2d25

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spinqualitylabelsall models 2d25, resolution 1.750Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

C-C-A-G-G-C-M5C-T-G-G; HELICAL FINE STRUCTURE, HYDRATION, AND COMPARISON WITH C-C-A-G-G-C-C-T-G-G

Overview

The self-complementary DNA duplex C-C-A-G-G-C-m5C-T-G-G has been refined, against 1.75-A x-ray diffraction data to an R value of 17.4%. In the, crystal of space group P6, 10-base pair DNA fragments with characteristic, sequence-related fine structure stack end to end to form long antiparallel, B-type double helices. As shown by a structure analysis at lower, resolution (Heinemann, U., and Alings, C. (1991) EMBO J. 10, 35-43), the, overall geometry of C-C-A-G-G-C-m5C-T-G-G is similar to that of the, unmethylated analog C-C-A-G-G-C-C-T-G-G despite a different crystal, environment. The present high resolution structure analysis permits a, detailed comparison of the two duplexes and their hydration spheres., Helical parameters are significantly correlated between both molecules, with the exception of the base pair propeller. Sugar pucker and backbone, torsion angles alpha, gamma, delta, and chi show similar mean values, but, their individual values deviate significantly between duplexes. In, contrast, torsion angles beta, epsilon, and zeta change along the strands, of both duplexes in much the same way. The effect of single-site, methylation on DNA conformation appears to be small and limited to the, base pairs directly involved. Methylation tends to push base pairs toward, the minor groove of the helix. A regular minor groove hydration pattern, involves dual hydrogen bonding of water molecules to O-4' and base atoms, of C-C-A-G-G-C-m5C-T-G-G.

About this Structure

2D25 is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.

Reference

C-C-A-G-G-C-m5C-T-G-G. Helical fine structure, hydration, and comparison with C-C-A-G-G-C-C-T-G-G., Heinemann U, Hahn M, J Biol Chem. 1992 Apr 15;267(11):7332-41. PMID:1559976

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