109d

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==VARIABILITY IN DNA MINOR GROOVE WIDTH RECOGNISED BY LIGAND BINDING: THE CRYSTAL STRUCTURE OF A BIS-BENZIMIDAZOLE COMPOUND BOUND TO THE DNA DUPLEX D(CGCGAATTCGCG)2==
==VARIABILITY IN DNA MINOR GROOVE WIDTH RECOGNISED BY LIGAND BINDING: THE CRYSTAL STRUCTURE OF A BIS-BENZIMIDAZOLE COMPOUND BOUND TO THE DNA DUPLEX D(CGCGAATTCGCG)2==
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<StructureSection load='109d' size='340' side='right' caption='[[109d]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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<StructureSection load='109d' size='340' side='right'caption='[[109d]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[109d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=109D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=109D FirstGlance]. <br>
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<table><tr><td colspan='2'>[[109d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=109D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=109D FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IBB:5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE'>IBB</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2&#8491;</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=109d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=109d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=109d RCSB], [http://www.ebi.ac.uk/pdbsum/109d PDBsum]</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=IBB:5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE'>IBB</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<table>
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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=109d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=109d OCA], [https://pdbe.org/109d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=109d RCSB], [https://www.ebi.ac.uk/pdbsum/109d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=109d ProSAT]</span></td></tr>
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<div style="background-color:#fffaf0;">
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</table>
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== Publication Abstract from PubMed ==
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An analogue of the DNA-binding compound Hoechst 33258, in which the piperazine ring has been replaced by an imidazoline group, has been cocrystallized with the dodecanucleotide sequence d(CGCGAATTCGCG)2. The structure has been solved by X-ray diffraction analysis and has been refined to an R-factor of 19.7% at a resolution of 2.0 A. The ligand is found to bind in the minor groove, at the central four AATT base pairs of the B-DNA double helix, with the involvement of a number of van der Waals contacts and hydrogen bonds. There are significant differences in minor groove width for the two compounds, along much of the AATT region. In particular this structure shows a narrower groove at the 3' end of the binding site consistent with the narrower cross-section of the imidazole group compared with the piperazine ring of Hoechst 33258 and therefore a smaller perturbation in groove width. The higher binding affinity to DNA shown by this analogue compared with Hoechst 33258 itself, has been rationalised in terms of these differences.
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Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2.,Wood AA, Nunn CM, Czarny A, Boykin DW, Neidle S Nucleic Acids Res. 1995 Sep 25;23(18):3678-84. PMID:7478996<ref>PMID:7478996</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: Boykin, D W.]]
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[[Category: Large Structures]]
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[[Category: Czarny, A.]]
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[[Category: Boykin DW]]
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[[Category: Neidle, S.]]
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[[Category: Czarny A]]
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[[Category: Nunn, C M.]]
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[[Category: Neidle S]]
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[[Category: Wilson, W D.]]
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[[Category: Nunn CM]]
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[[Category: Wood, A A.]]
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[[Category: Wilson WD]]
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[[Category: Zhao, M.]]
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[[Category: Wood AA]]
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[[Category: B-dna]]
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[[Category: Zhao M]]
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[[Category: Complexed with drug]]
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[[Category: Dna]]
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[[Category: Double helix]]
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Current revision

VARIABILITY IN DNA MINOR GROOVE WIDTH RECOGNISED BY LIGAND BINDING: THE CRYSTAL STRUCTURE OF A BIS-BENZIMIDAZOLE COMPOUND BOUND TO THE DNA DUPLEX D(CGCGAATTCGCG)2

PDB ID 109d

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