443d - Revision history

OCA at 00:35, 28 December 2023

2023-12-28T00:35:31Z

← Older revision		Revision as of 00:35, 28 December 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[443d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=443D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=443D FirstGlance]. <br>		<table><tr><td colspan='2'>[[443d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=443D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=443D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IA:2-(3-IODOPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>IA</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]] 1.6Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IA:2-(3-IODOPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>IA</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=443d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=443d OCA], [https://pdbe.org/443d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=443d RCSB], [https://www.ebi.ac.uk/pdbsum/443d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=443d 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=443d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=443d OCA], [https://pdbe.org/443d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=443d RCSB], [https://www.ebi.ac.uk/pdbsum/443d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=443d ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Baker~~, L J~~]]		[[Category: Baker LJ]]
	[[Category: Clark~~, G R~~]]		[[Category: Clark GR]]
	[[Category: Martin~~, R F~~]]		[[Category: Martin RF]]
	[[Category: Squire~~, C J~~]]		[[Category: Squire CJ]]
	[[Category: White, J]]		[[Category: White J]]
	~~[[Category: B-dna]]~~
	~~[[Category: Dna]]~~
	~~[[Category: Minor groove binding~~]]

OCA at 07:33, 18 August 2022

2022-08-18T07:33:32Z

← Older revision		Revision as of 07:33, 18 August 2022
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	<StructureSection load='443d' size='340' side='right'caption='[[443d]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='443d' size='340' side='right'caption='[[443d]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[443d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=443D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=443D FirstGlance]. <br>		<table><tr><td colspan='2'>[[443d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=443D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=443D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IA:2-(3-IODOPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>IA</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=IA:2-(3-IODOPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>IA</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=443d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=443d OCA], [~~http~~://pdbe.org/443d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=443d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/443d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=443d 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=443d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=443d OCA], [https://pdbe.org/443d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=443d RCSB], [https://www.ebi.ac.uk/pdbsum/443d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=443d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:16, 1 January 2020

2020-01-01T13:16:37Z

← Older revision		Revision as of 13:16, 1 January 2020
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	==5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3'/ BENZIMIDAZOLE DERIVATIVE COMPLEX==		==5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3'/ BENZIMIDAZOLE DERIVATIVE COMPLEX==
	<StructureSection load='443d' size='340' side='right' caption='[[443d]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='443d' size='340' side='right'caption='[[443d]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[443d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=443D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=443D FirstGlance]. <br>		<table><tr><td colspan='2'>[[443d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=443D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=443D FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Baker, L J]]		[[Category: Baker, L J]]
	[[Category: Clark, G R]]		[[Category: Clark, G R]]

OCA at 14:46, 11 August 2016

2016-08-11T14:46:42Z

← Older revision		Revision as of 14:46, 11 August 2016
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	==5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3'/ BENZIMIDAZOLE DERIVATIVE COMPLEX==		==5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3'/ BENZIMIDAZOLE DERIVATIVE COMPLEX==
	<StructureSection load='443d' size='340' side='right' caption='[[443d]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='443d' size='340' side='right' caption='[[443d]], [[Resolution\|resolution]] 1.60Å' scene=''>
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	<table><tr><td colspan='2'>[[443d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=443D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=443D FirstGlance]. <br>		<table><tr><td colspan='2'>[[443d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=443D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=443D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IA:2-(3-IODOPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>IA</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=IA:2-(3-IODOPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>IA</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=443d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=443d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=443d RCSB], [http://www.ebi.ac.uk/pdbsum/443d 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=443d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=443d OCA], [http://pdbe.org/443d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=443d RCSB], [http://www.ebi.ac.uk/pdbsum/443d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=443d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 15:
	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 443d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:56, 4 January 2015

2015-01-04T09:56:17Z

← Older revision		Revision as of 09:56, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[443d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=443D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=443D FirstGlance]. <br>		<table><tr><td colspan='2'>[[443d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=443D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=443D FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IA:2-(3-IODOPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>IA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IA:2-(3-IODOPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>IA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=443d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=443d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=443d RCSB], [http://www.ebi.ac.uk/pdbsum/443d 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=443d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=443d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=443d RCSB], [http://www.ebi.ac.uk/pdbsum/443d 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: Baker, L J.]]		[[Category: Baker, L J]]
	[[Category: Clark, G R.]]		[[Category: Clark, G R]]
	[[Category: Martin, R F.]]		[[Category: Martin, R F]]
	[[Category: Squire, C J.]]		[[Category: Squire, C J]]
	[[Category: White, J.]]		[[Category: White, J]]
	[[Category: B-dna]]		[[Category: B-dna]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Minor groove binding]]		[[Category: Minor groove binding]]

OCA at 09:16, 11 June 2014

2014-06-11T09:16:42Z

← Older revision		Revision as of 09:16, 11 June 2014
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	[[~~Image~~:443d.~~png\|left\|200px~~]]		==5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3'/ BENZIMIDAZOLE DERIVATIVE COMPLEX==
			<StructureSection load='443d' size='340' side='right' caption='[[443d]], [[Resolution\|resolution]] 1.60Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[443d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=443D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=443D FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IA:2-(3-IODOPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>IA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=443d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=443d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=443d RCSB], [http://www.ebi.ac.uk/pdbsum/443d PDBsum]</span></td></tr>
			<table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The DNA photosensitisers m-iodo Hoechst and m-iodo, p-methoxy Hoechst have been co-crystallised with the oligonucleotide d(CGCGAATTCGCG)(2)and their crystal structures determined. The crystals were then subjected to slow dehydration, which reduced their solvent contents from 40 (normal) to 30 (partially dehydrated) and then 20% (fully dehydrated) and caused a reduction in cell volume from 68,000 to 60,000 then 51,000 A(3). The dehydration resulted in a dramatic enhancement of diffraction resolution from approximately 2.6 to beyond 1.5 A. Crystal structures have also been determined for the partially and fully dehydrated states. The fully dehydrated crystals consist of an infinite polymeric network, in which neighbouring dodecamer duplexes are crosslinked through phosphate oxygens via direct bonding to bridging magnesium cations. This unique three-dimensional structure for DNA is described in detail in the following companion paper. The present paper details evidence from the sequence of crystal structures that the DNA is able to breathe locally, allowing the ligand to leave the minor groove, re-orient in the surrounding solvent medium and then re-enter the groove in a different orientation and location. The rearrangement of the minor groove binding ligands during the dehydration process mimics the binding behaviour of these ligands in solution and in vivo. We also present details of the DNA-ligand interactions that are consistent with a hydrogen atom ion mechanism for photocleavage of DNA.

	~~{{STRUCTURE_443d\| PDB=443d \| SCENE= }}~~		Structures of m-iodo Hoechst-DNA complexes in crystals with reduced solvent content: implications for minor groove binder drug design.,Squire CJ, Baker LJ, Clark GR, Martin RF, White J Nucleic Acids Res. 2000 Mar 1;28(5):1252-8. PMID:10666470<ref>PMID:10666470</ref>

	~~===5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3'~~/ ~~BENZIMIDAZOLE DERIVATIVE COMPLEX===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_10666470}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[443d]] is~~ a ~~2 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=443D OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:010666470<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Baker, L J.]]		[[Category: Baker, L J.]]
	[[Category: Clark, G R.]]		[[Category: Clark, G R.]]

OCA: Protected "443d" [edit=sysop:move=sysop]

2012-08-14T16:19:01Z

Protected "443d" [edit=sysop:move=sysop]

← Older revision	Revision as of 16:19, 14 August 2012
(No difference)

OCA at 16:19, 14 August 2012

2012-08-14T16:19:00Z

← Older revision		Revision as of 16:19, 14 August 2012
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	~~{{Seed}}~~
	[[Image:443d.png\|left\|200px]]		[[Image:443d.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_443d", 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_443d\| PDB=443d \| SCENE= }}		{{STRUCTURE_443d\| PDB=443d \| SCENE= }}

	===5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3'/ BENZIMIDAZOLE DERIVATIVE COMPLEX===		===5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3'/ BENZIMIDAZOLE DERIVATIVE COMPLEX===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_10666470}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 10666470 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_10666470}}		{{ABSTRACT_PUBMED_10666470}}

	==About this Structure==		==About this Structure==
	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=443D OCA].		[[443d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=443D OCA].

	==Reference==		==Reference==
	Structures of m-iodo Hoechst-DNA complexes in crystals with reduced solvent content: implications for minor groove binder drug design., Squire CJ, Baker LJ, Clark GR, Martin RF, White J, Nucleic Acids Res. 2000 Mar 1;28(5):1252-8. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~10666470 10666470]~~		<ref group="xtra">PMID:010666470</ref><references group="xtra"/>
	[[Category: Baker, L J.]]		[[Category: Baker, L J.]]
	[[Category: Clark, G R.]]		[[Category: Clark, G R.]]
Line 30:		Line 18:
	[[Category: White, J.]]		[[Category: White, J.]]
	[[Category: B-dna]]		[[Category: B-dna]]
			[[Category: Dna]]
	[[Category: Minor groove binding]]		[[Category: Minor groove binding]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 13:20:41 2008''~~

OCA at 10:20, 3 July 2008

2008-07-03T10:20:41Z

← Older revision		Revision as of 10:20, 3 July 2008
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	[[Image:443d.~~gif~~\|left\|200px]]		{{Seed}}
			[[Image:443d.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_443d\| PDB=443d \| SCENE= }}		{{STRUCTURE_443d\| PDB=443d \| SCENE= }}

	~~'''~~5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3'/ BENZIMIDAZOLE DERIVATIVE COMPLEX~~'''~~		===5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3'/ BENZIMIDAZOLE DERIVATIVE COMPLEX===


	~~==Overview==~~		<!--
	~~The DNA photosensitisers m~~-~~iodo Hoechst and m~~-~~iodo, p-methoxy Hoechst have been co-crystallised with the oligonucleotide d(CGCGAATTCGCG)(2)and their crystal structures determined.~~ The ~~crystals were then subjected to slow dehydration~~, ~~which reduced their solvent contents from 40 (normal) to 30 (partially dehydrated) and then 20% (fully dehydrated) and caused a reduction in cell volume from 68~~,~~000~~ to ~~60,000 then 51,000 A~~(3). ~~The dehydration resulted in a dramatic enhancement of diffraction resolution from approximately 2~~.~~6 to beyond 1.5 A. Crystal structures have also been determined for the partially and fully dehydrated states. The fully dehydrated crystals consist of an infinite polymeric network~~, ~~in which neighbouring dodecamer duplexes are crosslinked through phosphate oxygens via direct bonding to bridging magnesium cations. This unique three-dimensional structure for DNA~~ is ~~described in detail in~~ the ~~following companion paper~~. ~~The present paper details evidence from the sequence of crystal structures that the DNA is able to breathe locally, allowing the ligand to leave the minor groove, re~~-~~orient in the surrounding solvent medium and then re~~-enter the groove in a different orientation and location. The rearrangement of the minor groove binding ligands during the dehydration process mimics the binding behaviour of these ligands in solution and in vivo. We also present details of the DNA-ligand interactions that are consistent with a hydrogen atom ion mechanism for photocleavage of DNA.		The line below this paragraph, {{ABSTRACT_PUBMED_10666470}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 10666470 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_10666470}}

	==About this Structure==		==About this Structure==
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	[[Category: B-dna]]		[[Category: B-dna]]
	[[Category: Minor groove binding]]		[[Category: Minor groove binding]]
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:18:13 2008''
			''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 13:20:41 2008''

OCA at 19:18, 4 May 2008

2008-05-04T19:18:14Z

← Older revision		Revision as of 19:18, 4 May 2008
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	[[Image:443d.gif\|left\|200px]]		[[Image:443d.gif\|left\|200px]]

	~~{{Structure~~		<!--
	~~\|PDB= 443d \|SIZE=350\|CAPTION= <scene name='initialview01'>443d~~<~~/scene>, resolution 1.6Å~~		The line below this paragraph, containing "STRUCTURE_443d", 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=IA:2'-~~(~~3-IODOPHENYL~~)~~-5-~~(~~4-METHYL-1-PIPERAZINYL~~)-2,~~5'~~-BI-~~BENZIMIDAZOLE'>IA</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_443d\| PDB=443d \| SCENE= }}
	~~\|RELATEDENTRY=~~
	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=443d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=443d OCA], [http://www.ebi.ac.uk/pdbsum/443d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=443d RCSB]</span>
	}}

	'''5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3'/ BENZIMIDAZOLE DERIVATIVE COMPLEX'''		'''5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3'/ BENZIMIDAZOLE DERIVATIVE COMPLEX'''
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	==About this Structure==		==About this Structure==
	~~443D 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=443D OCA].		Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=443D OCA].

	==Reference==		==Reference==
	Structures of m-iodo Hoechst-DNA complexes in crystals with reduced solvent content: implications for minor groove binder drug design., Squire CJ, Baker LJ, Clark GR, Martin RF, White J, Nucleic Acids Res. 2000 Mar 1;28(5):1252-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10666470 10666470]		Structures of m-iodo Hoechst-DNA complexes in crystals with reduced solvent content: implications for minor groove binder drug design., Squire CJ, Baker LJ, Clark GR, Martin RF, White J, Nucleic Acids Res. 2000 Mar 1;28(5):1252-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10666470 10666470]
	~~[[Category: Protein complex]]~~
	[[Category: Baker, L J.]]		[[Category: Baker, L J.]]
	[[Category: Clark, G R.]]		[[Category: Clark, G R.]]
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	[[Category: Squire, C J.]]		[[Category: Squire, C J.]]
	[[Category: White, J.]]		[[Category: White, J.]]
	[[Category: b-dna]]		[[Category: B-dna]]
	[[Category: ~~minor~~ groove binding]]		[[Category: Minor groove binding]]
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