1qby - Revision history

OCA at 09:18, 6 December 2023

OCA — Wed, 06 Dec 2023 09:18:59 GMT

←Older revision		Revision as of 09:18, 6 December 2023
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	==THE SOLUTION STRUCTURE OF A BAY-REGION 1R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE==		==THE SOLUTION STRUCTURE OF A BAY-REGION 1R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE==
-	<StructureSection load='1qby' size='340' side='right'caption='[[1qby~~]], [[NMR_Ensembles_of_Models \| 1 NMR models~~]]' scene=''>	+	<StructureSection load='1qby' size='340' side='right'caption='[[1qby]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qby]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QBY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qby]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QBY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BZA:1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL'>BZA</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=BZA:1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL'>BZA</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=1qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qby OCA], [https://pdbe.org/1qby PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qby RCSB], [https://www.ebi.ac.uk/pdbsum/1qby PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qby 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=1qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qby OCA], [https://pdbe.org/1qby PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qby RCSB], [https://www.ebi.ac.uk/pdbsum/1qby PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qby ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Harris~~, C M~~]]	+	[[Category: Harris CM]]
-	[[Category: Harris~~, T M~~]]	+	[[Category: Harris TM]]
-	[[Category: Kim, H Y]]	+	[[Category: Kim H-Y]]
-	[[Category: Li, Z]]	+	[[Category: Li Z]]
-	[[Category: Mao, H]]	+	[[Category: Mao H]]
-	[[Category: Stone~~, M P~~]]	+	[[Category: Stone MP]]
-	[[Category: Tamura~~, P J]]~~	+	[[Category: Tamura PJ]]
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Intercalation~~]]	+

OCA at 09:40, 8 September 2021

OCA — Wed, 08 Sep 2021 09:40:39 GMT

←Older revision		Revision as of 09:40, 8 September 2021
Line 3:		Line 3:
	<StructureSection load='1qby' size='340' side='right'caption='[[1qby]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1qby' size='340' side='right'caption='[[1qby]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qby]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QBY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1QBY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qby]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QBY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BZA:1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL'>BZA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BZA:1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL'>BZA</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=1qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qby OCA], [~~http~~://pdbe.org/1qby PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1qby RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1qby PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1qby 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=1qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qby OCA], [https://pdbe.org/1qby PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qby RCSB], [https://www.ebi.ac.uk/pdbsum/1qby PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qby ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:37, 27 November 2019

OCA — Wed, 27 Nov 2019 10:37:44 GMT

←Older revision		Revision as of 10:37, 27 November 2019
Line 1:		Line 1:

	==THE SOLUTION STRUCTURE OF A BAY-REGION 1R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE==		==THE SOLUTION STRUCTURE OF A BAY-REGION 1R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE==
-	<StructureSection load='1qby' size='340' side='right' caption='[[1qby]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>	+	<StructureSection load='1qby' size='340' side='right'caption='[[1qby]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qby]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qby]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBY FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Harris, C M]]		[[Category: Harris, C M]]
	[[Category: Harris, T M]]		[[Category: Harris, T M]]

OCA at 08:35, 24 February 2018

OCA — Sat, 24 Feb 2018 08:35:14 GMT

←Older revision		Revision as of 08:35, 24 February 2018
Line 1:		Line 1:
		+
	==THE SOLUTION STRUCTURE OF A BAY-REGION 1R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE==		==THE SOLUTION STRUCTURE OF A BAY-REGION 1R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE==
	<StructureSection load='1qby' size='340' side='right' caption='[[1qby]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1qby' size='340' side='right' caption='[[1qby]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1qby]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qby]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BZA:1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL'>BZA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BZA:1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL'>BZA</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=1qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qby OCA], [http://pdbe.org/1qby PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qby RCSB], [http://www.ebi.ac.uk/pdbsum/1qby 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=1qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qby OCA], [http://pdbe.org/1qby PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qby RCSB], [http://www.ebi.ac.uk/pdbsum/1qby PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qby ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:10, 11 September 2015

OCA — Fri, 11 Sep 2015 05:10:27 GMT

←Older revision		Revision as of 05:10, 11 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1qby]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qby]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BZA:1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL'>BZA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BZA:1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL'>BZA</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=1qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qby OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qby RCSB], [http://www.ebi.ac.uk/pdbsum/1qby 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=1qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qby OCA], [http://pdbe.org/1qby PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qby RCSB], [http://www.ebi.ac.uk/pdbsum/1qby 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 1qby" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:24, 3 January 2015

OCA — Sat, 03 Jan 2015 22:24:50 GMT

←Older revision		Revision as of 22:24, 3 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qby]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qby]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BZA:1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL'>BZA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BZA:1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL'>BZA</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=1qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qby OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qby RCSB], [http://www.ebi.ac.uk/pdbsum/1qby 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=1qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qby OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qby RCSB], [http://www.ebi.ac.uk/pdbsum/1qby 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: Harris, C M.]]	+	[[Category: Harris, C M]]
-	[[Category: Harris, T M.]]	+	[[Category: Harris, T M]]
-	[[Category: Kim, H Y.]]	+	[[Category: Kim, H Y]]
-	[[Category: Li, Z.]]	+	[[Category: Li, Z]]
-	[[Category: Mao, H.]]	+	[[Category: Mao, H]]
-	[[Category: Stone, M P.]]	+	[[Category: Stone, M P]]
-	[[Category: Tamura, P J.]]	+	[[Category: Tamura, P J]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Intercalation]]		[[Category: Intercalation]]

OCA at 07:12, 9 June 2014

OCA — Mon, 09 Jun 2014 07:12:14 GMT

←Older revision		Revision as of 07:12, 9 June 2014
Line 1:		Line 1:
-	[[~~Image:~~1qby.~~png~~\|~~left\|200px~~]]	+	==THE SOLUTION STRUCTURE OF A BAY-REGION 1R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE==
		+	<StructureSection load='1qby' size='340' side='right' caption='[[1qby]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1qby]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BZA:1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL'>BZA</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=1qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qby OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qby RCSB], [http://www.ebi.ac.uk/pdbsum/1qby PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The solution structure of the (-)-(1R,2S,3R,4S)-N6-[1-(1,2,3, 4-tetrahydroxy-benz[a]anthracenyl)]-2'-deoxyadenosyl adduct at X6 of 5'-d(CGGACXAGAAG)-3'.5'-d(CTTCTTGTCCG)-3', incorporating codons 60, 61(italic), and 62 of the human N-ras protooncogene, was determined. This adduct results from the trans opening of 1S,2R,3R,4S-1, 2-epoxy-1,2,3,4-tetrahydro-benz[a]anthracenyl-3,4-diol by the exocyclic N6 of adenine. Molecular dynamics simulations were restrained by 509 NOEs from 1H NMR. The precision of the refined structures was monitored by pairwise root-mean-square deviations which were <1.2 A; accuracy was measured by complete relaxation matrix calculations, which yielded a sixth root R factor of 9.1 x 10(-)2 at 250 ms. The refined structure was a right-handed duplex, in which the benz[a]anthracene moiety intercalated from the major groove between C5.G18 and R,S,R,SA6.T17. In this orientation, the saturated ring of BA was oriented in the major groove of the duplex, with the aromatic rings inserted into the duplex such that the terminal ring of BA threaded the duplex and faced toward the minor groove direction. The duplex suffered localized distortion at and immediately adjacent to the adduct site, evidenced by the increased rise of 8.8 A as compared to the value of 3.5 A normally observed for B-DNA between base pairs C5.G18 and R,S,R,SA6.T17. These two base pairs also buckled in opposite directions away from the intercalated BA moiety. The refined structure was similar to the (-)-(7S,8R,9S,10R)-N6-[10-(7,8,9, 10)-tetrahydrobenzo[a]pyrenyl)]-2'-deoxyadenosyl adduct of corresponding stereochemistry at X6 of the same oligodeoxynucleotide [Zegar, I. S., Kim, S. J., Johansen, T. N., Horton, P. J., Harris, C. M., Harris, T. M., and Stone, M. P. (1996) Biochemistry 35, 6212-6224]. Both adducts intercalated toward the 5'-direction from the site of adduction. The similarities in solution structures were reflected in similar biological responses, when repair-deficient AB2480 Escherichia coli were transformed with M13mp7L2 DNA site-specifically modified with these two adducts.

-	~~{{STRUCTURE_1qby\| PDB=1qby \| SCENE= }}~~	+	Intercalation of the (-)-(1R,2S,3R, 4S)-N6-[1-benz[a]anthracenyl]-2'-deoxyadenosyl adduct in an oligodeoxynucleotide containing the human N-ras codon 61 sequence.,Li Z, Mao H, Kim HY, Tamura PJ, Harris CM, Harris TM, Stone MP Biochemistry. 1999 Mar 9;38(10):2969-81. PMID:10074349<ref>PMID:10074349</ref>

-	~~===THE SOLUTION STRUCTURE OF A BAY-REGION 1R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10074349}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1qby]] is~~ a ~~2 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1QBY OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010074349<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Harris, C M.]]		[[Category: Harris, C M.]]
	[[Category: Harris, T M.]]		[[Category: Harris, T M.]]

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

OCA — Tue, 14 Aug 2012 17:05:16 GMT

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

←Older revision

Revision as of 17:05, 14 August 2012

OCA at 17:05, 14 August 2012

OCA — Tue, 14 Aug 2012 17:05:14 GMT

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	[[Image:1qby.png\|left\|200px]]		[[Image:1qby.png\|left\|200px]]

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	{{STRUCTURE_1qby\| PDB=1qby \| SCENE= }}		{{STRUCTURE_1qby\| PDB=1qby \| SCENE= }}

	===THE SOLUTION STRUCTURE OF A BAY-REGION 1R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE===		===THE SOLUTION STRUCTURE OF A BAY-REGION 1R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE===

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	{{ABSTRACT_PUBMED_10074349}}		{{ABSTRACT_PUBMED_10074349}}

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

	==Reference==		==Reference==
-	Intercalation of the (-)-(1R,2S,3R, 4S)-N6-[1-benz[a]anthracenyl]-2'-deoxyadenosyl adduct in an oligodeoxynucleotide containing the human N-ras codon 61 sequence., Li Z, Mao H, Kim HY, Tamura PJ, Harris CM, Harris TM, Stone MP, Biochemistry. 1999 Mar 9;38(10):2969-81. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~10074349 10074349]~~	+	<ref group="xtra">PMID:010074349</ref><references group="xtra"/>
	[[Category: Harris, C M.]]		[[Category: Harris, C M.]]
	[[Category: Harris, T M.]]		[[Category: Harris, T M.]]
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	[[Category: Stone, M P.]]		[[Category: Stone, M P.]]
	[[Category: Tamura, P J.]]		[[Category: Tamura, P J.]]
		+	[[Category: Dna]]
	[[Category: Intercalation]]		[[Category: Intercalation]]
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OCA at 17:52, 28 July 2008

OCA — Mon, 28 Jul 2008 17:52:08 GMT

←Older revision		Revision as of 17:52, 28 July 2008
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	{{STRUCTURE_1qby\| PDB=1qby \| SCENE= }}		{{STRUCTURE_1qby\| PDB=1qby \| SCENE= }}

-	~~'''~~THE SOLUTION STRUCTURE OF A BAY-REGION 1R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE~~'''~~	+	===THE SOLUTION STRUCTURE OF A BAY-REGION 1R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE===


-	~~==Overview==~~	+	<!--
-	~~The solution structure of the (~~-)-(1R,2S,3R,4S)-N6-[1-(1,2,3, 4-tetrahydroxy-benz[a]anthracenyl)]-2'-deoxyadenosyl adduct at X6 of 5'-d(CGGACXAGAAG)-3'.5'-d(CTTCTTGTCCG)-3', incorporating codons 60, 61(italic), and 62 of the human N-ras protooncogene, was determined. This adduct results from the trans opening of 1S,2R,3R,4S-1, 2-epoxy-1,2,3,4-tetrahydro-benz[a]anthracenyl-3,4-diol by the exocyclic N6 of adenine. Molecular dynamics simulations were restrained by 509 NOEs from 1H NMR. The precision of the refined structures was monitored by pairwise root-mean-square deviations which were <1.2 A; accuracy was measured by complete relaxation matrix calculations, which yielded a sixth root R factor of 9.1 x 10(-)2 at 250 ms. The refined structure was a right-handed duplex, in which the benz[a]anthracene moiety intercalated from the major groove between C5.G18 and R,S,R,SA6.T17. In this ~~orientation~~, ~~the saturated ring of BA was oriented in the major groove of the duplex~~, ~~with~~ the aromatic rings inserted into the duplex such that the terminal ring of BA threaded the duplex and faced toward the minor groove direction. The duplex suffered localized distortion at and immediately adjacent to the ~~adduct site, evidenced by the increased rise of 8.8 A~~ as compared to the value of 3.5 A normally observed for B-DNA between base pairs C5.G18 and R,S,R,SA6.T17. These two base pairs also buckled in opposite directions away from the intercalated BA moiety. The refined structure was similar to the (-)-(7S,8R,9S,10R)-N6-[10-(7,8,9, 10)-tetrahydrobenzo[a]pyrenyl)]-2'-deoxyadenosyl adduct of corresponding stereochemistry at ~~X6 of the same oligodeoxynucleotide [Zegar, I~~. S.~~, Kim, S. J., Johansen, T. N., Horton, P. J., Harris, C. M., Harris, T. M., and Stone, M. P. (1996~~) ~~Biochemistry 35~~, ~~6212-6224]. Both adducts intercalated toward~~ the ~~5'-direction from the site of adduction~~. ~~The similarities in solution structures were reflected in similar biological responses, when repair~~-~~deficient AB2480 Escherichia coli were transformed with M13mp7L2 DNA site~~-~~specifically modified with these two adducts.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_10074349}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 10074349 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_10074349}}

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

	==Reference==		==Reference==
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	[[Category: Tamura, P J.]]		[[Category: Tamura, P J.]]
	[[Category: Intercalation]]		[[Category: Intercalation]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 06~~:06:45 2008''	+
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