459d

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|PDB= 459d |SIZE=350|CAPTION= <scene name='initialview01'>459d</scene>, resolution 2.3&Aring;
|PDB= 459d |SIZE=350|CAPTION= <scene name='initialview01'>459d</scene>, resolution 2.3&Aring;
|SITE=
|SITE=
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|LIGAND= <scene name='pdbligand=TBZ:2''-(4-METHOXYPHENYL)-5-(3-AMINO-1-PYRROLIDINYL)-2,5',2',5''-TRI-BENZIMIDAZOLE'>TBZ</scene>
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|LIGAND= <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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|ACTIVITY=
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[[Category: minor groove binding]]
[[Category: minor groove binding]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 19:08:29 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 16:03:56 2008''

Revision as of 14:03, 23 March 2008

Image:459d.gif


PDB ID 459d

Drag the structure with the mouse to rotate
, resolution 2.3Å
Ligands:
Coordinates: save as pdb, mmCIF, xml



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

459D is a Protein complex structure of sequences from [1]. 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

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