DSSR-PyMOL cartoon-block schematics: PDB entry 1xa2

PDB-id

1xa2; DSSR-derived features in text and JSON formats

Class

DNA

Method

X-ray (1.71 Å)

Summary

Cobalt hexammine induced tautomeric shift in z-DNA: the structure of d(cgcgca).d(tgcgcg) in two crystal forms

Reference

Thiyagarajan S, Rajan SS, Gautham N (2004): "Cobalt hexammine induced tautomeric shift in Z-DNA: the structure of d(CGCGCA)*d(TGCGCG) in two crystal forms." Nucleic Acids Res., 32, 5945-5953. doi: 10.1093/nar/gkh919.

Abstract

We report here the crystal structure of the DNA hexamer duplex d(CGCGCA)*d(TGCGCG) at 1.71 A resolution. The crystals, in orthorhombic space group, were grown in the presence of cobalt hexammine, a known inducer of the left-handed Z form of DNA. The interaction of this ion with the DNA helix results in a change of the adenine base from the common amino tautomeric form to the imino tautomer. Consequently the A:T base pair is disrupted from the normal Watson-Crick base pairing to a 'wobble' like base pairing. This change is accommodated easily within the helix, and the helical parameters are those expected for Z-DNA. When the cobalt hexammine concentration is decreased slightly in the crystallization conditions, the duplex crystallizes in a different, hexagonal space group, with two hexamer duplexes in the asymmetric unit. One of these is situated on a crystallographic 6-fold screw axis, leading to disorder. The tautomeric shift is not observed in this space group. We show that the change in inter-helix interactions that lead to the two different space groups probably arise from the small decrease in ion concentration, and consequently disordered positions for the ion.