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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[[Image:109d.jpg|left|200px]]
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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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{{Structure
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|PDB= 109d |SIZE=350|CAPTION= <scene name='initialview01'>109d</scene>, resolution 2.000&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=IBB:5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE'>IBB</scene> and <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>
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|ACTIVITY=
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|GENE=
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}}
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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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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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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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109D 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=109D OCA].
==Reference==
==Reference==
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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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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://www.ncbi.nlm.nih.gov/pubmed/7478996 7478996]
[[Category: Protein complex]]
[[Category: Protein complex]]
[[Category: Boykin, D W.]]
[[Category: Boykin, D W.]]
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[[Category: double helix]]
[[Category: double helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:37:29 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 09:48:30 2008''

Revision as of 07:48, 20 March 2008

Image:109d.jpg


PDB ID 109d

Drag the structure with the mouse to rotate
, resolution 2.000Å
Ligands: and
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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