2lfa - Revision history

OCA at 06:55, 1 May 2024

2024-05-01T06:55:29Z

←Older revision		Revision as of 06:55, 1 May 2024
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2lfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lfa OCA], [https://pdbe.org/2lfa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lfa RCSB], [https://www.ebi.ac.uk/pdbsum/2lfa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lfa 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=2lfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lfa OCA], [https://pdbe.org/2lfa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lfa RCSB], [https://www.ebi.ac.uk/pdbsum/2lfa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lfa ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Diastereomeric 8,5'-cyclopurine 2'-deoxynucleosides, containing a covalent bond between the deoxyribose and the purine base, represent an important class of DNA damage induced by ionizing radiation. The 8,5'-cyclo-2'-deoxyguanosine lesion (cdG) has been recently reported to be a strong block of replication and highly mutagenic in Escherichia coli. The 8,5'-cyclopurine-2'-deoxyriboses are suspected to play a role in the etiology of neurodegeneration in xeroderma pigmentosum patients. These lesions cannot be repaired by base excision repair, but they are substrates for nucleotide excision repair. The structure of an oligodeoxynucleotide duplex containing a site-specific S-cdG lesion placed opposite dC in the complementary strand was obtained by molecular dynamics calculations restrained by distance and dihedral angle restraints obtained from NMR spectroscopy. The S-cdG deoxyribose exhibited the O4'-exo (west) pseudorotation. Significant perturbations were observed for the beta, gamma, and chi torsion angles of the S-cdG nucleoside. Watson-Crick base pairing was conserved at the S-cdG.dC pair. However, the O4'-exo pseudorotation of the S-cdG deoxyribose perturbed the helical twist and base pair stacking at the lesion site and the 5'-neighbor dC.dG base pair. Thermodynamic destabilization of the duplex measured by UV melting experiments correlated with base stacking and structural perturbations involving the modified S-cdG.dC and 3'- neighbor dT.dA base pairs. These perturbations may be responsible for both the genotoxicity of this lesion and its ability to be recognized by nucleotide excision repair.
-
-	Structure of (5'S)-8,5'-Cyclo-2'-deoxyguanosine in DNA.,Huang H, Das RS, Basu AK, Stone MP J Am Chem Soc. 2011 Dec 21;133(50):20357-68. Epub 2011 Nov 21. PMID:22103478<ref>PMID:22103478</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2lfa" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:15, 15 November 2023

2023-11-15T12:15:50Z

←Older revision		Revision as of 12:15, 15 November 2023
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	==Oligonucleotide duplex contaning (5'S)-8,5'-cyclo-2'-deoxyguansine==		==Oligonucleotide duplex contaning (5'S)-8,5'-cyclo-2'-deoxyguansine==
-	<StructureSection load='2lfa' size='340' side='right'caption='[[2lfa~~]], [[NMR_Ensembles_of_Models \| 1 NMR models~~]]' scene=''>	+	<StructureSection load='2lfa' size='340' side='right'caption='[[2lfa]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2lfa]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LFA FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lfa]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LFA FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=2LF:(6S,7S,8S,10R)-2-AMINO-8-HYDROXY-4-OXO-3,6,7,8,9,10-HEXAHYDRO-4H-7,10-EPOXYAZEPINO[1,2-E]PURIN-6-YL+DIHYDROGEN+PHOSPHATE'>2LF</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=2LF:(6S,7S,8S,10R)-2-AMINO-8-HYDROXY-4-OXO-3,6,7,8,9,10-HEXAHYDRO-4H-7,10-EPOXYAZEPINO[1,2-E]PURIN-6-YL+DIHYDROGEN+PHOSPHATE'>2LF</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=2lfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lfa OCA], [https://pdbe.org/2lfa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lfa RCSB], [https://www.ebi.ac.uk/pdbsum/2lfa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lfa 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=2lfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lfa OCA], [https://pdbe.org/2lfa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lfa RCSB], [https://www.ebi.ac.uk/pdbsum/2lfa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lfa ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Basu, A]]	+	[[Category: Basu A]]
-	[[Category: Das~~, R S~~]]	+	[[Category: Das RS]]
-	[[Category: Huang, H]]	+	[[Category: Huang H]]
-	[[Category: Stone~~, M P]]~~	+	[[Category: Stone MP]]
-	~~[[Category: 5'-cyclo-2'-deoxyguanosine]]~~	+
-	~~[[Category: Cyclo-dg]]~~	+
-	~~[[Category: Cyclopurine]]~~	+
-	~~[[Category: Dna~~]]	+

OCA at 07:51, 9 February 2022

2022-02-09T07:51:15Z

←Older revision		Revision as of 07:51, 9 February 2022
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	<StructureSection load='2lfa' size='340' side='right'caption='[[2lfa]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='2lfa' size='340' side='right'caption='[[2lfa]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2lfa]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2LFA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2lfa]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LFA FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2LF:(6S,7S,8S,10R)-2-AMINO-8-HYDROXY-4-OXO-3,6,7,8,9,10-HEXAHYDRO-4H-7,10-EPOXYAZEPINO[1,2-E]PURIN-6-YL+DIHYDROGEN+PHOSPHATE'>2LF</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=2LF:(6S,7S,8S,10R)-2-AMINO-8-HYDROXY-4-OXO-3,6,7,8,9,10-HEXAHYDRO-4H-7,10-EPOXYAZEPINO[1,2-E]PURIN-6-YL+DIHYDROGEN+PHOSPHATE'>2LF</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2lfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lfa OCA], [~~http~~://pdbe.org/2lfa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2lfa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2lfa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2lfa 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=2lfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lfa OCA], [https://pdbe.org/2lfa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lfa RCSB], [https://www.ebi.ac.uk/pdbsum/2lfa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lfa ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:03, 6 May 2020

2020-05-06T07:03:30Z

←Older revision		Revision as of 07:03, 6 May 2020
Line 1:		Line 1:

	==Oligonucleotide duplex contaning (5'S)-8,5'-cyclo-2'-deoxyguansine==		==Oligonucleotide duplex contaning (5'S)-8,5'-cyclo-2'-deoxyguansine==
-	<StructureSection load='2lfa' size='340' side='right' caption='[[2lfa]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>	+	<StructureSection load='2lfa' size='340' side='right'caption='[[2lfa]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2lfa]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2LFA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2lfa]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2LFA FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2LF:(6S,7S,8S,10R)-2-AMINO-8-HYDROXY-4-OXO-3,6,7,8,9,10-HEXAHYDRO-4H-7,10-EPOXYAZEPINO[1,2-E]PURIN-6-YL+DIHYDROGEN+PHOSPHATE'>2LF</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=2LF:(6S,7S,8S,10R)-2-AMINO-8-HYDROXY-4-OXO-3,6,7,8,9,10-HEXAHYDRO-4H-7,10-EPOXYAZEPINO[1,2-E]PURIN-6-YL+DIHYDROGEN+PHOSPHATE'>2LF</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=2lfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lfa OCA], [http://pdbe.org/2lfa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lfa RCSB], [http://www.ebi.ac.uk/pdbsum/2lfa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2lfa ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2lfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lfa OCA], [http://pdbe.org/2lfa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lfa RCSB], [http://www.ebi.ac.uk/pdbsum/2lfa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2lfa ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Basu, A]]		[[Category: Basu, A]]
	[[Category: Das, R S]]		[[Category: Das, R S]]

OCA at 19:26, 1 August 2018

2018-08-01T19:26:20Z

←Older revision		Revision as of 19:26, 1 August 2018
Line 1:		Line 1:
		+
	==Oligonucleotide duplex contaning (5'S)-8,5'-cyclo-2'-deoxyguansine==		==Oligonucleotide duplex contaning (5'S)-8,5'-cyclo-2'-deoxyguansine==
	<StructureSection load='2lfa' size='340' side='right' caption='[[2lfa]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='2lfa' size='340' side='right' caption='[[2lfa]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2lfa]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LFA FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lfa]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LFA FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2LF:(6S,7S,8S,10R)-2-AMINO-8-HYDROXY-4-OXO-3,6,7,8,9,10-HEXAHYDRO-4H-7,10-EPOXYAZEPINO[1,2-E]PURIN-6-YL+DIHYDROGEN+PHOSPHATE'>2LF</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=2LF:(6S,7S,8S,10R)-2-AMINO-8-HYDROXY-4-OXO-3,6,7,8,9,10-HEXAHYDRO-4H-7,10-EPOXYAZEPINO[1,2-E]PURIN-6-YL+DIHYDROGEN+PHOSPHATE'>2LF</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=2lfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lfa OCA], [http://pdbe.org/2lfa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lfa RCSB], [http://www.ebi.ac.uk/pdbsum/2lfa 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=2lfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lfa OCA], [http://pdbe.org/2lfa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lfa RCSB], [http://www.ebi.ac.uk/pdbsum/2lfa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2lfa ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:13, 10 September 2015

2015-09-10T16:13:09Z

←Older revision		Revision as of 16:13, 10 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[2lfa]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LFA FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lfa]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LFA FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2LF:(6S,7S,8S,10R)-2-AMINO-8-HYDROXY-4-OXO-3,6,7,8,9,10-HEXAHYDRO-4H-7,10-EPOXYAZEPINO[1,2-E]PURIN-6-YL+DIHYDROGEN+PHOSPHATE'>2LF</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=2LF:(6S,7S,8S,10R)-2-AMINO-8-HYDROXY-4-OXO-3,6,7,8,9,10-HEXAHYDRO-4H-7,10-EPOXYAZEPINO[1,2-E]PURIN-6-YL+DIHYDROGEN+PHOSPHATE'>2LF</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=2lfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lfa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lfa RCSB], [http://www.ebi.ac.uk/pdbsum/2lfa 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=2lfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lfa OCA], [http://pdbe.org/2lfa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lfa RCSB], [http://www.ebi.ac.uk/pdbsum/2lfa 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 2lfa" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:02, 22 December 2014

2014-12-22T05:02:48Z

←Older revision		Revision as of 05:02, 22 December 2014
Line 2:		Line 2:
	<StructureSection load='2lfa' size='340' side='right' caption='[[2lfa]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='2lfa' size='340' side='right' caption='[[2lfa]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2lfa]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA]. <br>	+	<table><tr><td colspan='2'>[[2lfa]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LFA FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2LF:(6S,7S,8S,10R)-2-AMINO-8-HYDROXY-4-OXO-3,6,7,8,9,10-HEXAHYDRO-4H-7,10-EPOXYAZEPINO[1,2-E]PURIN-6-YL+DIHYDROGEN+PHOSPHATE'>2LF</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=2LF:(6S,7S,8S,10R)-2-AMINO-8-HYDROXY-4-OXO-3,6,7,8,9,10-HEXAHYDRO-4H-7,10-EPOXYAZEPINO[1,2-E]PURIN-6-YL+DIHYDROGEN+PHOSPHATE'>2LF</scene></td></tr>
-	<tr~~><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class~~='~~plainlinks~~'~~>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2lfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lfa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lfa RCSB], [http://www.ebi.ac.uk/pdbsum/2lfa PDBsum]</span></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=2lfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lfa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lfa RCSB], [http://www.ebi.ac.uk/pdbsum/2lfa 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 13:		Line 12:
	Structure of (5'S)-8,5'-Cyclo-2'-deoxyguanosine in DNA.,Huang H, Das RS, Basu AK, Stone MP J Am Chem Soc. 2011 Dec 21;133(50):20357-68. Epub 2011 Nov 21. PMID:22103478<ref>PMID:22103478</ref>		Structure of (5'S)-8,5'-Cyclo-2'-deoxyguanosine in DNA.,Huang H, Das RS, Basu AK, Stone MP J Am Chem Soc. 2011 Dec 21;133(50):20357-68. Epub 2011 Nov 21. PMID:22103478<ref>PMID:22103478</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 19:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Basu, A.]]	+	[[Category: Basu, A]]
-	[[Category: Das, R S.]]	+	[[Category: Das, R S]]
-	[[Category: Huang, H.]]	+	[[Category: Huang, H]]
-	[[Category: Stone, M P.]]	+	[[Category: Stone, M P]]
	[[Category: 5'-cyclo-2'-deoxyguanosine]]		[[Category: 5'-cyclo-2'-deoxyguanosine]]
	[[Category: Cyclo-dg]]		[[Category: Cyclo-dg]]
	[[Category: Cyclopurine]]		[[Category: Cyclopurine]]
	[[Category: Dna]]		[[Category: Dna]]

OCA at 09:48, 1 May 2014

2014-05-01T09:48:12Z

←Older revision		Revision as of 09:48, 1 May 2014
Line 2:		Line 2:
	<StructureSection load='2lfa' size='340' side='right' caption='[[2lfa]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='2lfa' size='340' side='right' caption='[[2lfa]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	[[2lfa]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA]. <br>	+	<table><tr><td colspan='2'>[[2lfa]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA]. <br>
-	<b>[[Non-Standard_Residue\|NonStd Res:]]</b> <scene name='pdbligand=2LF:(6S,7S,8S,10R)-2-AMINO-8-HYDROXY-4-OXO-3,6,7,8,9,10-HEXAHYDRO-4H-7,10-EPOXYAZEPINO[1,2-E]PURIN-6-YL+DIHYDROGEN+PHOSPHATE'>2LF</scene><br>	+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2LF:(6S,7S,8S,10R)-2-AMINO-8-HYDROXY-4-OXO-3,6,7,8,9,10-HEXAHYDRO-4H-7,10-EPOXYAZEPINO[1,2-E]PURIN-6-YL+DIHYDROGEN+PHOSPHATE'>2LF</scene></td></tr>
-	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>	+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
-	<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lfa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lfa RCSB], [http://www.ebi.ac.uk/pdbsum/2lfa PDBsum]</span><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=2lfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lfa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lfa RCSB], [http://www.ebi.ac.uk/pdbsum/2lfa PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	Diastereomeric 8,5'-cyclopurine 2'-deoxynucleosides, containing a covalent bond between the deoxyribose and the purine base, represent an important class of DNA damage induced by ionizing radiation. The 8,5'-cyclo-2'-deoxyguanosine lesion (cdG) has been recently reported to be a strong block of replication and highly mutagenic in Escherichia coli. The 8,5'-cyclopurine-2'-deoxyriboses are suspected to play a role in the etiology of neurodegeneration in xeroderma pigmentosum patients. These lesions cannot be repaired by base excision repair, but they are substrates for nucleotide excision repair. The structure of an oligodeoxynucleotide duplex containing a site-specific S-cdG lesion placed opposite dC in the complementary strand was obtained by molecular dynamics calculations restrained by distance and dihedral angle restraints obtained from NMR spectroscopy. The S-cdG deoxyribose exhibited the O4'-exo (west) pseudorotation. Significant perturbations were observed for the beta, gamma, and chi torsion angles of the S-cdG nucleoside. Watson-Crick base pairing was conserved at the S-cdG.dC pair. However, the O4'-exo pseudorotation of the S-cdG deoxyribose perturbed the helical twist and base pair stacking at the lesion site and the 5'-neighbor dC.dG base pair. Thermodynamic destabilization of the duplex measured by UV melting experiments correlated with base stacking and structural perturbations involving the modified S-cdG.dC and 3'- neighbor dT.dA base pairs. These perturbations may be responsible for both the genotoxicity of this lesion and its ability to be recognized by nucleotide excision repair.		Diastereomeric 8,5'-cyclopurine 2'-deoxynucleosides, containing a covalent bond between the deoxyribose and the purine base, represent an important class of DNA damage induced by ionizing radiation. The 8,5'-cyclo-2'-deoxyguanosine lesion (cdG) has been recently reported to be a strong block of replication and highly mutagenic in Escherichia coli. The 8,5'-cyclopurine-2'-deoxyriboses are suspected to play a role in the etiology of neurodegeneration in xeroderma pigmentosum patients. These lesions cannot be repaired by base excision repair, but they are substrates for nucleotide excision repair. The structure of an oligodeoxynucleotide duplex containing a site-specific S-cdG lesion placed opposite dC in the complementary strand was obtained by molecular dynamics calculations restrained by distance and dihedral angle restraints obtained from NMR spectroscopy. The S-cdG deoxyribose exhibited the O4'-exo (west) pseudorotation. Significant perturbations were observed for the beta, gamma, and chi torsion angles of the S-cdG nucleoside. Watson-Crick base pairing was conserved at the S-cdG.dC pair. However, the O4'-exo pseudorotation of the S-cdG deoxyribose perturbed the helical twist and base pair stacking at the lesion site and the 5'-neighbor dC.dG base pair. Thermodynamic destabilization of the duplex measured by UV melting experiments correlated with base stacking and structural perturbations involving the modified S-cdG.dC and 3'- neighbor dT.dA base pairs. These perturbations may be responsible for both the genotoxicity of this lesion and its ability to be recognized by nucleotide excision repair.
Line 12:		Line 14:

	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>		From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:11, 30 April 2014

2014-04-30T10:11:05Z

←Older revision		Revision as of 10:11, 30 April 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	[[2lfa]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA]. <br>		[[2lfa]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA]. <br>
		+	<b>[[Non-Standard_Residue\|NonStd Res:]]</b> <scene name='pdbligand=2LF:(6S,7S,8S,10R)-2-AMINO-8-HYDROXY-4-OXO-3,6,7,8,9,10-HEXAHYDRO-4H-7,10-EPOXYAZEPINO[1,2-E]PURIN-6-YL+DIHYDROGEN+PHOSPHATE'>2LF</scene><br>
	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>		<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
		+	<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lfa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lfa RCSB], [http://www.ebi.ac.uk/pdbsum/2lfa PDBsum]</span><br>
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	Diastereomeric 8,5'-cyclopurine 2'-deoxynucleosides, containing a covalent bond between the deoxyribose and the purine base, represent an important class of DNA damage induced by ionizing radiation. The 8,5'-cyclo-2'-deoxyguanosine lesion (cdG) has been recently reported to be a strong block of replication and highly mutagenic in Escherichia coli. The 8,5'-cyclopurine-2'-deoxyriboses are suspected to play a role in the etiology of neurodegeneration in xeroderma pigmentosum patients. These lesions cannot be repaired by base excision repair, but they are substrates for nucleotide excision repair. The structure of an oligodeoxynucleotide duplex containing a site-specific S-cdG lesion placed opposite dC in the complementary strand was obtained by molecular dynamics calculations restrained by distance and dihedral angle restraints obtained from NMR spectroscopy. The S-cdG deoxyribose exhibited the O4'-exo (west) pseudorotation. Significant perturbations were observed for the beta, gamma, and chi torsion angles of the S-cdG nucleoside. Watson-Crick base pairing was conserved at the S-cdG.dC pair. However, the O4'-exo pseudorotation of the S-cdG deoxyribose perturbed the helical twist and base pair stacking at the lesion site and the 5'-neighbor dC.dG base pair. Thermodynamic destabilization of the duplex measured by UV melting experiments correlated with base stacking and structural perturbations involving the modified S-cdG.dC and 3'- neighbor dT.dA base pairs. These perturbations may be responsible for both the genotoxicity of this lesion and its ability to be recognized by nucleotide excision repair.		Diastereomeric 8,5'-cyclopurine 2'-deoxynucleosides, containing a covalent bond between the deoxyribose and the purine base, represent an important class of DNA damage induced by ionizing radiation. The 8,5'-cyclo-2'-deoxyguanosine lesion (cdG) has been recently reported to be a strong block of replication and highly mutagenic in Escherichia coli. The 8,5'-cyclopurine-2'-deoxyriboses are suspected to play a role in the etiology of neurodegeneration in xeroderma pigmentosum patients. These lesions cannot be repaired by base excision repair, but they are substrates for nucleotide excision repair. The structure of an oligodeoxynucleotide duplex containing a site-specific S-cdG lesion placed opposite dC in the complementary strand was obtained by molecular dynamics calculations restrained by distance and dihedral angle restraints obtained from NMR spectroscopy. The S-cdG deoxyribose exhibited the O4'-exo (west) pseudorotation. Significant perturbations were observed for the beta, gamma, and chi torsion angles of the S-cdG nucleoside. Watson-Crick base pairing was conserved at the S-cdG.dC pair. However, the O4'-exo pseudorotation of the S-cdG deoxyribose perturbed the helical twist and base pair stacking at the lesion site and the 5'-neighbor dC.dG base pair. Thermodynamic destabilization of the duplex measured by UV melting experiments correlated with base stacking and structural perturbations involving the modified S-cdG.dC and 3'- neighbor dT.dA base pairs. These perturbations may be responsible for both the genotoxicity of this lesion and its ability to be recognized by nucleotide excision repair.

OCA at 08:31, 30 April 2014

2014-04-30T08:31:15Z

←Older revision		Revision as of 08:31, 30 April 2014
Line 1:		Line 1:
-	[[~~Image:~~2lfa~~.jpg~~\|~~left\|200px~~]]	+	==Oligonucleotide duplex contaning (5'S)-8,5'-cyclo-2'-deoxyguansine==
		+	<StructureSection load='2lfa' size='340' side='right' caption='[[2lfa]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	[[2lfa]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA]. <br>
		+	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
		+	== Publication Abstract from PubMed ==
		+	Diastereomeric 8,5'-cyclopurine 2'-deoxynucleosides, containing a covalent bond between the deoxyribose and the purine base, represent an important class of DNA damage induced by ionizing radiation. The 8,5'-cyclo-2'-deoxyguanosine lesion (cdG) has been recently reported to be a strong block of replication and highly mutagenic in Escherichia coli. The 8,5'-cyclopurine-2'-deoxyriboses are suspected to play a role in the etiology of neurodegeneration in xeroderma pigmentosum patients. These lesions cannot be repaired by base excision repair, but they are substrates for nucleotide excision repair. The structure of an oligodeoxynucleotide duplex containing a site-specific S-cdG lesion placed opposite dC in the complementary strand was obtained by molecular dynamics calculations restrained by distance and dihedral angle restraints obtained from NMR spectroscopy. The S-cdG deoxyribose exhibited the O4'-exo (west) pseudorotation. Significant perturbations were observed for the beta, gamma, and chi torsion angles of the S-cdG nucleoside. Watson-Crick base pairing was conserved at the S-cdG.dC pair. However, the O4'-exo pseudorotation of the S-cdG deoxyribose perturbed the helical twist and base pair stacking at the lesion site and the 5'-neighbor dC.dG base pair. Thermodynamic destabilization of the duplex measured by UV melting experiments correlated with base stacking and structural perturbations involving the modified S-cdG.dC and 3'- neighbor dT.dA base pairs. These perturbations may be responsible for both the genotoxicity of this lesion and its ability to be recognized by nucleotide excision repair.

-	<!--	+	Structure of (5'S)-8,5'-Cyclo-2'-deoxyguanosine in DNA.,Huang H, Das RS, Basu AK, Stone MP J Am Chem Soc. 2011 Dec 21;133(50):20357-68. Epub 2011 Nov 21. PMID:22103478<ref>PMID:22103478</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_2lfa"~~, ~~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_2lfa\| PDB=2lfa \| SCENE= }}~~	+

-	~~===Oligonucleotide duplex contaning (5'S)-8~~,~~5'-cyclo-2'-deoxyguansine===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	== References ==
-		+	<references/>
-	~~<!--~~	+	__TOC__
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22103478}}, adds~~ the ~~Publication Abstract to the page~~	+	</StructureSection>
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22103478 is the PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_22103478}}~~	+
-		+
-	==~~About this Structure~~==	+
-	~~[[2lfa]] is a 2 chain structure. Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2LFA OCA].~~	+
-		+
-	~~==Reference==~~	+
-	<~~ref group="xtra">PMID:022103478</ref><references group="xtra"~~/>	+
	[[Category: Basu, A.]]		[[Category: Basu, A.]]
	[[Category: Das, R S.]]		[[Category: Das, R S.]]