most striking finding is that the pairing modes of O(6)-CMG with T are quite different from those previously reported. In the present dodecamer, the T bases are displaced (wobbled) into the major groove to form a hydrogen bond between the thymine N(3) N-H and the carboxyl group of O(6)-CMG. In addition, a water molecule is bridged through two hydrogen bonds between the thymine O(2) atom and the 2-amino group of O(6)-CMG to stabilize the pairing. These interaction modes commonly occur in the four crystal forms, regardless of the differences in crystallization conditions. The previous and the present results show that O(6)-CMG can form a base pair with T in two alternative modes: the Watson-Crick type and a high-wobble type, the nature of which may depend on the DNA-sequence context.
-
-	O(6)-Carboxymethylguanine in DNA forms a sequence context-dependent wobble base-pair structure with thymine.,Zhang F, Tsunoda M, Kikuchi Y, Wilkinson O, Millington CL, Margison GP, Williams DM, Takenaka A Acta Crystallogr D Biol Crystallogr. 2014 Jun;70(Pt 6):1669-79. doi:, 10.1107/S1399004714006178. Epub 2014 May 30. PMID:24914978<ref>PMID:24914978</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4o5z" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:57, 18 January 2023

OCA — Wed, 18 Jan 2023 08:57:06 GMT

←Older revision		Revision as of 08:57, 18 January 2023
Line 3:		Line 3:
	<StructureSection load='4o5z' size='340' side='right'caption='[[4o5z]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='4o5z' size='340' side='right'caption='[[4o5z]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4o5z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4O5Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4o5z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O5Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=C6G:6-(CARBOXYMETHOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE'>C6G</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=C6G:6-(CARBOXYMETHOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE'>C6G</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=4o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5z OCA], [https://pdbe.org/4o5z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o5z RCSB], [https://www.ebi.ac.uk/pdbsum/4o5z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o5z ProSAT]</span></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[4ij0\|4ij0]], [[4itd\|4itd]], [[4o5w\|4o5w]], [[4o5x\|4o5x]], [[4o5y\|4o5y]]~~</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=4o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5z OCA], [~~http~~://pdbe.org/4o5z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4o5z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4o5z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4o5z ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kikuchi, Y]]	+	[[Category: Kikuchi Y]]
-	[[Category: Margison~~, G P~~]]	+	[[Category: Margison GP]]
-	[[Category: Millington~~, C L~~]]	+	[[Category: Millington CL]]
-	[[Category: Suzuki, K]]	+	[[Category: Suzuki K]]
-	[[Category: Takenaka, A]]	+	[[Category: Takenaka A]]
-	[[Category: Tsunoda, M]]	+	[[Category: Tsunoda M]]
-	[[Category: Wilkinson, O]]	+	[[Category: Wilkinson O]]
-	[[Category: Williams~~, D M~~]]	+	[[Category: Williams DM]]
-	[[Category: Zhang, F]]	+	[[Category: Zhang F]]
-	~~[[Category: Damaged dna]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: O6-carboxymethylguanine~~]]	+

OCA at 05:22, 13 February 2020

OCA — Thu, 13 Feb 2020 05:22:21 GMT

←Older revision		Revision as of 05:22, 13 February 2020
Line 1:		Line 1:

	==O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine==		==O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine==
-	<StructureSection load='4o5z' size='340' side='right' caption='[[4o5z]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='4o5z' size='340' side='right'caption='[[4o5z]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4o5z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O5Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[4o5z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O5Z FirstGlance]. <br>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Kikuchi, Y]]		[[Category: Kikuchi, Y]]
	[[Category: Margison, G P]]		[[Category: Margison, G P]]

OCA at 19:15, 11 August 2016

OCA — Thu, 11 Aug 2016 19:15:13 GMT

←Older revision		Revision as of 19:15, 11 August 2016
Line 1:		Line 1:
		+
	==O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine==		==O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine==
	<StructureSection load='4o5z' size='340' side='right' caption='[[4o5z]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='4o5z' size='340' side='right' caption='[[4o5z]], [[Resolution\|resolution]] 1.75Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=C6G:6-(CARBOXYMETHOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE'>C6G</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=C6G:6-(CARBOXYMETHOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE'>C6G</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ij0\|4ij0]], [[4itd\|4itd]], [[4o5w\|4o5w]], [[4o5x\|4o5x]], [[4o5y\|4o5y]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ij0\|4ij0]], [[4itd\|4itd]], [[4o5w\|4o5w]], [[4o5x\|4o5x]], [[4o5y\|4o5y]]</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=4o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o5z RCSB], [http://www.ebi.ac.uk/pdbsum/4o5z 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=4o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5z OCA], [http://pdbe.org/4o5z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4o5z RCSB], [http://www.ebi.ac.uk/pdbsum/4o5z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4o5z ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4o5z" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:40, 5 January 2015

OCA — Mon, 05 Jan 2015 09:40:17 GMT

←Older revision		Revision as of 09:40, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4o5z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O5Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[4o5z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O5Z FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=C6G:6-(CARBOXYMETHOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE'>C6G</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=C6G:6-(CARBOXYMETHOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE'>C6G</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ij0\|4ij0]], [[4itd\|4itd]], [[4o5w\|4o5w]], [[4o5x\|4o5x]], [[4o5y\|4o5y]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ij0\|4ij0]], [[4itd\|4itd]], [[4o5w\|4o5w]], [[4o5x\|4o5x]], [[4o5y\|4o5y]]</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=4o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o5z RCSB], [http://www.ebi.ac.uk/pdbsum/4o5z 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=4o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o5z RCSB], [http://www.ebi.ac.uk/pdbsum/4o5z 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 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Kikuchi, Y.]]	+	[[Category: Kikuchi, Y]]
-	[[Category: Margison, G P.]]	+	[[Category: Margison, G P]]
-	[[Category: Millington, C L.]]	+	[[Category: Millington, C L]]
-	[[Category: Suzuki, K.]]	+	[[Category: Suzuki, K]]
-	[[Category: Takenaka, A.]]	+	[[Category: Takenaka, A]]
-	[[Category: Tsunoda, M.]]	+	[[Category: Tsunoda, M]]
-	[[Category: Wilkinson, O.]]	+	[[Category: Wilkinson, O]]
-	[[Category: Williams, D M.]]	+	[[Category: Williams, D M]]
-	[[Category: Zhang, F.]]	+	[[Category: Zhang, F]]
	[[Category: Damaged dna]]		[[Category: Damaged dna]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: O6-carboxymethylguanine]]		[[Category: O6-carboxymethylguanine]]

OCA at 08:33, 2 July 2014

OCA — Wed, 02 Jul 2014 08:33:26 GMT

←Older revision		Revision as of 08:33, 2 July 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine==
		+	<StructureSection load='4o5z' size='340' side='right' caption='[[4o5z]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4o5z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O5Z FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=C6G:6-(CARBOXYMETHOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE'>C6G</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ij0\|4ij0]], [[4itd\|4itd]], [[4o5w\|4o5w]], [[4o5x\|4o5x]], [[4o5y\|4o5y]]</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=4o5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o5z RCSB], [http://www.ebi.ac.uk/pdbsum/4o5z PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	N-Nitrosation of glycine and its derivatives generates potent alkylating agents that can lead to the formation of O(6)-carboxymethylguanine (O(6)-CMG) in DNA. O(6)-CMG has been identified in DNA derived from human colon tissue and its occurrence has been linked to diets high in red and processed meats, implying an association with the induction of colorectal cancer. By analogy to O(6)-methylguanine, O(6)-CMG is expected to be mutagenic, inducing G-to-A mutations that may be the molecular basis of increased cancer risk. Previously, the crystal structure of the DNA dodecamer d(CGCG[O(6)-CMG]ATTCGCG) has been reported, in which O(6)-CMG forms a Watson-Crick-type pair with thymine similar to the canonical A:T pair. In order to further investigate the versatility of O(6)-CMG in base-pair formation, the structure of the DNA dodecamer d(CGC[O(6)-CMG]AATTTGCG) containing O(6)-CMG at a different position has been determined by X-ray crystallography using four crystal forms obtained under conditions containing different solvent ions (Sr(2+), Ba(2+), Mg(2+), K(+) or Na(+)) with and without Hoechst 33258. The most striking finding is that the pairing modes of O(6)-CMG with T are quite different from those previously reported. In the present dodecamer, the T bases are displaced (wobbled) into the major groove to form a hydrogen bond between the thymine N(3) N-H and the carboxyl group of O(6)-CMG. In addition, a water molecule is bridged through two hydrogen bonds between the thymine O(2) atom and the 2-amino group of O(6)-CMG to stabilize the pairing. These interaction modes commonly occur in the four crystal forms, regardless of the differences in crystallization conditions. The previous and the present results show that O(6)-CMG can form a base pair with T in two alternative modes: the Watson-Crick type and a high-wobble type, the nature of which may depend on the DNA-sequence context.

-	~~The entry 4o5z is ON HOLD until Dec 20 2015~~	+	O(6)-Carboxymethylguanine in DNA forms a sequence context-dependent wobble base-pair structure with thymine.,Zhang F, Tsunoda M, Kikuchi Y, Wilkinson O, Millington CL, Margison GP, Williams DM, Takenaka A Acta Crystallogr D Biol Crystallogr. 2014 Jun;70(Pt 6):1669-79. doi:, 10.1107/S1399004714006178. Epub 2014 May 30. PMID:24914978<ref>PMID:24914978</ref>

-	~~Authors: Zhang~~, F.~~, Tsunoda, M~~.~~, Suzuki, K~~., Kikuchi, Y., ~~Wilkinson, O~~., Millington, C.L., ~~Margison~~, G.P., Williams, D.M., ~~Takenaka, A~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: O6-carboxymethylguanine ~~in DNA forms a sequence context dependent wobble base pair structure with thymine~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kikuchi, Y.]]
		+	[[Category: Margison, G P.]]
		+	[[Category: Millington, C L.]]
		+	[[Category: Suzuki, K.]]
		+	[[Category: Takenaka, A.]]
		+	[[Category: Tsunoda, M.]]
		+	[[Category: Wilkinson, O.]]
		+	[[Category: Williams, D M.]]
		+	[[Category: Zhang, F.]]
		+	[[Category: Damaged dna]]
		+	[[Category: Dna]]
		+	[[Category: O6-carboxymethylguanine]]

OCA at 04:51, 4 June 2014

OCA — Wed, 04 Jun 2014 04:51:09 GMT

←Older revision		Revision as of 04:51, 4 June 2014
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4o5z is ON HOLD	+	The entry 4o5z is ON HOLD until Dec 20 2015

	Authors: Zhang, F., Tsunoda, M., Suzuki, K., Kikuchi, Y., Wilkinson, O., Millington, C.L., Margison, G.P., Williams, D.M., Takenaka, A.		Authors: Zhang, F., Tsunoda, M., Suzuki, K., Kikuchi, Y., Wilkinson, O., Millington, C.L., Margison, G.P., Williams, D.M., Takenaka, A.

	Description: O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine		Description: O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine

OCA at 06:46, 22 January 2014

OCA — Wed, 22 Jan 2014 06:46:06 GMT

←Older revision		Revision as of 06:46, 22 January 2014
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	Authors: Zhang, F., Tsunoda, M., Suzuki, K., Kikuchi, Y., Wilkinson, O., Millington, C.L., Margison, G.P., Williams, D.M., Takenaka, A.		Authors: Zhang, F., Tsunoda, M., Suzuki, K., Kikuchi, Y., Wilkinson, O., Millington, C.L., Margison, G.P., Williams, D.M., Takenaka, A.

-	Description: O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine.	+	Description: O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine

OCA: Protected "4o5z" [edit=sysop:move=sysop]

OCA — Wed, 08 Jan 2014 09:23:45 GMT

Protected "4o5z" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:23, 8 January 2014

OCA: New page: '''Unreleased structure''' The entry 4o5z is ON HOLD Authors: Zhang, F., Tsunoda, M., Suzuki, K., Kikuchi, Y., Wilkinson, O., Millington, C.L., Margison, G.P., Williams, D.M., Takenaka,...

OCA — Wed, 08 Jan 2014 09:23:44 GMT

New page: '''Unreleased structure''' The entry 4o5z is ON HOLD Authors: Zhang, F., Tsunoda, M., Suzuki, K., Kikuchi, Y., Wilkinson, O., Millington, C.L., Margison, G.P., Williams, D.M., Takenaka,...

New page

'''Unreleased structure'''

The entry 4o5z is ON HOLD

Authors: Zhang, F., Tsunoda, M., Suzuki, K., Kikuchi, Y., Wilkinson, O., Millington, C.L., Margison, G.P., Williams, D.M., Takenaka, A.

Description: O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine.