459d

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(New page: 200px<br /><applet load="459d" size="350" color="white" frame="true" align="right" spinBox="true" caption="459d, resolution 2.3&Aring;" /> '''DNA MINOR-GROOVE RECO...)
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[[Image:459d.gif|left|200px]]<br /><applet load="459d" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="459d, resolution 2.3&Aring;" />
 
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'''DNA MINOR-GROOVE RECOGNITION OF A TRIS-BENZIMIDAZOLE DRUG'''<br />
 
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==Overview==
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==DNA MINOR-GROOVE RECOGNITION OF A TRIS-BENZIMIDAZOLE DRUG==
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The crystal structure of the non-self-complementary dodecamer DNA duplex, formed by d(CG[5BrC]ATAT-TTGCG) and d(CGCAAATATGCG) has been solved to 2.3, A resolution, together with that of its complex with the, tris-benzimidazole minor groove binding ligand TRIBIZ. The inclusion of a, bromine atom on one strand in each structure enabled the possibility of, disorder to be discounted. The native structure has an exceptional narrow, minor groove, of 2.5-2.6 A in the central part of the A/T region, which is, increased in width by approximately 0.8 A on drug binding. The ligand, molecule binds in the central part of the sequence. The benzimidazole, subunits of the ligand participate in six bifurcated hydrogen bonds with, A:T base pair edges, three to each DNA strand. The presence of a pair of, C-H...O hydrogen bonds has been deduced from the close proximity of the, pyrrolidine group of the ligand to the TpA step in the sequence.
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<StructureSection load='459d' size='340' side='right'caption='[[459d]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[459d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=459D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=459D FirstGlance]. <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]] 2.3&#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=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=TBZ:2-(4-METHOXYPHENYL)-5-(3-AMINO-1-PYRROLIDINYL)-2,5,2,5-TRI-BENZIMIDAZOLE'>TBZ</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=459d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=459d OCA], [https://pdbe.org/459d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=459d RCSB], [https://www.ebi.ac.uk/pdbsum/459d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=459d ProSAT]</span></td></tr>
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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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The crystal structure of the non-self-complementary dodecamer DNA duplex formed by d(CG[5BrC]ATAT-TTGCG) and d(CGCAAATATGCG) has been solved to 2.3 A resolution, together with that of its complex with the tris-benzimidazole minor groove binding ligand TRIBIZ. The inclusion of a bromine atom on one strand in each structure enabled the possibility of disorder to be discounted. The native structure has an exceptional narrow minor groove, of 2.5-2.6 A in the central part of the A/T region, which is increased in width by approximately 0.8 A on drug binding. The ligand molecule binds in the central part of the sequence. The benzimidazole subunits of the ligand participate in six bifurcated hydrogen bonds with A:T base pair edges, three to each DNA strand. The presence of a pair of C-H...O hydrogen bonds has been deduced from the close proximity of the pyrrolidine group of the ligand to the TpA step in the sequence.
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==About this Structure==
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DNA minor groove recognition of a non-self-complementary AT-rich sequence by a tris-benzimidazole ligand.,Aymami J, Nunn CM, Neidle S Nucleic Acids Res. 1999 Jul 1;27(13):2691-8. PMID:10373586<ref>PMID:10373586</ref>
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459D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=TBZ:'>TBZ</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=459D OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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DNA minor groove recognition of a non-self-complementary AT-rich sequence by a tris-benzimidazole ligand., Aymami J, Nunn CM, Neidle S, Nucleic Acids Res. 1999 Jul 1;27(13):2691-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10373586 10373586]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 459d" style="background-color:#fffaf0;"></div>
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[[Category: Aymami, J.]]
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== References ==
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[[Category: Neidle, S.]]
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<references/>
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[[Category: Nunn, C.M.]]
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__TOC__
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[[Category: TBZ]]
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</StructureSection>
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[[Category: b-dna]]
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[[Category: Large Structures]]
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[[Category: complexed with tris-benzimidazole]]
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[[Category: Aymami J]]
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[[Category: deoxyribonucleic acid]]
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[[Category: Neidle S]]
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[[Category: minor groove binding]]
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[[Category: Nunn CM]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 21:44:22 2008''
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Current revision

DNA MINOR-GROOVE RECOGNITION OF A TRIS-BENZIMIDAZOLE DRUG

PDB ID 459d

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