459d

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[[Image:459d.gif|left|200px]]
[[Image:459d.gif|left|200px]]
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{{Structure
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<!--
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|PDB= 459d |SIZE=350|CAPTION= <scene name='initialview01'>459d</scene>, resolution 2.3&Aring;
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The line below this paragraph, containing "STRUCTURE_459d", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=CBR:5-BROMO-2&#39;-DEOXY-CYTIDINE-5&#39;-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=TBZ:2&#39;&#39;-(4-METHOXYPHENYL)-5-(3-AMINO-1-PYRROLIDINYL)-2,5&#39;,2&#39;,5&#39;&#39;-TRI-BENZIMIDAZOLE'>TBZ</scene>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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|ACTIVITY=
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or leave the SCENE parameter empty for the default display.
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|GENE=
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|DOMAIN=
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{{STRUCTURE_459d| PDB=459d | SCENE= }}
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|RELATEDENTRY=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=459d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=459d OCA], [http://www.ebi.ac.uk/pdbsum/459d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=459d RCSB]</span>
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}}
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'''DNA MINOR-GROOVE RECOGNITION OF A TRIS-BENZIMIDAZOLE DRUG'''
'''DNA MINOR-GROOVE RECOGNITION OF A TRIS-BENZIMIDAZOLE DRUG'''
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==About this Structure==
==About this Structure==
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459D is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=459D OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=459D OCA].
==Reference==
==Reference==
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://www.ncbi.nlm.nih.gov/pubmed/10373586 10373586]
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://www.ncbi.nlm.nih.gov/pubmed/10373586 10373586]
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[[Category: Protein complex]]
 
[[Category: Aymami, J.]]
[[Category: Aymami, J.]]
[[Category: Neidle, S.]]
[[Category: Neidle, S.]]
[[Category: Nunn, C M.]]
[[Category: Nunn, C M.]]
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[[Category: b-dna]]
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[[Category: B-dna]]
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[[Category: complexed with tris-benzimidazole]]
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[[Category: Complexed with tris-benzimidazole]]
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[[Category: deoxyribonucleic acid]]
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[[Category: Deoxyribonucleic acid]]
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[[Category: minor groove binding]]
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[[Category: Minor groove binding]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:18:53 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:37:33 2008''
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Revision as of 19:18, 4 May 2008

Image:459d.gif

Template:STRUCTURE 459d

DNA MINOR-GROOVE RECOGNITION OF A TRIS-BENZIMIDAZOLE DRUG


Overview

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.

About this Structure

Full crystallographic information is available from OCA.

Reference

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 Page seeded by OCA on Sun May 4 22:18:53 2008

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