2ADW

Crystal structure of Echinomycin-(ACGTACGT)2 solved by SAD

Summary for 2ADW

• Entry DOI: 10.2210/pdb2adw/pdb
• Related: 185D 193D 1PFE 1VS2 1XVK 1XVN 1XVR 2DA8 3GO3
• Related PRD ID: PRD_000491
• Descriptor: 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3', ECHINOMYCIN, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ... (7 entities in total)
• Functional Keywords: dna-antibiotic complex, bisintercalator, hoogsteen basepair, depsipeptide, quinoxaline, thioacetal, antibiotic, antitumor, dna/antibiotic
• Biological source: STREPTOMYCES ECHINATUS
• Total number of polymer chains: 8
• Total formula weight: 14655.09

Authors

Cuesta-Seijo, J.A.,Sheldrick, G.M. (deposition date: 2005-07-21, release date: 2006-03-28, Last modification date: 2025-03-26)

Primary citation

Cuesta-Seijo, J.A.,Weiss, M.S.,Sheldrick, G.M.
Serendipitous Sad Phasing of an Echinomycin-(Acgtacgt)2 Bisintercalation Complex.
Acta Crystallogr.,Sect.D, 62:417-, 2006

PubMed Abstract: A new crystal form was obtained for the complex between (ACGTACGT)2 and echinomycin and X-ray data were collected to 1.6 A. The structure was phased by the SAD method based on a single unexpected anomalous scatterer that could be identified as a mixture of nickel and zinc by measurements of the anomalous scattering at different wavelengths. This cation is coordinated by two guanines from two different duplexes and four water molecules. The structure resembles previously reported crystal structures of DNA-echinomycin complexes, except that three of the eight base pairs flanking the echinomycin bisintercalator sites have the Watson-Crick rather than the Hoogsteen configuration. Hoogsteen binding was found for the corresponding base pairs of the crystallographically independent duplex, indicating that the two configurations are very close in energy.

PubMed: 16552143
DOI: 10.1107/S0907444906003763

Experimental method

X-RAY DIFFRACTION (1.6 Å)