The crystal and molecular structure of a calcium salt of guanylyl-3',5'-cytidine (GpC)

Hingerty, B.; Subramanian, E.; Stellman, Steven D.; Sato, T.; Broyde, Suse B.; Langridge, R.

The calcium salt, Ca(C_19H_24N_8O_I2P)_2.18H_20, of guanylyl-3',5'-cytidine (GpC) has been refined to an R of 8·2 % for 2918 observed reflections (11% for 4237 reflections, including unobserved). The molecule crystallized in space group P2_1 with a=21·224, b=34·207, c=9·327 Å, β=90·527°, Z=4. The asymmetric unit contains four GpC, 36 waters and two Ca^2+ ions, for a total of 198 non-hydrogen atoms. The four GpC occur as two dimers related by a pseudo C-face-centering. Each dimer consists of two crystallographically independent GpC as Watson-Crick base-pairs, and possesses a pseudo twofold axis broken by a Ca^2+ ion and associated solvent. The structure was solved by an unusual series of steps including semi-empirical potential-energy methods, packing analysis, rigid-body refinement, least-squares and difference Fourier techniques, and direct-methods tangent-formula phase refinement. The four GpC have conformational angles in the range of helical RNA, but are not identical. The different crystallographic environments perturb the GpC from exact symmetry and demonstrate the range of the basic helical conformations. All eight bases are anti, sugars are all C(3’) endo, the C(4')-C(5') bond rotations are gauche-gauche, and the ω', ω angle pair about the O-P bonds is gauche—gauche-.


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Acta Crystallographica Section B

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May 9, 2014