109d
From Proteopedia
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|PDB= 109d |SIZE=350|CAPTION= <scene name='initialview01'>109d</scene>, resolution 2.000Å | |PDB= 109d |SIZE=350|CAPTION= <scene name='initialview01'>109d</scene>, resolution 2.000Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=IBB:5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE'>IBB</scene> | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=IBB:5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE'>IBB</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<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.ebi.ac.uk/pdbsum/109d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=109d RCSB]</span> | ||
}} | }} | ||
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[[Category: Wood, A A.]] | [[Category: Wood, A A.]] | ||
[[Category: Zhao, M.]] | [[Category: Zhao, M.]] | ||
| - | [[Category: IBB]] | ||
| - | [[Category: MG]] | ||
[[Category: b-dna]] | [[Category: b-dna]] | ||
[[Category: complexed with drug]] | [[Category: complexed with drug]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:26:33 2008'' |
Revision as of 15:26, 30 March 2008
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| , resolution 2.000Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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
Overview
An analogue of the DNA-binding compound Hoechst 33258, in which the piperazine ring has been replaced by an imidazoline group, has been cocrystallized with the dodecanucleotide sequence d(CGCGAATTCGCG)2.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.
About this Structure
109D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
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
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