4HIG

Ultrahigh-resolution crystal structure of Z-DNA in complex with Mn2+ ion.

4HIG の概要

• エントリーDOI: 10.2210/pdb4hig/pdb
• 関連するPDBエントリー: 1D39 1ICK 3FQ5 3G2R 3P4J 4HIF
• 分子名称: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3'), SPERMINE (FULLY PROTONATED FORM), MANGANESE (II) ION, ... (4 entities in total)
• 機能のキーワード: self-complementary dna, z-dna, dna
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 3881.72

構造登録者

Drozdzal, P.,Gilski, M.,Kierzek, R.,Lomozik, L.,Jaskolski, M. (登録日: 2012-10-11, 公開日: 2013-06-05, 最終更新日: 2023-09-20)

主引用文献

Drozdzal, P.,Gilski, M.,Kierzek, R.,Lomozik, L.,Jaskolski, M.
Ultrahigh-resolution crystal structures of Z-DNA in complex with Mn(2+) and Zn(2+) ions.
Acta Crystallogr.,Sect.D, 69:1180-1190, 2013

PubMed Abstract: X-ray crystal structures of the spermine(4+) form of the Z-DNA duplex with the self-complementary d(CG)3 sequence in complexes with Mn(2+) and Zn(2+) cations have been determined at the ultrahigh resolutions of 0.75 and 0.85 Å, respectively. Stereochemical restraints were only used for the sperminium cation (in both structures) and for nucleotides with dual conformation in the Zn(2+) complex. The Mn(2+) and Zn(2+) cations at the major site, designated M(2+)(1), bind at the N7 position of G6 by direct coordination. The coordination geometry of this site was octahedral, with complete hydration shells. An additional Zn(2+)(2) cation was bis-coordinated in a tetrahedral fashion by the N7 atoms of G10 and G12 from a symmetry-related molecule. The coordination distances of Zn(2+)(1) and Zn(2+)(2) to the O6 atom of the guanine residues were 3.613 (6) and 3.258 (5) Å, respectively. Moreover, a chloride ion was also identified in the coordination sphere of Zn(2+)(2). Alternate conformations were observed in the Z-DNA-Zn(2+) structure not only at internucleotide linkages but also at the terminal C3'-OH group of G12. The conformation of the sperminium chain in the Z-DNA-Mn(2+) complex is similar to the spermine(4+) conformation in analogous Z-DNA-Mg(2+) structures. In the Z-DNA-Zn(2+) complex the sperminium cation is disordered and partially invisible in electron-density maps. In the Z-DNA-Zn(2+) complex the sperminium cation only interacts with the phosphate groups of the Z-DNA molecules, while in the Z-DNA-Mn(2+) structure it forms hydrogen bonds to both the phosphate groups and DNA bases.

PubMed: 23695262
DOI: 10.1107/S0907444913007798

実験手法

X-RAY DIFFRACTION (0.75 Å)