109d

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[[Image:109d.jpg|left|200px]]<br /><applet load="109d" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="109d, resolution 2.000&Aring;" />
 
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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'''<br />
 
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==Overview==
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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==
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An analogue of the DNA-binding compound Hoechst 33258, in which the, piperazine ring has been replaced by an imidazoline group, has been, cocrystallized with the dodecanucleotide sequence d(CGCGAATTCGCG)2.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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<StructureSection load='109d' size='340' side='right'caption='[[109d]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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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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109D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=IBB:'>IBB</scene> and <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=109D OCA].
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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 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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==Reference==
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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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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7478996 7478996]
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</table>
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[[Category: Protein complex]]
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__TOC__
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[[Category: Boykin, D.W.]]
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</StructureSection>
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[[Category: Czarny, A.]]
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[[Category: Large Structures]]
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[[Category: Neidle, S.]]
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[[Category: Boykin DW]]
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[[Category: Nunn, C.M.]]
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[[Category: Czarny A]]
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[[Category: Wilson, W.D.]]
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[[Category: Neidle S]]
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[[Category: Wood, A.A.]]
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[[Category: Nunn CM]]
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[[Category: Zhao, M.]]
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[[Category: Wilson WD]]
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[[Category: IBB]]
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[[Category: Wood AA]]
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[[Category: MG]]
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[[Category: Zhao M]]
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[[Category: b-dna]]
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[[Category: complexed with drug]]
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[[Category: double helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Feb 15 15:27:57 2008''
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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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