DSSR-PyMOL cartoon-block schematics: PDB entry 362d

PDB-id

362d; DSSR-derived features in text and JSON formats

Class

DNA

Method

X-ray (1.3 Å)

Summary

The structure of d(tgcgca)2 and a comparison to other z-DNA hexamers

Reference

Harper A, Brannigan JA, Buck M, Hewitt L, Lewis RJ, Moore MH, Schneider B (1998): "Structure of d(TGCGCA)2 and a comparison to other DNA hexamers." Acta Crystallogr.,Sect.D, 54, 1273-1284. doi: 10.1107/S0907444998002807.

Abstract

The X-ray crystal structure of d(TGCGCA)2 has been determined at 120 K to a resolution of 1.3 A. Hexamer duplexes, in the Z-DNA conformation, pack in an arrangement similar to the 'pure spermine form' [Egli et al. (1991). Biochemistry, 30, 11388-11402] but with significantly different cell dimensions. The phosphate backbone exists in two equally populated discrete conformations at one nucleotide step, around phosphate 11. The structure contains two ordered cobalt hexammine molecules which have roles in stabilization of both the Z-DNA conformation of the duplex and in crystal packing. A comparison of d(TGCGCA)2 with other Z-DNA hexamer structures available in the Nucleic Acid Database illustrates the elusive nature of crystal packing. A review of the interactions with the metal cations Na+, Mg2+ and Co3+ reveals a relatively small proportion of phosphate binding and that close contacts between metal ions are common. A prediction of the water structure is compared with the observed pattern in the reported structure.