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

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.