1D63

CRYSTAL STRUCTURE OF A BERENIL-D(CGCAAATTTGCG) COMPLEX; AN EXAMPLE OF DRUG-DNA RECOGNITION BASED ON SEQUENCE-DEPENDENT STRUCTURAL FEATURES

1D63 の概要

• エントリーDOI: 10.2210/pdb1d63/pdb
• 分子名称: DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3'), MAGNESIUM ION, BERENIL, ... (4 entities in total)
• 機能のキーワード: b-dna, double helix, complexed with drug, dna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 7630.43

構造登録者

Brown, D.G.,Sanderson, M.R.,Garman, E.,Neidle, S. (登録日: 1992-03-02, 公開日: 1993-01-15, 最終更新日: 2024-02-07)

主引用文献

Brown, D.G.,Sanderson, M.R.,Garman, E.,Neidle, S.
Crystal structure of a berenil-d(CGCAAATTTGCG) complex. An example of drug-DNA recognition based on sequence-dependent structural features.
J.Mol.Biol., 226:481-490, 1992

PubMed Abstract: The AT-selective drug berenil has been co-crystallized with the dodecanucleotide sequence d(CGCAAATTTGCG)2. The crystal structure has been solved to a resolution of 2.0 A and an R factor of 18.3%, with the location of 65 water molecules. The drug is symmetrically bound in the 5'-AATT region of the minor groove, with its amidinium groups hydrogen-bonding to O-2 atoms of the thymine base at each end of the binding site. This arrangement is distinct from that previously found for berenil with the sequence d(CGCGAATTCGCG)2, which has the drug bound to the sequencing 5'-ATT via hydrogen bonds to adenine N-3 atoms with the involvement of a bridging water molecule at one end of the binding site. The reasons for these differences are discussed in terms of changes in helical parameters; in particular propeller twist and base-pair roll are considered to be important. The conformational and base-pair geometry of the dodecanucleotide in the structure reported here, is closely similar to that for the native structure, suggesting that the 5'-AAATTT sequence does not significantly alter during drug binding, either because of its inflexibility or because its geometry is nearly ideal for berenil binding.

PubMed: 1640462
DOI: 10.1016/0022-2836(92)90962-J

実験手法

X-RAY DIFFRACTION (2 Å)