Serendipitous SAD phasing of an echinomycin-(ACGTACGT)2 bisintercalation complex.
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.
Department of Structural Chemistry, University of Göttingen, Tammannstrasse 4, D37077 Göttingen, Germany.
Jose A
JA
Cuesta-Seijo
Manfred S
MS
Weiss
George M
GM
Sheldrick
D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D003460:Crystallization; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004448:Echinomycin / Q000737:chemistry* / Q000378:metabolism; D004583:Electrons; D006860:Hydrogen Bonding; D007364:Intercalating Agents / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D009532:Nickel / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012542:Scattering, Radiation; D013052:Spectrometry, X-Ray Emission; D055672:Static Electricity; D015032:Zinc / Q000737:chemistry
D007364:Intercalating Agents; D009838:Oligodeoxyribonucleotides; D004448:Echinomycin; D009532:Nickel; D004247:DNA; D015032:Zinc