1JO2

Crystal Structure of the B-DNA Hexamer (CgATCG).Daunomycin Complex Containing a Ribose at the Intercalation Site

Summary for 1JO2

• Entry DOI: 10.2210/pdb1jo2/pdb
• Descriptor: 5'-D(*C)-R(P*G)-D(P*AP*TP*CP*G)-3', DAUNOMYCIN (3 entities in total)
• Functional Keywords: intercalation, dna/rna chimer, dna, rna
• Total number of polymer chains: 1
• Total formula weight: 2352.74

Authors

Shi, K.,Pan, B.,Sundaralingam, M. (deposition date: 2001-07-26, release date: 2003-07-29, Last modification date: 2024-02-07)

Primary citation

Shi, K.,Pan, B.,Sundaralingam, M.
Structure of a B-form DNA/RNA chimera (dC)(rG)d(ATCG) complexed with daunomycin at 1.5 A resolution.
Acta Crystallogr.,Sect.D, 59:1377-1383, 2003

PubMed Abstract: The crystal structure of a DNA/RNA chimera (dC)(rG)d(ATCG) complexed with the anticancer drug daunomycin has been determined at 1.5 A resolution with R(work) and R(free) of 19.7 and 23.3%, respectively, for 2767 reflections. The complex crystallizes in space group P4(1)2(1)2, with unit-cell parameters a = b = 28.05, c = 53.16 A, and contains one nucleic acid strand and one daunomycin molecule in the asymmetric unit. To our knowledge, this is the first crystal structure of a DNA/RNA chimera complexed with an intercalating drug. The DNA/RNA chimera adopts the B-form helical conformation, with the 2'-hydroxyl group in the major groove of the duplex, forming hydrogen bonds to N7 and the anionic phosphate oxygen of its 3'-side adenine. The present results indicate that the replacement by the ribose sugar in the DNA sequence does not change the geometry and intercalation pattern of daunomycin. A model of B-form RNA has been built based on the present structure. The model indicates that the interactions of the 2'-hydroxyl groups in the B-form duplex depend on their 3'-side nucleotides.

PubMed: 12876339
DOI: 10.1107/S0907444903011788

Experimental method

X-RAY DIFFRACTION (1.5 Å)