1z5t

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==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.==
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<StructureSection load='1z5t' size='340' side='right' caption='[[1z5t]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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<StructureSection load='1z5t' size='340' side='right'caption='[[1z5t]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<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>
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<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>
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</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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
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<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>
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<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>
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<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>
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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=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>
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<table>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Gold, B.]]
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[[Category: Large Structures]]
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[[Category: Komeda, S.]]
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[[Category: Gold B]]
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[[Category: Li, J S.]]
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[[Category: Komeda S]]
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[[Category: Lountos, G T.]]
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[[Category: Li JS]]
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[[Category: Maehigashi, T.]]
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[[Category: Lountos GT]]
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[[Category: Marky, L A.]]
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[[Category: Maehigashi T]]
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[[Category: Moulaei, T.]]
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[[Category: Marky LA]]
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[[Category: Stone, M P.]]
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[[Category: Moulaei T]]
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[[Category: Watkins, D.]]
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[[Category: Stone MP]]
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[[Category: Williams, L D.]]
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[[Category: Watkins D]]
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[[Category: B-dna]]
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[[Category: Williams LD]]
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[[Category: Cation]]
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[[Category: Dna]]
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[[Category: Modified dna]]
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[[Category: Modified thymine]]
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[[Category: Thallium]]
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[[Category: Tl+]]
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Current revision

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

PDB ID 1z5t

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