1agk - Revision history

OCA at 11:32, 22 November 2023

OCA — Wed, 22 Nov 2023 11:32:37 GMT

←Older revision		Revision as of 11:32, 22 November 2023
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	==THE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE SECOND POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE==		==THE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE SECOND POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE==
-	<StructureSection load='1agk' size='340' side='right'caption='[[1agk~~]], [[NMR_Ensembles_of_Models \| 1 NMR models~~]]' scene=''>	+	<StructureSection load='1agk' size='340' side='right'caption='[[1agk]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1agk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AGK FirstGlance]. <br>		<table><tr><td colspan='2'>[[1agk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AGK FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=R:2-DEOXY-N6-(R)STYRENE+OXIDE+ADENOSINE+MONOPHOSPHATE'>R</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;~~'>~~[[1agz\|1agz]], [[1ago\|1ago]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=R:2-DEOXY-N6-(R)STYRENE+OXIDE+ADENOSINE+MONOPHOSPHATE'>R</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=1agk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1agk OCA], [https://pdbe.org/1agk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1agk RCSB], [https://www.ebi.ac.uk/pdbsum/1agk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1agk 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=1agk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1agk OCA], [https://pdbe.org/1agk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1agk RCSB], [https://www.ebi.ac.uk/pdbsum/1agk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1agk ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Feng, B]]	+	[[Category: Feng B]]
-	[[Category: Stone~~, M P]]~~	+	[[Category: Stone MP]]
-	~~[[Category: B-dna]]~~	+
-	~~[[Category: Codon 61 sequence]]~~	+
-	~~[[Category: Deoxyribonucleic acid]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Dna duplex]]~~	+
-	~~[[Category: Human n-ras gene]]~~	+
-	~~[[Category: Major groove]]~~	+
-	~~[[Category: N6-adenine]]~~	+
-	~~[[Category: R-styrene oxide adduct~~]]	+

OCA at 10:20, 17 February 2021

OCA — Wed, 17 Feb 2021 10:20:27 GMT

←Older revision		Revision as of 10:20, 17 February 2021
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	<StructureSection load='1agk' size='340' side='right'caption='[[1agk]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1agk' size='340' side='right'caption='[[1agk]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1agk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AGK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1AGK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1agk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AGK FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=R:2-DEOXY-N6-(R)STYRENE+OXIDE+ADENOSINE+MONOPHOSPHATE'>R</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=R:2-DEOXY-N6-(R)STYRENE+OXIDE+ADENOSINE+MONOPHOSPHATE'>R</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1agz\|1agz]], [[1ago\|1ago]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1agz\|1agz]], [[1ago\|1ago]]</div></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=1agk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1agk OCA], [~~http~~://pdbe.org/1agk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1agk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1agk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1agk 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=1agk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1agk OCA], [https://pdbe.org/1agk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1agk RCSB], [https://www.ebi.ac.uk/pdbsum/1agk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1agk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:44, 10 May 2019

OCA — Fri, 10 May 2019 14:44:27 GMT

←Older revision		Revision as of 14:44, 10 May 2019
Line 1:		Line 1:

	==THE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE SECOND POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE==		==THE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE SECOND POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE==
-	<StructureSection load='1agk' size='340' side='right' caption='[[1agk]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>	+	<StructureSection load='1agk' size='340' side='right'caption='[[1agk]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1agk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AGK FirstGlance]. <br>		<table><tr><td colspan='2'>[[1agk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AGK FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Feng, B]]		[[Category: Feng, B]]
	[[Category: Stone, M P]]		[[Category: Stone, M P]]

OCA at 09:12, 9 August 2017

OCA — Wed, 09 Aug 2017 09:12:38 GMT

←Older revision		Revision as of 09:12, 9 August 2017
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		+
	==THE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE SECOND POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE==		==THE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE SECOND POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE==
	<StructureSection load='1agk' size='340' side='right' caption='[[1agk]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1agk' size='340' side='right' caption='[[1agk]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
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	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=R:2-DEOXY-N6-(R)STYRENE+OXIDE+ADENOSINE+MONOPHOSPHATE'>R</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=R:2-DEOXY-N6-(R)STYRENE+OXIDE+ADENOSINE+MONOPHOSPHATE'>R</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1agz\|1agz]], [[1ago\|1ago]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1agz\|1agz]], [[1ago\|1ago]]</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=1agk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1agk OCA], [http://pdbe.org/1agk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1agk RCSB], [http://www.ebi.ac.uk/pdbsum/1agk 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=1agk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1agk OCA], [http://pdbe.org/1agk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1agk RCSB], [http://www.ebi.ac.uk/pdbsum/1agk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1agk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:20, 11 September 2015

OCA — Fri, 11 Sep 2015 06:20:31 GMT

←Older revision		Revision as of 06:20, 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=R:2-DEOXY-N6-(R)STYRENE+OXIDE+ADENOSINE+MONOPHOSPHATE'>R</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=R:2-DEOXY-N6-(R)STYRENE+OXIDE+ADENOSINE+MONOPHOSPHATE'>R</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1agz\|1agz]], [[1ago\|1ago]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1agz\|1agz]], [[1ago\|1ago]]</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=1agk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1agk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1agk RCSB], [http://www.ebi.ac.uk/pdbsum/1agk 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=1agk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1agk OCA], [http://pdbe.org/1agk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1agk RCSB], [http://www.ebi.ac.uk/pdbsum/1agk PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 1agk" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:02, 22 December 2014

OCA — Mon, 22 Dec 2014 11:02:04 GMT

←Older revision		Revision as of 11:02, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1agk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AGK FirstGlance]. <br>		<table><tr><td colspan='2'>[[1agk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AGK FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=R:2-DEOXY-N6-(R)STYRENE+OXIDE+ADENOSINE+MONOPHOSPHATE'>R</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=R:2-DEOXY-N6-(R)STYRENE+OXIDE+ADENOSINE+MONOPHOSPHATE'>R</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1agz\|1agz]], [[1ago\|1ago]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1agz\|1agz]], [[1ago\|1ago]]</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=1agk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1agk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1agk RCSB], [http://www.ebi.ac.uk/pdbsum/1agk 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=1agk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1agk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1agk RCSB], [http://www.ebi.ac.uk/pdbsum/1agk 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 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Feng, B.]]	+	[[Category: Feng, B]]
-	[[Category: Stone, M P.]]	+	[[Category: Stone, M P]]
	[[Category: B-dna]]		[[Category: B-dna]]
	[[Category: Codon 61 sequence]]		[[Category: Codon 61 sequence]]

OCA at 08:07, 30 July 2014

OCA — Wed, 30 Jul 2014 08:07:35 GMT

←Older revision		Revision as of 08:07, 30 July 2014
Line 1:		Line 1:
-	[[~~Image:~~1agk.~~png~~\|~~left~~\|~~200px~~]]	+	==THE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE SECOND POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE==
		+	<StructureSection load='1agk' size='340' side='right' caption='[[1agk]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1agk]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AGK FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=R:2-DEOXY-N6-(R)STYRENE+OXIDE+ADENOSINE+MONOPHOSPHATE'>R</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1agz\|1agz]], [[1ago\|1ago]]</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=1agk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1agk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1agk RCSB], [http://www.ebi.ac.uk/pdbsum/1agk PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Conformations of (R)-alpha-(N6-adenyl)styrene oxide adducts at positions X6 in d(CGGACXAGAAG).d(CTTCTTGTCCG) and X7 in d(CGGACAXGAAG).d(CTTCTTGTCCG), incorporating codons 60, 61 (underlined), and 62 of the human n-ras protooncogene, were refined from 1H NMR data. These were the R(61,2) and R(61,3) adducts. Chemical shift perturbations were in the 5'-direction from the sites of adduction; large changes were observed for C5 H5 and H6 in the R(61,2) adduct. The styrene moieties were only partially defined by NOE data. Spectral overlap, particularly for the R(61,2) adduct, prevented complete assignments of the aromatic resonances; likewise, there were insufficient data to orient the CH2OH moieties. Ring flips were slow on the NMR time scale. For the R(61,2) adduct 260 restraints were obtained from NOE data at three mixing times using relaxation matrix analysis; for the R(61,3) adduct 230 restraints were obtained. Structures emergent from molecular dynamics/simulated annealing for the R(61,2) adduct converged to average and maximum pairwise rms differences of 1.3 and 1.7 A, respectively, while those for the R(61,3) adduct converged to average and maximum pairwise rms differences of 1.2 and 1.6 A. Sixth root residual indices of 7.5 and 6.8 x 10(-2) were measured between the refined structures and NOE intensities using relaxation matrix calculations for the R(61,2) and R(61,3) adducts, respectively. The styrene rings were in the 5'-direction from the lesion sites in the major groove. The preferred orientation calculated for the R(61,2) adduct placed the styrene ring edgewise and approximately orthogonal to C5, while that calculated for the R(61,3) duplex had the styrene ring approximately orthogonal to the major groove edges of base pairs A6.T17 and R-SOA7.T16.

-	~~{{STRUCTURE_1agk\| PDB=1agk \| SCENE= }}~~	+	Major groove (R)-alpha-(N6-adenyl)styrene oxide adducts in an oligodeoxynucleotide containing the human N-ras codon 61 sequence: conformations of the R(61,2) and R(61,3) sequence isomers from 1H NMR.,Feng B, Zhou L, Passarelli M, Harris CM, Harris TM, Stone MP Biochemistry. 1995 Oct 31;34(43):14021-36. PMID:7578000<ref>PMID:7578000</ref>

-	~~===THE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE SECOND POSITION OF THE CODON 61 REGION~~, ~~MINIMIZED AVERAGE STRUCTURE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_7578000}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1agk]] is~~ a ~~2 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1AGK OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:007578000<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Feng, B.]]		[[Category: Feng, B.]]
	[[Category: Stone, M P.]]		[[Category: Stone, M P.]]

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

OCA — Sun, 21 Oct 2012 11:44:24 GMT

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

←Older revision

Revision as of 11:44, 21 October 2012

OCA at 11:44, 21 October 2012

OCA — Sun, 21 Oct 2012 11:44:21 GMT

←Older revision		Revision as of 11:44, 21 October 2012
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-	{{Seed}}
	[[Image:1agk.png\|left\|200px]]		[[Image:1agk.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1agk", creates the "Structure Box" on the page.
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	{{STRUCTURE_1agk\| PDB=1agk \| SCENE= }}		{{STRUCTURE_1agk\| PDB=1agk \| SCENE= }}

	===THE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE SECOND POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE===		===THE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE SECOND POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE===

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	{{ABSTRACT_PUBMED_7578000}}		{{ABSTRACT_PUBMED_7578000}}

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

	==Reference==		==Reference==
-	Major groove (R)-alpha-(N6-adenyl)styrene oxide adducts in an oligodeoxynucleotide containing the human N-ras codon 61 sequence: conformations of the R(61,2) and R(61,3) sequence isomers from 1H NMR., Feng B, Zhou L, Passarelli M, Harris CM, Harris TM, Stone MP, Biochemistry. 1995 Oct 31;34(43):14021-36. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~7578000 7578000]~~	+	<ref group="xtra">PMID:007578000</ref><references group="xtra"/>
	[[Category: Feng, B.]]		[[Category: Feng, B.]]
	[[Category: Stone, M P.]]		[[Category: Stone, M P.]]
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	[[Category: Codon 61 sequence]]		[[Category: Codon 61 sequence]]
	[[Category: Deoxyribonucleic acid]]		[[Category: Deoxyribonucleic acid]]
		+	[[Category: Dna]]
	[[Category: Dna duplex]]		[[Category: Dna duplex]]
	[[Category: Human n-ras gene]]		[[Category: Human n-ras gene]]
	[[Category: Major groove]]		[[Category: Major groove]]
	[[Category: N6-adenine]]		[[Category: N6-adenine]]
-	[[Category: Nmr]]
	[[Category: R-styrene oxide adduct]]		[[Category: R-styrene oxide adduct]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 16:48:08 2008''

OCA at 13:48, 30 June 2008

OCA — Mon, 30 Jun 2008 13:48:10 GMT

←Older revision		Revision as of 13:48, 30 June 2008
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-	[[Image:1agk.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1agk.png\|left\|200px]]

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	{{STRUCTURE_1agk\| PDB=1agk \| SCENE= }}		{{STRUCTURE_1agk\| PDB=1agk \| SCENE= }}

-	~~'''~~THE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE SECOND POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE~~'''~~	+	===THE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE SECOND POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE===


-	~~==Overview==~~	+	<!--
-	~~Conformations of (R)~~-~~alpha~~-(N6-adenyl)styrene oxide adducts at positions X6 in d(CGGACXAGAAG).d(CTTCTTGTCCG) and X7 in d(CGGACAXGAAG).d(CTTCTTGTCCG), incorporating codons 60, 61 (underlined), and 62 of the human n-ras protooncogene, were refined from 1H NMR data. These were the R(61,2) and R(61,3) adducts. Chemical shift perturbations were in the 5'-direction from the sites of adduction; large changes were observed for C5 H5 and H6 in the R(61,2) adduct. The ~~styrene moieties were only partially defined by NOE data. Spectral overlap~~, ~~particularly for the R(61,2) adduct~~, ~~prevented complete assignments of~~ the ~~aromatic resonances; likewise, there were insufficient data~~ to ~~orient~~ the ~~CH2OH moieties. Ring flips were slow~~ on ~~the NMR time scale. For the R(61,2) adduct 260 restraints were obtained from NOE data~~ at ~~three mixing times using relaxation matrix analysis; for the R(61,3) adduct 230 restraints were obtained. Structures emergent from molecular dynamics~~/~~simulated annealing for the R(61,2) adduct converged to average and maximum pairwise rms differences of 1~~.~~3 and 1~~.~~7 A~~, ~~respectively, while those for~~ the ~~R(61,3) adduct converged to average and maximum pairwise rms differences of 1~~.~~2 and 1.6 A. Sixth root residual indices of 7.5 and 6.8 x 10(~~-~~2) were measured between the refined structures and NOE intensities using relaxation matrix calculations for the R(61,2) and R(61,3) adducts, respectively. The styrene rings were in the 5'~~-direction from the lesion sites in the major groove. The preferred orientation calculated for the R(61,2) adduct placed the styrene ring edgewise and approximately orthogonal to C5, while that calculated for the R(61,3) duplex had the styrene ring approximately orthogonal to the major groove edges of base pairs A6.T17 and R-SOA7.T16.	+	The line below this paragraph, {{ABSTRACT_PUBMED_7578000}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 7578000 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_7578000}}

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

	==Reference==		==Reference==
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	[[Category: Nmr]]		[[Category: Nmr]]
	[[Category: R-styrene oxide adduct]]		[[Category: R-styrene oxide adduct]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri May 2 10~~:14:32 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 16:48:08 2008''