SNAP output for PDB entry 3go3 [SNAP web server]

PDB-id

3go3; SNAP-derived features in text and JSON formats; DNAproDB

Class

DNA-antibiotic

Method

X-ray (1.1 Å)

Summary

Interactions of an echinomycin-DNA complex with manganese(ii) ions

Reference

Pfoh R, Cuesta-Seijo JA, Sheldrick GM (2009): "Interaction of an Echinomycin-DNA Complex with Manganese Ion." Acta Crystallogr.,Sect.F, 65, 660. doi: 10.1107/S1744309109019654.

Abstract

The crystal structure of an echinomycin-d(ACGTACGT) duplex interacting with manganese(II) was solved by Mn-SAD using in-house data and refined to 1.1 A resolution against synchrotron data. This complex crystallizes in a different space group compared with related complexes and shows a different mode of base pairing next to the bis-intercalation site, suggesting that the energy difference between Hoogsteen and Watson-Crick pairing is rather small. The binding of manganese to N7 of guanine is only possible because of DNA unwinding induced by the echinomycin, which might help to explain the mode of action of the drug.