378D

STRUCTURE OF THE SIDE-BY-SIDE BINDING OF DISTAMYCIN TO DNA

Summary for 378D

• Entry DOI: 10.2210/pdb378d/pdb
• Descriptor: DNA (5'-D(*GP*TP*AP*TP*AP*TP*AP*C)-3'), DISTAMYCIN A, SODIUM ION, ... (4 entities in total)
• Functional Keywords: right handed dna, double helix, double drug in minor groove, dna
• Total number of polymer chains: 4
• Total formula weight: 11651.54

Authors

Mitra, S.N.,Wahl, M.C.,Sundaralingam, M. (deposition date: 1998-01-28, release date: 1999-03-04, Last modification date: 2024-04-03)

Primary citation

Mitra, S.N.,Wahl, M.C.,Sundaralingam, M.
Structure of the side-by-side binding of distamycin to d(GTATATAC)2.
Acta Crystallogr.,Sect.D, 55:602-609, 1999

PubMed Abstract: The 2.40 A resolution crystal structure of a side-by-side binding of distamycin A molecules to a DNA octamer d(GTATATAC)2 with an extended alternating TA sequence has been determined. The unit-cell parameters are a = 29.55, b = 42.18, c = 43.38 A, beta = 96.56 degrees, space group P21, with two molecules in the asymmetric unit, in contrast to all previous side-by-side distamycin-DNA complexes which have only a single DNA strand and one drug molecule in the asymmetric unit. The structure was solved by the molecular-replacement method and refined to an R index of 21.0% using 3467 reflections [>/= 2sigma(F)]. The minor grooves of the DNA molecules bind two side-by-side antiparallel staggered distamycins spanning about five base pairs and virtually covering the entire length of the DNA. The octamer duplexes exhibit low-high alternations in the helical twist, sugar puckering and the C-O3' and O3'-P torsion angles, similar to the earlier side-by-side complexes containing inosine bases. The molecules are stacked one over the other along the ac diagonal in an infinite pseudo-continuous helical column with no lateral interactions.

PubMed: 10089456
DOI: 10.1107/S0907444998012475

Experimental method

X-RAY DIFFRACTION (2.4 Å)