Acta Crystallographica Section D

Biological Crystallography

Volume 69, Part 6 (June 2013)

research papers

Acta Cryst. (2013). D69, 1180-1190    [ doi:10.1107/S0907444913007798 ]

Ultrahigh-resolution crystal structures of Z-DNA in complex with Mn2+ and Zn2+ ions

P. Drozdzal, M. Gilski, R. Kierzek, L. Lomozik and M. Jaskolski

Abstract: X-ray crystal structures of the spermine4+ form of the Z-DNA duplex with the self-complementary d(CG)3 sequence in complexes with Mn2+ and Zn2+ 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 Zn2+ complex. The Mn2+ and Zn2+ cations at the major site, designated M2+(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 Zn2+(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 Zn2+(1) and Zn2+(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 Zn2+(2). Alternate conformations were observed in the Z-DNA-Zn2+ 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-Mn2+ complex is similar to the spermine4+ conformation in analogous Z-DNA-Mg2+ structures. In the Z-DNA-Zn2+ complex the sperminium cation is disordered and partially invisible in electron-density maps. In the Z-DNA-Zn2+ complex the sperminium cation only interacts with the phosphate groups of the Z-DNA molecules, while in the Z-DNA-Mn2+ structure it forms hydrogen bonds to both the phosphate groups and DNA bases.

PDB references: 4hig and 4hif

Keywords: Z-DNA; d(CG)3; Mn2+; Zn2+.

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