Stereochemistry of nucleic acid constituents: I. Refinement of the structure of cytidylic acid b‡

Add time:09/06/2019    Source:sciencedirect.com

The crystal structure of cytidylic acid b,‡ cytidine-3′-phosphate, has been refined by the method of full matrix least-squares to an R factor of 0·045, R = Σ|Fo| − Σ|Fc|/Σ|Fo| where |Fo| and |Fc| are respectively the observed and calculated diffraction amplitudes. The nucleotide is found to exist as a zwitter ion. The cytosine ring is slightly nonplanar, with N(3) protonated. The ribose ring is puckered with C(2′)-endo, and displaced (on the same side of C(5′)) about 0·6 Å from the plane of the remaining ring atoms. These latter appear to deviate slightly from a plane. Because the base in nucleic acids need not necessarily be planar and because C(1′) can be significantly displaced from the least-squares plane of the base, we suggest that the definition of the torsion angle ΦCN defined by Donohue & Trueblood (1960), be modified as follows. The torsion angle ΦCN of the bond C(1′)−N is the angle formed by the projection of C(1′)−O(1′) relative to the projection of N(1′)−C(6) (in pyrimidine ring) and N(9)−C(8) (in purine ring) when viewed along C(1′)−N. This angle is taken as zero when O(1′) is anti-planar to C(2) of the pyrimidine or C(4) of the purine ring, and positive angles are taken as those measured in a clockwise direction when viewing from C(1′) to N. For this structure ΦCN = −42·1° and the conformation anti. All 14 hydrogen atoms in the structure appear in a ΔF synthesis and their parameters have also been refined. Several of the hydrogen isotropic thermal parameters have an anomalously low value. The standard deviation of the atomic co-ordinates from the least-squares refinement are P = 0·0011 Å, O = 0·0036 Å, N = 0·0042 A, C = 0·005 Å and H = 0·06 Å.

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