1cr3 - Revision history

OCA at 11:40, 22 November 2023

OCA — Wed, 22 Nov 2023 11:40:16 GMT

←Older revision		Revision as of 11:40, 22 November 2023
Line 1:		Line 1:

	==SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX==		==SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX==
-	<StructureSection load='1cr3' size='340' side='right'caption='[[1cr3~~]], [[NMR_Ensembles_of_Models \| 7 NMR models~~]]' scene=''>	+	<StructureSection load='1cr3' size='340' side='right'caption='[[1cr3]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1cr3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CR3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1cr3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CR3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BC:BENZO[G]CHRYSENE'>BC</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BC:BENZO[G]CHRYSENE'>BC</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=1cr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cr3 OCA], [https://pdbe.org/1cr3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cr3 RCSB], [https://www.ebi.ac.uk/pdbsum/1cr3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cr3 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=1cr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cr3 OCA], [https://pdbe.org/1cr3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cr3 RCSB], [https://www.ebi.ac.uk/pdbsum/1cr3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cr3 ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Amin, S]]	+	[[Category: Amin S]]
-	[[Category: Geacintov~~, N E~~]]	+	[[Category: Geacintov NE]]
-	[[Category: Mao, B]]	+	[[Category: Mao B]]
-	[[Category: Patel~~, D J~~]]	+	[[Category: Patel DJ]]
-	[[Category: Suri~~, A K]]~~	+	[[Category: Suri AK]]
-	~~[[Category: Carcinogen adduct]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Dna duplex~~]]	+

OCA at 15:18, 3 March 2021

OCA — Wed, 03 Mar 2021 15:18:29 GMT

←Older revision		Revision as of 15:18, 3 March 2021
Line 3:		Line 3:
	<StructureSection load='1cr3' size='340' side='right'caption='[[1cr3]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>		<StructureSection load='1cr3' size='340' side='right'caption='[[1cr3]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1cr3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1CR3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1cr3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CR3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BC:BENZO[G]CHRYSENE'>BC</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BC:BENZO[G]CHRYSENE'>BC</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=1cr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cr3 OCA], [~~http~~://pdbe.org/1cr3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1cr3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1cr3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1cr3 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=1cr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cr3 OCA], [https://pdbe.org/1cr3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cr3 RCSB], [https://www.ebi.ac.uk/pdbsum/1cr3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cr3 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:24, 29 May 2019

OCA — Wed, 29 May 2019 07:24:15 GMT

←Older revision		Revision as of 07:24, 29 May 2019
Line 1:		Line 1:

	==SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX==		==SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX==
-	<StructureSection load='1cr3' size='340' side='right' caption='[[1cr3]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>	+	<StructureSection load='1cr3' size='340' side='right'caption='[[1cr3]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1cr3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CR3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1cr3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CR3 FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Amin, S]]		[[Category: Amin, S]]
	[[Category: Geacintov, N E]]		[[Category: Geacintov, N E]]

OCA at 11:10, 24 August 2017

OCA — Thu, 24 Aug 2017 11:10:13 GMT

←Older revision		Revision as of 11:10, 24 August 2017
Line 1:		Line 1:
		+
	==SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX==		==SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX==
	<StructureSection load='1cr3' size='340' side='right' caption='[[1cr3]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>		<StructureSection load='1cr3' size='340' side='right' caption='[[1cr3]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1cr3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CR3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1cr3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CR3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BC:BENZO[G]CHRYSENE'>BC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BC:BENZO[G]CHRYSENE'>BC</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=1cr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cr3 OCA], [http://pdbe.org/1cr3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1cr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1cr3 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=1cr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cr3 OCA], [http://pdbe.org/1cr3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1cr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1cr3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1cr3 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:31, 11 September 2015

OCA — Fri, 11 Sep 2015 11:31:58 GMT

←Older revision		Revision as of 11:31, 11 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1cr3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CR3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1cr3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CR3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BC:BENZO[G]CHRYSENE'>BC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BC:BENZO[G]CHRYSENE'>BC</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=1cr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cr3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1cr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1cr3 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=1cr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cr3 OCA], [http://pdbe.org/1cr3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1cr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1cr3 PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	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 1cr3" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:32, 22 December 2014

OCA — Mon, 22 Dec 2014 06:32:29 GMT

←Older revision		Revision as of 06:32, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1cr3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CR3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1cr3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CR3 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BC:BENZO[G]CHRYSENE'>BC</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BC:BENZO[G]CHRYSENE'>BC</scene></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=1cr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cr3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1cr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1cr3 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=1cr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cr3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1cr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1cr3 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 18:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Amin, S.]]	+	[[Category: Amin, S]]
-	[[Category: Geacintov, N E.]]	+	[[Category: Geacintov, N E]]
-	[[Category: Mao, B.]]	+	[[Category: Mao, B]]
-	[[Category: Patel, D J.]]	+	[[Category: Patel, D J]]
-	[[Category: Suri, A K.]]	+	[[Category: Suri, A K]]
	[[Category: Carcinogen adduct]]		[[Category: Carcinogen adduct]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Dna duplex]]		[[Category: Dna duplex]]

OCA at 05:36, 8 June 2014

OCA — Sun, 08 Jun 2014 05:36:02 GMT

←Older revision		Revision as of 05:36, 8 June 2014
Line 1:		Line 1:
-	[[~~Image:~~1cr3.~~png~~\|~~left\|200px~~]]	+	==SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX==
		+	<StructureSection load='1cr3' size='340' side='right' caption='[[1cr3]], [[NMR_Ensembles_of_Models \| 7 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1cr3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CR3 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BC:BENZO[G]CHRYSENE'>BC</scene><br>
		+	<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=1cr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cr3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1cr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1cr3 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The solution structure of the adduct derived from the covalent bonding of the fjord region (+)-(11S, 12R, 13R, 14S) stereoisomer of anti -11,12-dihydroxy-13,14-epoxy-11,12,13, 14-tetrahydrobenzo[g]chrysene, (+)- anti -B[g]CDE, to the exocyclic N(6)amino group of the adenine residue dA6, (designated (+)- trans-anti -(B[g]C)dA6), positioned opposite a thymine residue dT17 in the DNA sequence context d(C1-T2-C3-T4-C5-(B[g]C)A6-C7-T8-T9-C10-C11). d(G12-G13-A14-A15-G16-T17-G18-A19-G20++ +-A21-G22) (designated (B[g]C)dA. dT 11-mer duplex), has been studied using structural information derived from NMR data in combination with molecular dynamics (MD) calculations. The solution structure of the (+)- trans-anti -(B[g]C)dA.dT 11-mer duplex has been determined using an MD protocol where both interproton distance and dihedral angle restraints deduced from NOESY and COSY spectra are used during the refinement process, followed by additional relaxation matrix refinement to the observed NOESY intensities to account for spin diffusion effects. The results established that the covalently attached benzo[g]chrysene ring intercalates into the DNA helix directed towards the 5'-side of the modified strand and stacks predominantly with dT17 when intercalated between dC5.dG18 and (B[g]C)dA6.dT17 base-pairs. All base-pairs, including the modified (B[g]C)dA6.dT17 base-pair, are aligned through Watson-Crick pairing as in normal B -DNA. In addition, the potential strain associated with the highly sterically hindered fjord region of the aromatic portion of the benzo[g]chrysenyl ring is relieved through the adoption of a non-planar, propeller-like geometry within the chrysenyl ring system. This conformation shares common structural features with the related (+)- trans-anti -(B[c]Ph)dA adduct in the identical base sequence context, derived from the fjord region (+)-(1S,2R,3R,4S)-3, 4-dihydroxy-1,2-epoxy-1,2,3,4-tetrahydrobenzo[c]phenanthrene stereoisomer, in which intercalation is also observed towards the 5'-side of the modified dA6.dT17 base-pair.

-	~~{{STRUCTURE_1cr3\| PDB=1cr3 \| SCENE= }}~~	+	Solution conformation of the (+)-trans-anti-benzo[g]chrysene-dA adduct opposite dT in a DNA duplex.,Suri AK, Mao B, Amin S, Geacintov NE, Patel DJ J Mol Biol. 1999 Sep 17;292(2):289-307. PMID:10493876<ref>PMID:10493876</ref>

-	~~===SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10493876}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1cr3]] is~~ a ~~2 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1CR3 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010493876<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Amin, S.]]		[[Category: Amin, S.]]
	[[Category: Geacintov, N E.]]		[[Category: Geacintov, N E.]]

OCA: Protected "1cr3" [edit=sysop:move=sysop]

OCA — Tue, 14 Aug 2012 18:43:52 GMT

Protected "1cr3" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:43, 14 August 2012

OCA at 18:43, 14 August 2012

OCA — Tue, 14 Aug 2012 18:43:51 GMT

←Older revision		Revision as of 18:43, 14 August 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1cr3.png\|left\|200px]]		[[Image:1cr3.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1cr3", 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_1cr3\| PDB=1cr3 \| SCENE= }}		{{STRUCTURE_1cr3\| PDB=1cr3 \| SCENE= }}

	===SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX===		===SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_10493876}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 10493876 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_10493876}}		{{ABSTRACT_PUBMED_10493876}}

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA].	+	[[1cr3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA].

	==Reference==		==Reference==
-	~~Solution conformation of the (+)-trans-anti-benzo[g]chrysene-dA adduct opposite dT in a DNA duplex., Suri AK, Mao B, Amin S, Geacintov NE, Patel DJ, J Mol Biol. 1999 Sep 17;292(2):289-307.~~ PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~10493876 10493876]~~	+	<ref group="xtra">PMID:010493876</ref><references group="xtra"/>
	[[Category: Amin, S.]]		[[Category: Amin, S.]]
	[[Category: Geacintov, N E.]]		[[Category: Geacintov, N E.]]
Line 30:		Line 18:
	[[Category: Suri, A K.]]		[[Category: Suri, A K.]]
	[[Category: Carcinogen adduct]]		[[Category: Carcinogen adduct]]
		+	[[Category: Dna]]
	[[Category: Dna duplex]]		[[Category: Dna duplex]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 21:11:47 2008''

OCA at 18:11, 30 June 2008

OCA — Mon, 30 Jun 2008 18:11:48 GMT

←Older revision		Revision as of 18:11, 30 June 2008
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-	[[Image:1cr3.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1cr3.png\|left\|200px]]

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	{{STRUCTURE_1cr3\| PDB=1cr3 \| SCENE= }}		{{STRUCTURE_1cr3\| PDB=1cr3 \| SCENE= }}

-	~~'''~~SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX~~'''~~	+	===SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX===


-	~~==Overview==~~	+	<!--
-	The ~~solution structure of the adduct derived from the covalent bonding of the fjord region (+)-(11S~~, ~~12R, 13R, 14S) stereoisomer of anti -11,12-dihydroxy-13,14-epoxy-11,12,13, 14-tetrahydrobenzo[g]chrysene, (+)- anti -B[g]CDE~~, to the ~~exocyclic N~~(~~6)amino group of the adenine residue dA6, (designated (+)- trans-anti -(B[g]C)dA6), positioned opposite a thymine residue dT17 in the DNA sequence context d(C1-T2-C3-T4-C5-(B[g]C)A6-C7-T8-T9-C10-C11)~~. ~~d(G12-G13-A14-A15-G16-T17-G18-A19-G20++ +-A21-G22) (designated (B[g]C)dA~~. ~~dT 11-mer duplex~~), has been studied using structural information derived from NMR data in combination with molecular dynamics (MD) calculations. The solution structure of the (+)- trans-anti -(B[g]C)dA.dT 11-mer duplex has been determined using an MD protocol where both interproton distance and dihedral angle restraints deduced from NOESY and COSY spectra are used during the refinement process, followed by additional relaxation matrix refinement to the observed NOESY intensities to account for spin diffusion effects. The results established that the covalently attached benzo[g]chrysene ring intercalates into the DNA helix directed towards the 5'-side of the modified strand and stacks predominantly with dT17 when intercalated between dC5.dG18 and (B[g]C)dA6.dT17 base-pairs. All base-pairs, including the modified (B[g]C)dA6.dT17 base-pair, are aligned through Watson-Crick pairing as in normal B -DNA. In addition, the potential strain associated with the highly sterically hindered fjord region of the aromatic portion of the benzo[g]chrysenyl ring is ~~relieved through~~ the ~~adoption of a non-planar, propeller-like geometry within the chrysenyl ring system~~. ~~This conformation shares common structural features with the related (+)~~- ~~trans~~-anti -(B[c]Ph)dA adduct in the identical base sequence context, derived from the fjord region (+)-(1S,2R,3R,4S)-3, 4-dihydroxy-1,2-epoxy-1,2,3,4-tetrahydrobenzo[c]phenanthrene stereoisomer, in which intercalation is also observed towards the 5'-side of the modified dA6.dT17 base-pair.	+	The line below this paragraph, {{ABSTRACT_PUBMED_10493876}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 10493876 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_10493876}}

	==About this Structure==		==About this Structure==
-	Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA].	+	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CR3 OCA].

	==Reference==		==Reference==
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	[[Category: Carcinogen adduct]]		[[Category: Carcinogen adduct]]
	[[Category: Dna duplex]]		[[Category: Dna duplex]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri May 2 13~~:01:52 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 21:11:47 2008''