DSSR-PyMOL cartoon-block schematics: PDB entry 1da4

PDB-id

1da4; DSSR-derived features in text and JSON formats

Class

DNA

Method

NMR

Summary

Solution structure of a DNA duplex containing the cis-pt(nh3)2[d(-gtg-)-n7-(g)-n7(g)n7(g)]adduct as determined with high field NMR and molecular mechanics-dynamics

Reference

van Garderen CJ, van Houte LP (1994): "The solution structure of a DNA duplex containing the cis-Pt(NH3)2[d(-GTG-)-N7(G),N7(G)] adduct, as determined with high-field NMR and molecular mechanics/dynamics." Eur.J.Biochem., 225, 1169-1179. doi: 10.1111/j.1432-1033.1994.1169b.x.

Abstract

The solution structure of the cis-Pt-GTG adduct in the double-stranded oligomer d(CTCTAGTGCTCAC).td(GTGAGCACTAGAG) was studied with high-resolution NMR techniques. For model building, the distance information obtained from two-dimensional NOE experiments was used in molecular mechanic computations and molecular dynamic structure refinements. The structural distortion upon platination appears to be restricted to the base pairs Pt-G6.C21 and T7.A20; Pt-G8.C19 forms a normal Watson-Crick base pair. T7 is positioned in the minor groove and stacks with the highly propeller-twisted Pt-G6. There is no hydrogen bonding between T7 and A20. The complementary strand is undistorted; A20 stacks with its flanking cytidines (C19 and C21) as in regular B-DNA. The duplex is locally unwound (from base pair A5.T22 to G8.C19: 19 degrees) and is slightly kinked (20 degrees) at the platination site. The platinum coordination distorts the DNA structure at the 5' side of the platinated-GTG-sequence and changes the minor groove face.