1z5t - Revision history

OCA at 09:02, 14 February 2024

OCA — Wed, 14 Feb 2024 09:02:34 GMT

←Older revision		Revision as of 09:02, 14 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1z5t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z5T FirstGlance]. <br>		<table><tr><td colspan='2'>[[1z5t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z5T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene>, <scene name='pdbligand=ZDU:5-(3-AMINOPROPYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>ZDU</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=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene>, <scene name='pdbligand=ZDU:5-(3-AMINOPROPYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>ZDU</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=1z5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5t OCA], [https://pdbe.org/1z5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z5t RCSB], [https://www.ebi.ac.uk/pdbsum/1z5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z5t 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=1z5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5t OCA], [https://pdbe.org/1z5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z5t RCSB], [https://www.ebi.ac.uk/pdbsum/1z5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z5t ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Here, we describe the 1.6-A X-ray structure of the DDD (Dickerson-Drew dodecamer), which has been covalently modified by the tethering of four cationic charges. This modified version of the DDD, called here the DDD(4+), is composed of [d(CGCGAAXXCGCG)](2), where X is effectively a thymine residue linked at the 5 position to an n-propyl-amine. The structure was determined from crystals soaked with thallium(I), which has been broadly used as a mimic of K(+) in X-ray diffraction experiments aimed at determining positions of cations adjacent to nucleic acids. Three of the tethered cations are directed radially out from the DNA. The radially directed tethered cations do not appear to induce structural changes or to displace counterions. One of the tethered cations is directed in the 3' direction, toward a phosphate group near one end of the duplex. This tethered cation appears to interact electrostatically with the DNA. This interaction is accompanied by changes in helical parameters rise, roll, and twist and by a displacement of the backbone relative to a control oligonucleotide. In addition, these interactions appear to be associated with displacement of counterions from the major groove of the DNA.
-
-	Structure of B-DNA with cations tethered in the major groove.,Moulaei T, Maehigashi T, Lountos GT, Komeda S, Watkins D, Stone MP, Marky LA, Li JS, Gold B, Williams LD Biochemistry. 2005 May 24;44(20):7458-68. PMID:15895989<ref>PMID:15895989</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1z5t" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:25, 1 February 2023

OCA — Wed, 01 Feb 2023 12:25:56 GMT

←Older revision		Revision as of 12:25, 1 February 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1z5t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z5T FirstGlance]. <br>		<table><tr><td colspan='2'>[[1z5t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z5T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene>, <scene name='pdbligand=ZDU:5-(3-AMINOPROPYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>ZDU</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=ZDU:5-(3-AMINOPROPYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>ZDU</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=1z5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5t OCA], [https://pdbe.org/1z5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z5t RCSB], [https://www.ebi.ac.uk/pdbsum/1z5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z5t 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=1z5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5t OCA], [https://pdbe.org/1z5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z5t RCSB], [https://www.ebi.ac.uk/pdbsum/1z5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z5t ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gold, B]]	+	[[Category: Gold B]]
-	[[Category: Komeda, S]]	+	[[Category: Komeda S]]
-	[[Category: Li~~, J S~~]]	+	[[Category: Li JS]]
-	[[Category: Lountos~~, G T~~]]	+	[[Category: Lountos GT]]
-	[[Category: Maehigashi, T]]	+	[[Category: Maehigashi T]]
-	[[Category: Marky~~, L A~~]]	+	[[Category: Marky LA]]
-	[[Category: Moulaei, T]]	+	[[Category: Moulaei T]]
-	[[Category: Stone~~, M P~~]]	+	[[Category: Stone MP]]
-	[[Category: Watkins, D]]	+	[[Category: Watkins D]]
-	[[Category: Williams~~, L D]]~~	+	[[Category: Williams LD]]
-	~~[[Category: B-dna]]~~	+
-	~~[[Category: Cation]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Modified dna]]~~	+
-	~~[[Category: Modified thymine]]~~	+
-	~~[[Category: Thallium]]~~	+
-	~~[[Category: Tl+~~]]	+

OCA at 06:07, 28 April 2021

OCA — Wed, 28 Apr 2021 06:07:59 GMT

←Older revision		Revision as of 06:07, 28 April 2021
Line 3:		Line 3:
	<StructureSection load='1z5t' size='340' side='right'caption='[[1z5t]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1z5t' size='340' side='right'caption='[[1z5t]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1z5t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z5T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Z5T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1z5t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z5T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZDU:5-(3-AMINOPROPYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>ZDU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZDU:5-(3-AMINOPROPYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>ZDU</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=1z5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5t OCA], [~~http~~://pdbe.org/1z5t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1z5t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1z5t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1z5t 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=1z5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5t OCA], [https://pdbe.org/1z5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z5t RCSB], [https://www.ebi.ac.uk/pdbsum/1z5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z5t ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:57, 24 July 2019

OCA — Wed, 24 Jul 2019 08:57:32 GMT

←Older revision		Revision as of 08:57, 24 July 2019
Line 1:		Line 1:

	==Crystal Structure of [d(CGCGAA(Z3dU)(Z3dU)CGCG)]2, Z3dU:5-(3-aminopropyl)-2'-deoxyuridine, in presence of thallium I.==		==Crystal Structure of [d(CGCGAA(Z3dU)(Z3dU)CGCG)]2, Z3dU:5-(3-aminopropyl)-2'-deoxyuridine, in presence of thallium I.==
-	<StructureSection load='1z5t' size='340' side='right' caption='[[1z5t]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='1z5t' size='340' side='right'caption='[[1z5t]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1z5t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z5T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z5T FirstGlance]. <br>		<table><tr><td colspan='2'>[[1z5t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z5T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z5T FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Gold, B]]		[[Category: Gold, B]]
	[[Category: Komeda, S]]		[[Category: Komeda, S]]

OCA at 10:21, 12 October 2017

OCA — Thu, 12 Oct 2017 10:21:09 GMT

←Older revision		Revision as of 10:21, 12 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of [d(CGCGAA(Z3dU)(Z3dU)CGCG)]2, Z3dU:5-(3-aminopropyl)-2'-deoxyuridine, in presence of thallium I.==		==Crystal Structure of [d(CGCGAA(Z3dU)(Z3dU)CGCG)]2, Z3dU:5-(3-aminopropyl)-2'-deoxyuridine, in presence of thallium I.==
	<StructureSection load='1z5t' size='340' side='right' caption='[[1z5t]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1z5t' size='340' side='right' caption='[[1z5t]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZDU:5-(3-AMINOPROPYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>ZDU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZDU:5-(3-AMINOPROPYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>ZDU</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=1z5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5t OCA], [http://pdbe.org/1z5t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z5t RCSB], [http://www.ebi.ac.uk/pdbsum/1z5t 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=1z5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5t OCA], [http://pdbe.org/1z5t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z5t RCSB], [http://www.ebi.ac.uk/pdbsum/1z5t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1z5t ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:32, 10 September 2015

OCA — Thu, 10 Sep 2015 07:32:54 GMT

←Older revision		Revision as of 07:32, 10 September 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZDU:5-(3-AMINOPROPYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>ZDU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZDU:5-(3-AMINOPROPYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>ZDU</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=1z5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1z5t RCSB], [http://www.ebi.ac.uk/pdbsum/1z5t 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=1z5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5t OCA], [http://pdbe.org/1z5t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z5t RCSB], [http://www.ebi.ac.uk/pdbsum/1z5t PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		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 1z5t" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:35, 3 January 2015

OCA — Sat, 03 Jan 2015 22:35:21 GMT

←Older revision		Revision as of 22:35, 3 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1z5t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z5T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z5T FirstGlance]. <br>		<table><tr><td colspan='2'>[[1z5t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z5T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z5T FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZDU:5-(3-AMINOPROPYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>ZDU</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZDU:5-(3-AMINOPROPYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>ZDU</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=1z5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1z5t RCSB], [http://www.ebi.ac.uk/pdbsum/1z5t 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=1z5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1z5t RCSB], [http://www.ebi.ac.uk/pdbsum/1z5t PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Gold, B.]]	+	[[Category: Gold, B]]
-	[[Category: Komeda, S.]]	+	[[Category: Komeda, S]]
-	[[Category: Li, J S.]]	+	[[Category: Li, J S]]
-	[[Category: Lountos, G T.]]	+	[[Category: Lountos, G T]]
-	[[Category: Maehigashi, T.]]	+	[[Category: Maehigashi, T]]
-	[[Category: Marky, L A.]]	+	[[Category: Marky, L A]]
-	[[Category: Moulaei, T.]]	+	[[Category: Moulaei, T]]
-	[[Category: Stone, M P.]]	+	[[Category: Stone, M P]]
-	[[Category: Watkins, D.]]	+	[[Category: Watkins, D]]
-	[[Category: Williams, L D.]]	+	[[Category: Williams, L D]]
	[[Category: B-dna]]		[[Category: B-dna]]
	[[Category: Cation]]		[[Category: Cation]]

OCA at 06:47, 9 June 2014

OCA — Mon, 09 Jun 2014 06:47:58 GMT

←Older revision		Revision as of 06:47, 9 June 2014
Line 1:		Line 1:
-	[~~[Image~~:1z5t.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal Structure of [d(CGCGAA(Z3dU)(Z3dU)CGCG)]2, Z3dU:5-(3-aminopropyl)-2'-deoxyuridine, in presence of thallium I.==
		+	<StructureSection load='1z5t' size='340' side='right' caption='[[1z5t]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1z5t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z5T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z5T FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZDU:5-(3-AMINOPROPYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>ZDU</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=1z5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1z5t RCSB], [http://www.ebi.ac.uk/pdbsum/1z5t PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Here, we describe the 1.6-A X-ray structure of the DDD (Dickerson-Drew dodecamer), which has been covalently modified by the tethering of four cationic charges. This modified version of the DDD, called here the DDD(4+), is composed of [d(CGCGAAXXCGCG)](2), where X is effectively a thymine residue linked at the 5 position to an n-propyl-amine. The structure was determined from crystals soaked with thallium(I), which has been broadly used as a mimic of K(+) in X-ray diffraction experiments aimed at determining positions of cations adjacent to nucleic acids. Three of the tethered cations are directed radially out from the DNA. The radially directed tethered cations do not appear to induce structural changes or to displace counterions. One of the tethered cations is directed in the 3' direction, toward a phosphate group near one end of the duplex. This tethered cation appears to interact electrostatically with the DNA. This interaction is accompanied by changes in helical parameters rise, roll, and twist and by a displacement of the backbone relative to a control oligonucleotide. In addition, these interactions appear to be associated with displacement of counterions from the major groove of the DNA.

-	~~{{STRUCTURE_1z5t\| PDB=1z5t \| SCENE= }}~~	+	Structure of B-DNA with cations tethered in the major groove.,Moulaei T, Maehigashi T, Lountos GT, Komeda S, Watkins D, Stone MP, Marky LA, Li JS, Gold B, Williams LD Biochemistry. 2005 May 24;44(20):7458-68. PMID:15895989<ref>PMID:15895989</ref>

-	~~===Crystal Structure of [d(CGCGAA(Z3dU)(Z3dU)CGCG)]2~~, ~~Z3dU:5-(3-aminopropyl)-2'-deoxyuridine, in presence~~ of ~~thallium I~~.~~===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15895989}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1z5t]] is a 2 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann.ac.il~~/~~oca-bin/ocashort?id=1Z5T OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015895989<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Gold, B.]]		[[Category: Gold, B.]]
	[[Category: Komeda, S.]]		[[Category: Komeda, S.]]

OCA: Protected "1z5t" [edit=sysop:move=sysop]

OCA — Tue, 14 Aug 2012 17:22:40 GMT

Protected "1z5t" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:22, 14 August 2012

OCA at 17:22, 14 August 2012

OCA — Tue, 14 Aug 2012 17:22:39 GMT

←Older revision		Revision as of 17:22, 14 August 2012
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-	{{Seed}}
	[[Image:1z5t.png\|left\|200px]]		[[Image:1z5t.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_1z5t\| PDB=1z5t \| SCENE= }}		{{STRUCTURE_1z5t\| PDB=1z5t \| SCENE= }}

	===Crystal Structure of [d(CGCGAA(Z3dU)(Z3dU)CGCG)]2, Z3dU:5-(3-aminopropyl)-2'-deoxyuridine, in presence of thallium I.===		===Crystal Structure of [d(CGCGAA(Z3dU)(Z3dU)CGCG)]2, Z3dU:5-(3-aminopropyl)-2'-deoxyuridine, in presence of thallium I.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15895989}}, adds the Publication Abstract to the page
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	{{ABSTRACT_PUBMED_15895989}}		{{ABSTRACT_PUBMED_15895989}}

	==About this Structure==		==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z5T OCA].	+	[[1z5t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z5T OCA].

	==Reference==		==Reference==
-	Structure of B-DNA with cations tethered in the major groove., Moulaei T, Maehigashi T, Lountos GT, Komeda S, Watkins D, Stone MP, Marky LA, Li JS, Gold B, Williams LD, Biochemistry. 2005 May 24;44(20):7458-68. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~15895989 15895989]~~	+	<ref group="xtra">PMID:015895989</ref><references group="xtra"/>
	[[Category: Gold, B.]]		[[Category: Gold, B.]]
	[[Category: Komeda, S.]]		[[Category: Komeda, S.]]
Line 36:		Line 24:
	[[Category: B-dna]]		[[Category: B-dna]]
	[[Category: Cation]]		[[Category: Cation]]
		+	[[Category: Dna]]
	[[Category: Modified dna]]		[[Category: Modified dna]]
	[[Category: Modified thymine]]		[[Category: Modified thymine]]
	[[Category: Thallium]]		[[Category: Thallium]]
	[[Category: Tl+]]		[[Category: Tl+]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 22:47:46 2008''