403d - Revision history

OCA at 10:35, 1 March 2024

OCA — Fri, 01 Mar 2024 10:35:59 GMT

←Older revision		Revision as of 10:35, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[403d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=403D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=403D FirstGlance]. <br>		<table><tr><td colspan='2'>[[403d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=403D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=403D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HT1:2-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>HT1</scene>, <scene name='pdbligand=MG:~~MAGNESIUM+ION~~'>MG</scene>~~</td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.4Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~IGU~~:~~2-DEOXYISOGUANINE-5-MONOPHOSPHATE~~'>~~IGU~~</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HT1:2-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>HT1</scene>, <scene name='pdbligand=IGU:2-DEOXYISOGUANINE-5-MONOPHOSPHATE'>IGU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=403d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=403d OCA], [https://pdbe.org/403d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=403d RCSB], [https://www.ebi.ac.uk/pdbsum/403d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=403d 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=403d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=403d OCA], [https://pdbe.org/403d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=403d RCSB], [https://www.ebi.ac.uk/pdbsum/403d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=403d ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The questions of whether different tautomeric forms of nucleic acid bases exist to any significant extent in DNA, or what their possible roles in mutation may be, are under intense scrutiny. 2'-Deoxyisoguanosine (iG) has been suggested to have a propensity to adopt the enol form. Isoguanine (also called 2-hydroxyadenine) can be found in oxidatively damaged DNA generated from treating DNA with a Fenton-type reactive oxygen-generating system and is known to cause mutation. We have analyzed the three-dimensional structure of the DNA dodecamer d(CGC[iG]AATTTGCG) (denoted iG-DODE) by X-ray crystallography and NMR. The crystal structure of the iG-DODE complexed with the minor groove binder Hoechst 33342, refined to 1.4 A resolution, showed that the two independent iG.T base pairs in the dodecamer duplex adopt different (one in Watson-Crick and the other in wobble) conformations. The high-resolution nature of the structure also affords unprecedented clear information about the conformation and interactions of the Hoechst drug. The Hoechst 33342 binds in the narrow minor groove at the iGAATT site, with the N-methylpiperazine ring near the iG4.T21 base pair. Three hydrogen bonds are found between the NH of the Hoechst ligand and T-O2 DNA atoms. In solution, the two iG.T base pairs in iG-DODE predominantly are in the wobble form at 2 degreesC. At higher temperatures, another duplex form (likely involving the enol form of iG) is in slow exchange with the keto form and becomes significantly populated, reaching approximately 40% at 40 degreesC. Our data support the conclusion that iG pairs with T in a Watson-Crick configuration to a significant extent at physiological temperature (37 degreesC), which may explain the facile incorporation rate of T across from an iG during in vitro DNA replication.
-
-	2'-Deoxyisoguanosine adopts more than one tautomer to form base pairs with thymidine observed by high-resolution crystal structure analysis.,Robinson H, Gao YG, Bauer C, Roberts C, Switzer C, Wang AH Biochemistry. 1998 Aug 4;37(31):10897-905. PMID:9692982<ref>PMID:9692982</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 403d" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bauer, C]]	+	[[Category: Bauer C]]
-	[[Category: Gao, Y G]]	+	[[Category: Gao Y-G]]
-	[[Category: Roberts, C]]	+	[[Category: Roberts C]]
-	[[Category: Robinson, H]]	+	[[Category: Robinson H]]
-	[[Category: Switzer, C]]	+	[[Category: Switzer C]]
-	[[Category: Wang~~, A H.~~J]]	+	[[Category: Wang AH-J]]
-	~~[[Category: B-dna double helix]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Dna-drug complex~~]]	+

OCA at 07:31, 18 August 2022

OCA — Thu, 18 Aug 2022 07:31:32 GMT

←Older revision		Revision as of 07:31, 18 August 2022
Line 1:		Line 1:

	==5'-D(CPGPCP(HYD)APAPAPTPTPTPGPCPG)-3', 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE==		==5'-D(CPGPCP(HYD)APAPAPTPTPTPGPCPG)-3', 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE==
-	<StructureSection load='403d' size='340' side='right' caption='[[403d]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='403d' size='340' side='right'caption='[[403d]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[403d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=403D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=403D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[403d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=403D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=403D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HT1:2-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>HT1</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HT1:2-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>HT1</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IGU:2-DEOXYISOGUANINE-5-MONOPHOSPHATE'>IGU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IGU:2-DEOXYISOGUANINE-5-MONOPHOSPHATE'>IGU</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=403d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=403d OCA], [~~http~~://pdbe.org/403d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=403d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/403d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=403d 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=403d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=403d OCA], [https://pdbe.org/403d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=403d RCSB], [https://www.ebi.ac.uk/pdbsum/403d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=403d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 403d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 403d" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Temperature value vs. resolution\|Temperature value vs. resolution]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Bauer, C]]		[[Category: Bauer, C]]
	[[Category: Gao, Y G]]		[[Category: Gao, Y G]]

OCA at 15:23, 4 August 2016

OCA — Thu, 04 Aug 2016 15:23:46 GMT

←Older revision		Revision as of 15:23, 4 August 2016
Line 1:		Line 1:
		+
	==5'-D(CPGPCP(HYD)APAPAPTPTPTPGPCPG)-3', 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE==		==5'-D(CPGPCP(HYD)APAPAPTPTPTPGPCPG)-3', 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE==
	<StructureSection load='403d' size='340' side='right' caption='[[403d]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='403d' size='340' side='right' caption='[[403d]], [[Resolution\|resolution]] 1.40Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HT1:2-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>HT1</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HT1:2-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>HT1</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IGU:2-DEOXYISOGUANINE-5-MONOPHOSPHATE'>IGU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IGU:2-DEOXYISOGUANINE-5-MONOPHOSPHATE'>IGU</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=403d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=403d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=403d RCSB], [http://www.ebi.ac.uk/pdbsum/403d 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=403d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=403d OCA], [http://pdbe.org/403d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=403d RCSB], [http://www.ebi.ac.uk/pdbsum/403d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=403d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 403d" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 08:42, 18 December 2014

OCA — Thu, 18 Dec 2014 08:42:36 GMT

←Older revision		Revision as of 08:42, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_403d\| PDB=403d \| SCENE= }}~~	+	==5'-D(CPGPCP(HYD)APAPAPTPTPTPGPCPG)-3', 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE==
-	===5'-D(CPGPCP(HYD)APAPAPTPTPTPGPCPG)-3', 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE===	+	<StructureSection load='403d' size='340' side='right' caption='[[403d]], [[Resolution\|resolution]] 1.40Å' scene=''>
-	~~{{ABSTRACT_PUBMED_9692982}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[403d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=403D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=403D FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HT1:2-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>HT1</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IGU:2-DEOXYISOGUANINE-5-MONOPHOSPHATE'>IGU</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=403d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=403d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=403d RCSB], [http://www.ebi.ac.uk/pdbsum/403d PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The questions of whether different tautomeric forms of nucleic acid bases exist to any significant extent in DNA, or what their possible roles in mutation may be, are under intense scrutiny. 2'-Deoxyisoguanosine (iG) has been suggested to have a propensity to adopt the enol form. Isoguanine (also called 2-hydroxyadenine) can be found in oxidatively damaged DNA generated from treating DNA with a Fenton-type reactive oxygen-generating system and is known to cause mutation. We have analyzed the three-dimensional structure of the DNA dodecamer d(CGC[iG]AATTTGCG) (denoted iG-DODE) by X-ray crystallography and NMR. The crystal structure of the iG-DODE complexed with the minor groove binder Hoechst 33342, refined to 1.4 A resolution, showed that the two independent iG.T base pairs in the dodecamer duplex adopt different (one in Watson-Crick and the other in wobble) conformations. The high-resolution nature of the structure also affords unprecedented clear information about the conformation and interactions of the Hoechst drug. The Hoechst 33342 binds in the narrow minor groove at the iGAATT site, with the N-methylpiperazine ring near the iG4.T21 base pair. Three hydrogen bonds are found between the NH of the Hoechst ligand and T-O2 DNA atoms. In solution, the two iG.T base pairs in iG-DODE predominantly are in the wobble form at 2 degreesC. At higher temperatures, another duplex form (likely involving the enol form of iG) is in slow exchange with the keto form and becomes significantly populated, reaching approximately 40% at 40 degreesC. Our data support the conclusion that iG pairs with T in a Watson-Crick configuration to a significant extent at physiological temperature (37 degreesC), which may explain the facile incorporation rate of T across from an iG during in vitro DNA replication.

-	~~==About this Structure==~~	+	2'-Deoxyisoguanosine adopts more than one tautomer to form base pairs with thymidine observed by high-resolution crystal structure analysis.,Robinson H, Gao YG, Bauer C, Roberts C, Switzer C, Wang AH Biochemistry. 1998 Aug 4;37(31):10897-905. PMID:9692982<ref>PMID:9692982</ref>
-	~~[[403d]] is a~~ 2 ~~chain~~ structure. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=403D OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Temperature value vs. resolution\|Temperature value vs. resolution]]		*[[Temperature value vs. resolution\|Temperature value vs. resolution]]
-	[[Category: Bauer, C.]]	+	== References ==
-	[[Category: Gao, Y G.]]	+	<references/>
-	[[Category: Roberts, C.]]	+	__TOC__
-	[[Category: Robinson, H.]]	+	</StructureSection>
-	[[Category: Switzer, C.]]	+	[[Category: Bauer, C]]
-	[[Category: Wang, A H.J.]]	+	[[Category: Gao, Y G]]
		+	[[Category: Roberts, C]]
		+	[[Category: Robinson, H]]
		+	[[Category: Switzer, C]]
		+	[[Category: Wang, A H.J]]
	[[Category: B-dna double helix]]		[[Category: B-dna double helix]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Dna-drug complex]]		[[Category: Dna-drug complex]]

OCA: Protected "403d" [edit=sysop:move=sysop]

OCA — Mon, 11 Mar 2013 10:37:59 GMT

Protected "403d" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:37, 11 March 2013

OCA at 10:37, 11 March 2013

OCA — Mon, 11 Mar 2013 10:37:55 GMT

←Older revision		Revision as of 10:37, 11 March 2013
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-	{{Seed}}
-	[[Image:403d.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_403d", 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_403d\| PDB=403d \| SCENE= }}		{{STRUCTURE_403d\| PDB=403d \| SCENE= }}
-
	===5'-D(CPGPCP(HYD)APAPAPTPTPTPGPCPG)-3', 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE===		===5'-D(CPGPCP(HYD)APAPAPTPTPTPGPCPG)-3', 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_9692982}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 9692982 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_9692982}}		{{ABSTRACT_PUBMED_9692982}}

	==About this Structure==		==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=403D OCA].	+	[[403d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=403D OCA].

-	==~~Reference~~==	+	==See Also==
-	2'-Deoxyisoguanosine adopts more than one tautomer to form base pairs with thymidine observed by high-resolution crystal structure analysis., Robinson H, Gao YG, Bauer C, Roberts C, Switzer C, Wang AH, Biochemistry. 1998 Aug 4;37(31):10897-905. PMID:[~~http://www~~.~~ncbi~~.~~nlm.nih.gov/pubmed/9692982 9692982~~]	+	*[[Temperature value vs. resolution\|Temperature value vs. resolution]]
	[[Category: Bauer, C.]]		[[Category: Bauer, C.]]
	[[Category: Gao, Y G.]]		[[Category: Gao, Y G.]]
Line 31:		Line 15:
	[[Category: Wang, A H.J.]]		[[Category: Wang, A H.J.]]
	[[Category: B-dna double helix]]		[[Category: B-dna double helix]]
-	[[Category: Dna~~/drug complex~~]]	+	[[Category: Dna]]
-		+	[[Category: Dna-drug complex]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Thu Jul 3 13:14:43 2008''~~	+

OCA at 10:14, 3 July 2008

OCA — Thu, 03 Jul 2008 10:14:44 GMT

←Older revision		Revision as of 10:14, 3 July 2008
Line 1:		Line 1:
-	[[Image:403d.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:403d.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_403d\| PDB=403d \| SCENE= }}		{{STRUCTURE_403d\| PDB=403d \| SCENE= }}

-	~~'''~~5'-D(CPGPCP(HYD)APAPAPTPTPTPGPCPG)-3', 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE~~'''~~	+	===5'-D(CPGPCP(HYD)APAPAPTPTPTPGPCPG)-3', 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE===


-	~~==Overview==~~	+	<!--
-	The ~~questions of whether different tautomeric forms of nucleic acid bases exist to any significant extent in DNA~~, ~~or what their possible roles in mutation may be~~, ~~are under intense scrutiny. 2'-Deoxyisoguanosine (iG) has been suggested to have a propensity to adopt~~ the ~~enol form. Isoguanine (also called 2-hydroxyadenine) can be found in oxidatively damaged DNA generated from treating DNA with a Fenton-type reactive oxygen-generating system and is known~~ to ~~cause mutation. We have analyzed~~ the ~~three-dimensional structure of the DNA dodecamer d~~(~~CGC[iG]AATTTGCG) (denoted iG-DODE) by X-ray crystallography and NMR~~. ~~The crystal structure of the iG-DODE complexed with the minor groove binder Hoechst 33342, refined to 1~~.~~4 A resolution, showed that the two independent iG.T base pairs in the dodecamer duplex adopt different (one in Watson-Crick and the other in wobble~~) conformations. The high-resolution nature of the structure also affords unprecedented clear information about the conformation and interactions of the Hoechst drug. The Hoechst 33342 binds in the narrow minor groove at the iGAATT site, ~~with~~ the ~~N-methylpiperazine ring near the iG4~~.~~T21 base pair. Three hydrogen bonds are found between the NH of the Hoechst ligand and T~~-~~O2 DNA atoms. In solution, the two iG.T base pairs in iG~~-DODE predominantly are in the wobble form at 2 degreesC. At higher temperatures, another duplex form (likely involving the enol form of iG) is in slow exchange with the keto form and becomes significantly populated, reaching approximately 40% at 40 degreesC. Our data support the conclusion that iG pairs with T in a Watson-Crick configuration to a significant extent at physiological temperature (37 degreesC), which may explain the facile incorporation rate of T across from an iG during in vitro DNA replication.	+	The line below this paragraph, {{ABSTRACT_PUBMED_9692982}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 9692982 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_9692982}}

	==About this Structure==		==About this Structure==
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	[[Category: B-dna double helix]]		[[Category: B-dna double helix]]
	[[Category: Dna/drug complex]]		[[Category: Dna/drug complex]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:16:12 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 13:14:43 2008''

OCA at 19:16, 4 May 2008

OCA — Sun, 04 May 2008 19:16:14 GMT

←Older revision		Revision as of 19:16, 4 May 2008
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	[[Image:403d.gif\|left\|200px]]		[[Image:403d.gif\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 403d \|SIZE=350\|CAPTION=~~ <~~scene name='initialview01'>403d</scene>, resolution 1.400Å~~	+	The line below this paragraph, containing "STRUCTURE_403d", 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=HT1:2'-~~(~~4-ETHOXYPHENYL~~)~~-5-~~(~~4-METHYL-1-PIPERAZINYL~~)-2,~~5'~~-BI-~~BENZIMIDAZOLE'>HT1</scene>, <scene name='pdbligand=IGU:2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE'>IGU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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_403d\| PDB=403d \| SCENE= }}
-	~~\|RELATEDENTRY=~~	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=403d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=403d OCA], [http://www.ebi.ac.uk/pdbsum/403d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=403d RCSB]</span>	+
-	}}	+

	'''5'-D(CPGPCP(HYD)APAPAPTPTPTPGPCPG)-3', 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE'''		'''5'-D(CPGPCP(HYD)APAPAPTPTPTPGPCPG)-3', 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE'''
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	==About this Structure==		==About this Structure==
-	~~403D 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=403D OCA].	+	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=403D OCA].

	==Reference==		==Reference==
	2'-Deoxyisoguanosine adopts more than one tautomer to form base pairs with thymidine observed by high-resolution crystal structure analysis., Robinson H, Gao YG, Bauer C, Roberts C, Switzer C, Wang AH, Biochemistry. 1998 Aug 4;37(31):10897-905. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9692982 9692982]		2'-Deoxyisoguanosine adopts more than one tautomer to form base pairs with thymidine observed by high-resolution crystal structure analysis., Robinson H, Gao YG, Bauer C, Roberts C, Switzer C, Wang AH, Biochemistry. 1998 Aug 4;37(31):10897-905. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9692982 9692982]
-	[[Category: Protein complex]]
	[[Category: Bauer, C.]]		[[Category: Bauer, C.]]
	[[Category: Gao, Y G.]]		[[Category: Gao, Y G.]]
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	[[Category: Switzer, C.]]		[[Category: Switzer, C.]]
	[[Category: Wang, A H.J.]]		[[Category: Wang, A H.J.]]
-	[[Category: b-dna double helix]]	+	[[Category: B-dna double helix]]
-	[[Category: ~~dna~~/drug complex]]	+	[[Category: Dna/drug complex]]
-		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:16:12 2008''
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:36:49 2008''	+

OCA at 02:36, 31 March 2008

OCA — Mon, 31 Mar 2008 02:36:50 GMT

←Older revision		Revision as of 02:36, 31 March 2008
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	\|PDB= 403d \|SIZE=350\|CAPTION= <scene name='initialview01'>403d</scene>, resolution 1.400Å		\|PDB= 403d \|SIZE=350\|CAPTION= <scene name='initialview01'>403d</scene>, resolution 1.400Å
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=HT1:2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE'>HT1</scene> ~~and~~ <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>	+	\|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=HT1:2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE'>HT1</scene>, <scene name='pdbligand=IGU:2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE'>IGU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE=		\|GENE=
		+	\|DOMAIN=
		+	\|RELATEDENTRY=
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=403d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=403d OCA], [http://www.ebi.ac.uk/pdbsum/403d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=403d RCSB]</span>
	}}		}}

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	[[Category: Switzer, C.]]		[[Category: Switzer, C.]]
	[[Category: Wang, A H.J.]]		[[Category: Wang, A H.J.]]
-	[[Category: HT1]]
-	[[Category: MG]]
	[[Category: b-dna double helix]]		[[Category: b-dna double helix]]
	[[Category: dna/drug complex]]		[[Category: dna/drug complex]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun~~ Mar ~~23 16~~:03:42 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:36:49 2008''

OCA at 14:03, 23 March 2008

OCA — Sun, 23 Mar 2008 14:03:43 GMT

←Older revision		Revision as of 14:03, 23 March 2008
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	\|PDB= 403d \|SIZE=350\|CAPTION= <scene name='initialview01'>403d</scene>, resolution 1.400Å		\|PDB= 403d \|SIZE=350\|CAPTION= <scene name='initialview01'>403d</scene>, resolution 1.400Å
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=HT1:2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE'>HT1</scene> and <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>	+	\|LIGAND= <scene name='pdbligand=HT1:2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE'>HT1</scene> and <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE=		\|GENE=
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	[[Category: dna/drug complex]]		[[Category: dna/drug complex]]

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