2dbe

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{{STRUCTURE_2dbe| PDB=2dbe | SCENE= }}
{{STRUCTURE_2dbe| PDB=2dbe | SCENE= }}
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'''CRYSTAL STRUCTURE OF A BERENIL-DODECANUCLEOTIDE COMPLEX: THE ROLE OF WATER IN SEQUENCE-SPECIFIC LIGAND BINDING'''
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===CRYSTAL STRUCTURE OF A BERENIL-DODECANUCLEOTIDE COMPLEX: THE ROLE OF WATER IN SEQUENCE-SPECIFIC LIGAND BINDING===
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==Overview==
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The three-dimensional structure of a complex between the dodecanucleotide d(CGCGAATTCGCG) and the anti-trypanocidal drug berenil, has been determined to a resolution of 2.5 A. The structure has been solved by molecular replacement and refined to an R factor of 0.177. A total of 49 water molecules have been located. The drug is bound at the 5'-AAT-3' region of the oligonucleotide. At one end of the drug the amidinium group is in hydrogen-bonded contact with N3 of the adenine base complementary to the thymine of the AAT. The other amidinium group does not make direct interactions with the DNA. Instead, a water molecule mediates between them. This is in hydrogen-bonded contact with an amidinium nitrogen atom, N3 of the 5' end adenine base and the ring oxygen atom of an adjacent deoxyribose. Molecular mechanics calculations have been performed on this complex, with the drug at various positions along the sequence. These show that the observed position is only 0.8 kcal/mol higher in energy than the best position. It is suggested that there is a broad energy well in the AATT region for this drug, and that water molecules as well as the neighbouring sequence, will determine precise positioning. More general aspects of minor groove binding are discussed.
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(as it appears on PubMed at http://www.pubmed.gov), where 2323343 is the PubMed ID number.
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{{ABSTRACT_PUBMED_2323343}}
==About this Structure==
==About this Structure==
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[[Category: Complexed with drug]]
[[Category: Complexed with drug]]
[[Category: Double helix]]
[[Category: Double helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 00:05:42 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 17:43:11 2008''

Revision as of 14:43, 27 July 2008

Image:2dbe.png

Template:STRUCTURE 2dbe

CRYSTAL STRUCTURE OF A BERENIL-DODECANUCLEOTIDE COMPLEX: THE ROLE OF WATER IN SEQUENCE-SPECIFIC LIGAND BINDING

Template:ABSTRACT PUBMED 2323343

About this Structure

Full crystallographic information is available from OCA.

Reference

Crystal structure of a berenil-dodecanucleotide complex: the role of water in sequence-specific ligand binding., Brown DG, Sanderson MR, Skelly JV, Jenkins TC, Brown T, Garman E, Stuart DI, Neidle S, EMBO J. 1990 Apr;9(4):1329-34. PMID:2323343

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