1XCS

structure of oligonucleotide/drug complex

Summary for 1XCS

• Entry DOI: 10.2210/pdb1xcs/pdb
• Descriptor: 5'-D(*CP*GP*TP*AP*CP*G)-3', COBALT (II) ION, 9-[(5-(ACETYLAMINO)-6-{[(1S,4R)-8-AMINO-4-[((2R)-6-AMINO-2-{2-[(1S)-5-AMINO-1-FORMYLPENTYL]HYDRAZINO}HEXANOYL)AMINO]-1-(4-AMINOBUTYL)-2,3-DIOXOOCTYL]AMINO}-6-OXOHEXYL)AMINO]-6-CHLORO-2-METHOXYACRIDINIUM, ... (5 entities in total)
• Functional Keywords: drug-dna complex, double helix, co2+, dna
• Total number of polymer chains: 2
• Total formula weight: 4801.22

Authors

Valls, N.,Steiner, R.A.,Wright, G.,Murshudov, G.N.,Subirana, J.A. (deposition date: 2004-09-03, release date: 2005-07-19, Last modification date: 2024-02-14)

Primary citation

Valls, N.,Steiner, R.A.,Wright, G.,Murshudov, G.N.,Subirana, J.A.
Variable role of ions in two drug intercalation complexes of DNA
J.Biol.Inorg.Chem., 10:476-482, 2005

PubMed Abstract: The crystal structures of the hexamer duplex d(CGTACG)(2) complexed with the intercalating anthraquinone derivative 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione and the acridine derivative 9-acridinyl tetralysine have been solved at 2.0- and 1.4-A resolution, respectively. In both cases, the drugs adopt multiple orientations within a large DNA cavity constituted by two groups of four approximately coplanar bases. Cations play a pivotal role in the crystal structure. Both complexes crystallise in the presence of Co(2+), Ba(2+) and Na(+) ions. They reveal at least two different types of coordination environments: (1) specific sites for Co(2+) interacting with N7 of guanine; (2) a central ionic site formed by four phosphate groups, which can be occupied by different ions. One more ionic site that is not always occupied by ions is also visible in the electron density map. All of them play a role in the crystal structure.

PubMed: 15926069
DOI: 10.1007/s00775-005-0655-3

Experimental method

X-RAY DIFFRACTION (1.4 Å)