3GO3

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

Summary for 3GO3

• Entry DOI: 10.2210/pdb3go3/pdb
• Related: 185D 193D 1PFE 1VS2 1XVK 1XVN 1XVR 2ADW 2DA8
• Related PRD ID: PRD_000491
• Descriptor: 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3', ECHINOMYCIN, MANGANESE (II) ION, ... (6 entities in total)
• Functional Keywords: bisintercalator, hoogsteen basepair, depsipeptide, quinoxaline, thioacetal, antibiotic, antitumor, dna-antibiotic complex, dna/antibiotic
• Biological source: STREPTOMYCES ECHINATUS
• Total number of polymer chains: 4
• Total formula weight: 7383.87

Authors

Pfoh, R.,Cuesta-Seijo, J.A.,Sheldrick, G.M. (deposition date: 2009-03-18, release date: 2009-03-31, Last modification date: 2025-03-26)

Primary citation

Pfoh, R.,Cuesta-Seijo, J.A.,Sheldrick, G.M.
Interaction of an Echinomycin-DNA Complex with Manganese Ion
Acta Crystallogr.,Sect.F, 65:660-, 2009

PubMed 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.

PubMed: 19574634
DOI: 10.1107/S1744309109019654

Experimental method

X-RAY DIFFRACTION (1.1 Å)