1kxs - Revision history

OCA at 04:10, 11 September 2015

2015-09-11T04:10:19Z

←Older revision		Revision as of 04:10, 11 September 2015
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	<table><tr><td colspan='2'>[[1kxs]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KXS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kxs]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KXS FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEU:3-(2-HYDROXYETHYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>HEU</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=HEU:3-(2-HYDROXYETHYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>HEU</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=1kxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kxs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kxs RCSB], [http://www.ebi.ac.uk/pdbsum/1kxs 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=1kxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kxs OCA], [http://pdbe.org/1kxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kxs RCSB], [http://www.ebi.ac.uk/pdbsum/1kxs 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 1kxs" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:53, 5 January 2015

2015-01-05T16:53:02Z

←Older revision		Revision as of 16:53, 5 January 2015
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kxs]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KXS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kxs]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KXS FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEU:3-(2-HYDROXYETHYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>HEU</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=HEU:3-(2-HYDROXYETHYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>HEU</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=1kxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kxs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kxs RCSB], [http://www.ebi.ac.uk/pdbsum/1kxs 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=1kxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kxs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kxs RCSB], [http://www.ebi.ac.uk/pdbsum/1kxs PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Boulard, Y.]]	+	[[Category: Boulard, Y]]
-	[[Category: Fazakerley, G V.]]	+	[[Category: Fazakerley, G V]]
-	[[Category: Sowers, L C.]]	+	[[Category: Sowers, L C]]
	[[Category: Deoxyribonucleic acid]]		[[Category: Deoxyribonucleic acid]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Modified base]]		[[Category: Modified base]]
	[[Category: Mutagenesis]]		[[Category: Mutagenesis]]

OCA at 18:20, 28 September 2014

2014-09-28T18:20:49Z

←Older revision		Revision as of 18:20, 28 September 2014
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-	[[~~Image:~~1kxs.~~png~~\|~~left\|200px~~]]	+	==NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE)==
		+	<StructureSection load='1kxs' size='340' side='right' caption='[[1kxs]], [[NMR_Ensembles_of_Models \| 2 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1kxs]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KXS FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEU:3-(2-HYDROXYETHYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>HEU</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=1kxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kxs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kxs RCSB], [http://www.ebi.ac.uk/pdbsum/1kxs PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Determination of the solution structure of the duplex d(GCAAGTC(HE)AAAACG)d(CGTTTTAGACTTGC) containing a 3-(2-hydroxyethyl)-2'-deoxyuridinedeoxyadenine (HEA) base pair is reported. The three-dimensional solution structure, determined starting from 512 models via restrained molecular mechanics using inter-proton distances and torsion angles, converged to two final families of structures. For both families the HE and the opposite A residues are intrahelical and in the anti conformation. The hydroxyethyl chain lies close to the helix axis and for one family the hydroxyl group is above the HEA plane and in the other case it is below. These two models were used to start molecular dynamic calculations with explicit solvent to explore the hydrogen bonding possibilities of the HE*A base pair. The dynamics calculations converge finally to one model structure in which two hydrogen bonds are formed. The first is formed all the time and is between HEO4 and the amino group of A, and the second, an intermittent one, is between the hydroxyl group and the N1 of A. When this second hydrogen bond is not formed a weak interaction CH...N is possible between HEC7H2 and N1A21. All the best structures show an increase in the C1'-C1' distance relative to a Watson-Crick base pair.

-	~~{{STRUCTURE_1kxs\| PDB=1kxs \| SCENE= }}~~	+	The solution structure of an oligonucleotide duplex containing a 2'-deoxyadenosine-3-(2-hydroxyethyl)- 2'-deoxyuridine base pair determined by NMR and molecular dynamics studies.,Boulard Y, Fazakerley GV, Sowers LC Nucleic Acids Res. 2002 Mar 15;30(6):1371-8. PMID:11884635<ref>PMID:11884635</ref>

-	~~===NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11884635}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[1kxs]] is a 2 chain structure. Full experimental information is available from [http:~~//~~oca.weizmann.ac.il/oca-bin/ocashort?id=1KXS OCA].~~	+	</StructureSection>
	[[Category: Boulard, Y.]]		[[Category: Boulard, Y.]]
	[[Category: Fazakerley, G V.]]		[[Category: Fazakerley, G V.]]

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

2012-12-05T21:10:51Z

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

←Older revision

Revision as of 21:10, 5 December 2012

OCA at 21:10, 5 December 2012

2012-12-05T21:10:48Z

←Older revision		Revision as of 21:10, 5 December 2012
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-	{{Seed}}
	[[Image:1kxs.png\|left\|200px]]		[[Image:1kxs.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1kxs", 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_1kxs\| PDB=1kxs \| SCENE= }}		{{STRUCTURE_1kxs\| PDB=1kxs \| SCENE= }}

	===NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE)===		===NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11884635}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11884635 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11884635}}		{{ABSTRACT_PUBMED_11884635}}

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KXS OCA].	+	[[1kxs]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KXS OCA].
-		+
-	~~==Reference==~~	+
-	The solution structure of an oligonucleotide duplex containing a 2'-deoxyadenosine-3-(2-hydroxyethyl)- 2'-deoxyuridine base pair determined by NMR and molecular dynamics studies., Boulard Y, Fazakerley GV, Sowers LC, Nucleic Acids Res. 2002 Mar 15;30(6):1371-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11884635 11884635]	+
	[[Category: Boulard, Y.]]		[[Category: Boulard, Y.]]
	[[Category: Fazakerley, G V.]]		[[Category: Fazakerley, G V.]]
	[[Category: Sowers, L C.]]		[[Category: Sowers, L C.]]
	[[Category: Deoxyribonucleic acid]]		[[Category: Deoxyribonucleic acid]]
		+	[[Category: Dna]]
	[[Category: Modified base]]		[[Category: Modified base]]
	[[Category: Mutagenesis]]		[[Category: Mutagenesis]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 2 11:15:06 2008''

OCA at 08:15, 2 July 2008

2008-07-02T08:15:10Z

←Older revision		Revision as of 08:15, 2 July 2008
Line 1:		Line 1:
-	[[Image:1kxs.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1kxs.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_1kxs\| PDB=1kxs \| SCENE= }}		{{STRUCTURE_1kxs\| PDB=1kxs \| SCENE= }}

-	~~'''~~NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE)~~'''~~	+	===NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE)===


-	~~==Overview==~~	+	<!--
-	~~Determination of the solution structure of the duplex d(GCAAGTC(HE)AAAACG)d(CGTTTTAGACTTGC) containing a 3~~-(2-~~hydroxyethyl)-2'-deoxyuridinedeoxyadenine (HEA) base pair is reported.~~ The ~~three-dimensional solution structure~~, ~~determined starting from 512 models via restrained molecular mechanics using inter-proton distances and torsion angles~~, ~~converged to two final families of structures. For both families~~ the ~~HE and the opposite A residues are intrahelical and in the anti conformation. The hydroxyethyl chain lies close~~ to the ~~helix axis and for one family the hydroxyl group is above the HEA plane and in the other case~~ it ~~is below~~. ~~These two models were used to start molecular dynamic calculations with explicit solvent to explore the hydrogen bonding possibilities of the HE*A base pair~~. The dynamics calculations converge finally to one model structure in which two hydrogen bonds are formed. The first is formed all the time and is between HEO4 and the amino group of A, and the second, an intermittent one, is ~~between~~ the ~~hydroxyl group and the N1 of A~~. ~~When this second hydrogen bond is not formed a weak interaction CH...N is possible between HEC7H2 and N1A21. All the best structures show an increase in the C1'~~-~~C1' distance relative to a Watson~~-~~Crick base pair.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_11884635}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 11884635 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_11884635}}

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

	==Reference==		==Reference==
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	[[Category: Modified base]]		[[Category: Modified base]]
	[[Category: Mutagenesis]]		[[Category: Mutagenesis]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri May~~ 2 23:18:09 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 2 11:15:06 2008''

OCA at 20:18, 2 May 2008

2008-05-02T20:18:10Z

←Older revision		Revision as of 20:18, 2 May 2008
Line 1:		Line 1:
	[[Image:1kxs.gif\|left\|200px]]		[[Image:1kxs.gif\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 1kxs \|SIZE=350\|CAPTION=~~ <~~scene name='initialview01'>1kxs</scene>~~	+	The line below this paragraph, containing "STRUCTURE_1kxs", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <scene name='pdbligand=DA:2'~~-~~DEOXYADENOSINE~~-~~5'-MONOPHOSPHATE'>DA</scene>~~, ~~<scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>~~, <scene ~~name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>~~, ~~<scene name='pdbligand=DT:THYMIDINE~~-~~5'~~-~~MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=HEU:3-(2-HYDROXYETHYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE'>HEU</scene~~>	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	\|~~ACTIVITY~~=	+	or leave the SCENE parameter empty for the default display.
-	\|~~GENE~~=	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_1kxs\| PDB=1kxs \| SCENE= }}
-	~~\|RELATEDENTRY=~~	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kxs OCA], [http://www.ebi.ac.uk/pdbsum/1kxs PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kxs RCSB]</span>	+
-	}}	+

	'''NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE)'''		'''NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE)'''
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	==About this Structure==		==About this Structure==
-	~~1KXS is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KXS OCA].	+	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KXS OCA].

	==Reference==		==Reference==
	The solution structure of an oligonucleotide duplex containing a 2'-deoxyadenosine-3-(2-hydroxyethyl)- 2'-deoxyuridine base pair determined by NMR and molecular dynamics studies., Boulard Y, Fazakerley GV, Sowers LC, Nucleic Acids Res. 2002 Mar 15;30(6):1371-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11884635 11884635]		The solution structure of an oligonucleotide duplex containing a 2'-deoxyadenosine-3-(2-hydroxyethyl)- 2'-deoxyuridine base pair determined by NMR and molecular dynamics studies., Boulard Y, Fazakerley GV, Sowers LC, Nucleic Acids Res. 2002 Mar 15;30(6):1371-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11884635 11884635]
-	[[Category: Protein complex]]
	[[Category: Boulard, Y.]]		[[Category: Boulard, Y.]]
	[[Category: Fazakerley, G V.]]		[[Category: Fazakerley, G V.]]
	[[Category: Sowers, L C.]]		[[Category: Sowers, L C.]]
-	[[Category: ~~deoxyribonucleic~~ acid]]	+	[[Category: Deoxyribonucleic acid]]
-	[[Category: ~~modified~~ base]]	+	[[Category: Modified base]]
-	[[Category: ~~mutagenesis~~]]	+	[[Category: Mutagenesis]]
-		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 23:18:09 2008''
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Mar 30 21~~:55:10 2008''	+

OCA at 18:55, 30 March 2008

2008-03-30T18:55:10Z

←Older revision		Revision as of 18:55, 30 March 2008
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	\|PDB= 1kxs \|SIZE=350\|CAPTION= <scene name='initialview01'>1kxs</scene>		\|PDB= 1kxs \|SIZE=350\|CAPTION= <scene name='initialview01'>1kxs</scene>
	\|SITE=		\|SITE=
-	\|LIGAND=	+	\|LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=HEU:3-(2-HYDROXYETHYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE'>HEU</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE=		\|GENE=
		+	\|DOMAIN=
		+	\|RELATEDENTRY=
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kxs OCA], [http://www.ebi.ac.uk/pdbsum/1kxs PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kxs RCSB]</span>
	}}		}}

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	[[Category: mutagenesis]]		[[Category: mutagenesis]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar ~~20 12~~:23:36 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:55:10 2008''

OCA at 10:23, 20 March 2008

2008-03-20T10:23:37Z

←Older revision		Revision as of 10:23, 20 March 2008
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-	[[Image:1kxs.gif\|left\|200px]]~~<br /><applet load~~="1kxs~~" size~~="350~~" color~~=~~"white" frame~~=~~"true" align~~=~~"right" spinBox~~=~~"true"~~	+	[[Image:1kxs.gif\|left\|200px]]
-	~~caption~~=~~"1kxs" />~~	+
-	'''NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE)'''~~<br />~~	+	{{Structure
		+	\|PDB= 1kxs \|SIZE=350\|CAPTION= <scene name='initialview01'>1kxs</scene>
		+	\|SITE=
		+	\|LIGAND=
		+	\|ACTIVITY=
		+	\|GENE=
		+	}}
		+
		+	'''NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE)'''
		+

	==Overview==		==Overview==
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	==About this Structure==		==About this Structure==
-	1KXS is a [~~http://en.wikipedia.org/wiki/Protein_complex~~ Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KXS OCA].	+	1KXS is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KXS OCA].

	==Reference==		==Reference==
-	The solution structure of an oligonucleotide duplex containing a 2'-deoxyadenosine-3-(2-hydroxyethyl)- 2'-deoxyuridine base pair determined by NMR and molecular dynamics studies., Boulard Y, Fazakerley GV, Sowers LC, Nucleic Acids Res. 2002 Mar 15;30(6):1371-8. PMID:[http://~~ispc~~.~~weizmann~~.ac.~~il/~~/~~pmbin~~/~~getpm?pmid=~~11884635 11884635]	+	The solution structure of an oligonucleotide duplex containing a 2'-deoxyadenosine-3-(2-hydroxyethyl)- 2'-deoxyuridine base pair determined by NMR and molecular dynamics studies., Boulard Y, Fazakerley GV, Sowers LC, Nucleic Acids Res. 2002 Mar 15;30(6):1371-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11884635 11884635]
	[[Category: Protein complex]]		[[Category: Protein complex]]
	[[Category: Boulard, Y.]]		[[Category: Boulard, Y.]]
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	[[Category: mutagenesis]]		[[Category: mutagenesis]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu ~~Feb 21 13~~:39:07 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:23:36 2008''

OCA at 11:39, 21 February 2008

2008-02-21T11:39:15Z

←Older revision		Revision as of 11:39, 21 February 2008
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-	[[Image:1kxs.gif\|left\|200px]]<br /><applet load="1kxs" size="~~450~~" color="white" frame="true" align="right" spinBox="true"	+	[[Image:1kxs.gif\|left\|200px]]<br /><applet load="1kxs" size="350" color="white" frame="true" align="right" spinBox="true"
	caption="1kxs" />		caption="1kxs" />
	'''NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE)'''<br />		'''NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE)'''<br />

	==Overview==		==Overview==
-	Determination of the solution structure of the duplex, d(GCAAGTC(HE)AAAACG)d(CGTTTTAGACTTGC) containing a, 3-(2-hydroxyethyl)-2'-deoxyuridinedeoxyadenine (HEA) base pair is, reported. The three-dimensional solution structure, determined starting, from 512 models via restrained molecular mechanics using inter-proton, distances and torsion angles, converged to two final families of, structures. For both families the HE and the opposite A residues are, intrahelical and in the anti conformation. The hydroxyethyl chain lies, close to the helix axis and for one family the hydroxyl group is above the, HEA plane and in the other case it is below. These two models were used, to start molecular dynamic calculations with explicit solvent to explore, the hydrogen bonding possibilities of the HE*A base pair. The dynamics, calculations converge finally to one model structure in which two hydrogen, bonds are formed. The first is formed all the time and is between HEO4 and, the amino group of A, and the second, an intermittent one, is between the, hydroxyl group and the N1 of A. When this second hydrogen bond is not, formed a weak interaction CH...N is possible between HEC7H2 and N1A21. All, the best structures show an increase in the C1'-C1' distance relative to a, Watson-Crick base pair.	+	Determination of the solution structure of the duplex d(GCAAGTC(HE)AAAACG)d(CGTTTTAGACTTGC) containing a 3-(2-hydroxyethyl)-2'-deoxyuridinedeoxyadenine (HEA) base pair is reported. The three-dimensional solution structure, determined starting from 512 models via restrained molecular mechanics using inter-proton distances and torsion angles, converged to two final families of structures. For both families the HE and the opposite A residues are intrahelical and in the anti conformation. The hydroxyethyl chain lies close to the helix axis and for one family the hydroxyl group is above the HEA plane and in the other case it is below. These two models were used to start molecular dynamic calculations with explicit solvent to explore the hydrogen bonding possibilities of the HE*A base pair. The dynamics calculations converge finally to one model structure in which two hydrogen bonds are formed. The first is formed all the time and is between HEO4 and the amino group of A, and the second, an intermittent one, is between the hydroxyl group and the N1 of A. When this second hydrogen bond is not formed a weak interaction CH...N is possible between HEC7H2 and N1A21. All the best structures show an increase in the C1'-C1' distance relative to a Watson-Crick base pair.

	==About this Structure==		==About this Structure==
-	1KXS is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=1KXS OCA].	+	1KXS is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KXS OCA].

	==Reference==		==Reference==
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	[[Category: Protein complex]]		[[Category: Protein complex]]
	[[Category: Boulard, Y.]]		[[Category: Boulard, Y.]]
-	[[Category: Fazakerley, G.V.]]	+	[[Category: Fazakerley, G V.]]
-	[[Category: Sowers, L.C.]]	+	[[Category: Sowers, L C.]]
	[[Category: deoxyribonucleic acid]]		[[Category: deoxyribonucleic acid]]
	[[Category: modified base]]		[[Category: modified base]]
	[[Category: mutagenesis]]		[[Category: mutagenesis]]

-	''Page seeded by [http://~~ispc~~.weizmann.ac.il/oca OCA ] on ~~Sun Nov 25 02~~:09:~~04 2007~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:39:07 2008''