5ls8

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Current revision (18:44, 18 October 2023) (edit) (undo)
 
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<StructureSection load='5ls8' size='340' side='right'caption='[[5ls8]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
<StructureSection load='5ls8' size='340' side='right'caption='[[5ls8]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5ls8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LS8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LS8 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5ls8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LS8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LS8 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=QHL:delta-[Ru(tap2-dppz-CN]2+'>QHL</scene></td></tr>
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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]] 1.78&#8491;</td></tr>
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<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=5ls8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ls8 OCA], [http://pdbe.org/5ls8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ls8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ls8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ls8 ProSAT]</span></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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=QHL:delta-[Ru(tap2-dppz-CN]2+'>QHL</scene></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=5ls8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ls8 OCA], [https://pdbe.org/5ls8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ls8 RCSB], [https://www.ebi.ac.uk/pdbsum/5ls8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ls8 ProSAT]</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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The new complexes [Ru(TAP)2 (11-CN-dppz)](2+) , [Ru(TAP)2 (11-Br-dppz)](2+) and [Ru(TAP)2 (11,12-diCN-dppz)](2+) are reported. The addition of nitrile substituents to the dppz ligand of the DNA photo-oxidising complex [Ru(TAP)2 (dppz)](2+) promote pi-stacking interactions and ordered binding to DNA, as shown by X-ray crystallography. The structure of Lambda-[Ru(TAP)2 (11-CN-dppz)](2+) with the DNA duplex d(TCGGCGCCGA)2 shows, for the first time with this class of complex, a closed intercalation cavity with an AT base pair at the terminus. The structure obtained is compared to that formed with the 11-Br and 11,12-dinitrile derivatives, highlighting the stabilization of syn guanine by this enantiomer when the terminal base pair is GC. In contrast the AT base pair has the normal Watson-Crick orientation, highlighting the difference in charge distribution between the two purine bases and the complementarity of the dppz-purine interaction. The asymmetry of the cavity highlights the importance of the purine-dppz-purine stacking interaction.
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By using X-ray crystallography, we show that the complexes Lambda/Delta-[Ru(TAP)(2) (11-CN-dppz)](2+) (TAP=1,4,5,8-tetraazaphenanthrene, dppz=dipyridophenazine) bind DNA G-quadruplex in an enantiospecific manner that parallels the specificity of these complexes with duplex DNA. The Lambda complex crystallises with the normally parallel stranded d(TAGGGTTA) tetraplex to give the first such antiparallel strand assembly in which syn-guanosine is adjacent to the complex at the 5' end of the quadruplex core. SRCD measurements confirm that the same conformational switch occurs in solution. The Delta enantiomer, by contrast, is present in the structure but stacked at the ends of the assembly. In addition, we report the structure of Lambda-[Ru(phen)(2) (11-CN-dppz)](2+) bound to d(TCGGCGCCGA), a duplex-forming sequence, and use both structural models to provide insight into the motif-specific luminescence response of the isostructural phen analogue enantiomers.
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X-ray Crystal Structures Show DNA Stacking Advantage of Terminal Nitrile Substitution in Ru-dppz Complexes.,McQuaid K, Hall JP, Brazier JA, Cardin DJ, Cardin CJ Chemistry. 2018 Oct 22;24(59):15859-15867. doi: 10.1002/chem.201803021. Epub 2018, Oct 1. PMID:30063271<ref>PMID:30063271</ref>
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Structural Studies Reveal Enantiospecific Recognition of a DNA G-Quadruplex by a Ruthenium Polypyridyl Complex.,McQuaid K, Abell H, Gurung SP, Allan DR, Winter G, Sorensen T, Cardin DJ, Brazier JA, Cardin CJ, Hall JP Angew Chem Int Ed Engl. 2019 Jul 15;58(29):9881-9885. doi: , 10.1002/anie.201814502. Epub 2019 Jun 12. PMID:30958918<ref>PMID:30958918</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Abell, H]]
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[[Category: Synthetic construct]]
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[[Category: Cardin, C J]]
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[[Category: Abell H]]
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[[Category: Hall, J P]]
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[[Category: Cardin CJ]]
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[[Category: McQuaid, K T]]
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[[Category: Hall JP]]
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[[Category: Chiral recognition]]
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[[Category: McQuaid KT]]
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[[Category: Dna]]
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[[Category: Quadruplex]]
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[[Category: Ruthenium]]
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Current revision

Light-activated ruthenium complex bound to a DNA quadruplex

PDB ID 5ls8

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