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spinqualitylabelsall models 1d56, resolution 1.700Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

ALTERNATIVE STRUCTURES FOR ALTERNATING POLY(DA-DT) TRACTS: THE STRUCTURE OF THE B-DNA DECAMER C-G-A-T-A-T-A-T-C-G

Overview

The X-ray crystal structure of the decamer C-G-A-T-A-T-A-T-C-G has been, solved with two contrasting cations, Ca2+ and Mg2+. Crystals with calcium, are space group P2(1)2(1)2(1), cell dimensions a = 38.76 A, b = 40.06 A, and c = 33.73 A, and diffract to 1.7-A resolution. Crystals with magnesium, have the same space group, cell dimensions a = 38.69 A, b = 39.56 A, and c, = 33.64 A, and diffract to 2.0 A. Their structures were solved, independently by molecular replacement, beginning with idealized Arnott, B-DNA geometry. The calcium structure refined to R = 17.8% for the 3683, reflections greater than 2 sigma, with 404 DNA atoms, 95 solvent peaks, and 1 Ca(H2O)7(2+) ion. The magnesium structure refined to R = 16.5% for, the 1852 reflections greater than 2 sigma, with 404 DNA atoms, 62 solvent, peaks, and 1 Mg(H2O)6(2+) ion. The two structures are virtually identical, and are isostructural with C-G-A-T-C-G-A-T-C-G [Grzeskowiak et al. (1991), J. Biol. Chem. 266, 8861-8883] and C-G-A-T-T-A-A-T-C-G [Quintana et al., (1992) J. Mol. Biol. 225, 375-395]. Comparison of C-G-A-T-A-T-A-T-C-G with, C-G-C-A-T-A-T-A-T-G-C-G [Yoon et al. (1988) Proc. Natl. Acad. Sci. U.S.A., 85, 6332-6336] shows that the expected alternation of twist angles is, found in the central A-T-A-T-A-T region of the decamer (A-T small, T-A, large), but the minor groove remains wide at the center, rather than, narrow. Minor groove narrowing is produced, in these two structures, not, by overwinding of the helix, but by an increase in base pair propeller., This analysis confirms the concept that poly(dA-dT).poly(dA-dT) is, polymorphous, with different local conformations possible in different, local environments.

About this Structure

1D56 is a Protein complex structure of sequences from [1] with CA as ligand. Full crystallographic information is available from OCA.

Reference

Alternative structures for alternating poly(dA-dT) tracts: the structure of the B-DNA decamer C-G-A-T-A-T-A-T-C-G., Yuan H, Quintana J, Dickerson RE, Biochemistry. 1992 Sep 1;31(34):8009-21. PMID:1510987

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