1VTF

STRUCTURE OF 5'-D(*(BRO)CP*GP*(BRO)CP*G)-3' IN COMPLEX WITH PROFLAVINE

Summary for 1VTF

• Entry DOI: 10.2210/pdb1vtf/pdb
• Descriptor: DNA (5'-D(*(BRO)CP*GP*(BRO)CP*G)-3'), PROFLAVIN (3 entities in total)
• Functional Keywords: right handed dna, double helix, complexed with drug, modified, deoxyribonucleic acid, dna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 3954.70

Authors

Westhof, E.,Hosur, M.V.,Sundaralingam, M. (deposition date: 1988-12-13, release date: 2011-07-13, Last modification date: 2023-12-27)

Primary citation

Westhof, E.,Hosur, M.V.,Sundaralingam, M.
Nonintercalative binding of proflavin to Z-DNA: structure of a complex between d(5BrC-G-5BrC-G) and proflavin.
Biochemistry, 27:5742-5747, 1988

PubMed Abstract: The crystal structure of a disordered 1:1 complex between the tetradeoxyoligomer d(5BrC-G-5BrC-G) and proflavin has been determined and refined to an R factor of 26.9% for 474 reflections initially in space group P6(5) and to an R factor of 22.2% for 475 reflections in space group P2(1), both at 2-A resolution with Fobsd greater than or equal to 4.0. The unit cell constants are a = b = 17.9 A, c = 44.5 A, and gamma = 120 degrees. The final models are essentially the same in the two space groups with greater disorder in space group P6(5). In space group P2(1), the asymmetric unit is a tetranucleotide duplex, two sandwiched proflavin molecules, and four "outside-bound" proflavins. The tetranucleotide duplex is in the Z conformation and is located at the origin of the unit cell with a pair of proflavins sandwiched between the tetranucleotides. Thus, the tetranucleotides and proflavin dimers stack alternatively forming a quasi-continuous helix with the helix axis coincident with the c axis. The structure analysis revealed the presence of outside-bound proflavins as well. It is interesting that one type of outside-bound proflavins occupies a similar environment as the cobalt hexaammines in their complex with the decadeoxyoligomer d(CGTACGTACG) [Brennan, R. G., Westhof, E., & Sundaralingam, M. (1986) J. Biomol. Struct. Dyn. 3, 649]. Crystals of the latter are isomorphous to the present complex. The outside-bound proflavins penetrate the deep minor groove, thereby closing it off, and provide a visualization of a quasi-internal mode of binding of proflavin to a nucleic acid.

PubMed: 3179273

Experimental method

X-RAY DIFFRACTION (2 Å)