High-resolution crystal structure of Z-DNA in complex with Cr(3+) cations

Abstract

This work is part of our project aimed at characterizing metal-binding properties of left-handed Z-DNA helices. The three Cr(3+) cations found in the asymmetric unit of the d(CGCGCG)2-Cr(3+) crystal structure do not form direct coordination bonds with atoms of the Z-DNA molecule. Instead, the hydrated Cr(3+) ions are engaged in outer-sphere interactions with phosphate groups and O6 and N7 guanine atoms of the DNA. The Cr(3+)(1) and Cr(3+)(2) ions have disordered coordination spheres occupied by six water molecules each. These partial-occupancy chromium cations are 2.354(15) Å apart and are bridged by three water molecules from their hydration spheres. The Cr(3+)(3) cation has distorted square pyramidal geometry. In addition to the high degree of disorder of the DNA backbone, alternate conformations are also observed for the deoxyribose and base moieties of the G2 nucleotide. Our work illuminates the question of conformational flexibility of Z-DNA and its interaction mode with transition-metal cations.

Fig. 1

Stereoview of the d(CGCGCG)₂–Cr³⁺ structure with anomalous difference map for the three Cr³⁺ cations (purple spheres). The map is contoured at 6.5σ. Note the alternate conformations (I, green; II, orange) along the DNA chains

Fig. 2

A portion of the Z-DNA duplex in the d(CGCGCG)₂–Cr³⁺ complex at the G2 nucleotide with two alternative conformations (I, green; II, orange) shown in 2mFo-DFc map contoured at 1.0σ

Fig. 3

a The coordination spheres of the hydrated Cr³⁺(1) and Cr³⁺(2) ions. The 2mFo-DFc map is contoured at the 1.0σ level. b The distorted square pyramidal coordination sphere of the Cr³⁺(3) cation. The 2mFo-DFc map is contoured at the 1.0σ level. Water molecules are represented by red spheres. The coordination and hydrogen bonds are represented by gray and red dashed lines, respectively