X-ray structure of cytidine-5'-O-dimethylphosphate. Novel stacking between the ribosyl O(2') hydroxyl oxygen atom and the base.
X-ray structure of cytidine-5'-O-dimethylphosphate. Novel stacking between the ribosyl O(2') hydroxyl oxygen atom and the base.
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5-O-二甲基磷酸胞苷的 X 射线结构。
DOI：
10.1093/nar/12.17.6813
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发表时间：
1984
影响因子：
14.9
通讯作者：
Sundaralingam,M
中科院分区：
文献类型：
--
作者：
Brennan,RG;Kondo,NS;Sundaralingam,M
RNA和DNA的磷酸二酯主链的阴离子氧原子特别容易被许多致突变和致癌的烷基化剂酯化。为了更好地了解烷基化磷酸糖部分的几何、电子和构象性质，对磷酸三酯化核苷酸cytidine-5′-O-dimethylphos-phate （C11H18N3O8P）进行了x射线结构研究。化合物在单斜空间群P2中结晶，晶胞参数为a=5.741(2),b=11.625(1),c=11.425(1)Å， β=94.43(2)°。采用直接法求解，采用块对角线最小二乘法对结构进行细化，R指数为0.034 （Rw=0.046）。d -核呋喃基环为T2twist构象(P=13.1（2)°，τm=36.7(2)°），C（1’）-N（1)糖基键的构象为XCN=8.3(2)°）。四个P-O键的长度明显短于非烷基化的核苷酸。三组磷酸二酯键(ω，和（ω）分别为（g,t）、（t,g）和（g,t）构象。然而，在核糖基0（2’）羟基氧原子和邻近的嘧啶环之间发现了一种新的分子间堆叠。这种羟基基叠加相互作用方式对核糖核酸和核酸-蛋白复合物的三级和四级结构的稳定具有重要意义。
The anionic oxygen atoms of the phosphodiester backbone of RNA and DNA are particularly susceptible to esterification by many mutagenic and carcinogenic alkylating agents. To better understand the geometric, electronic and conformational properties of the alkylated sugar phosphate moiety, the X-ray structure of the phosphotriesterified nucleotide, cytidine-5′-O-dimethylphos-phate (C11H18N3O8P), was undertaken. The compound crystallizes in the monoclinic space group P2, with unit cell parameters ofa=5.741(2),b=11.625(1),c=11.425(1)Å, β=94.43(2)°. The structure was solved by direct methods and refined by block-diagonal least-squares technique to an R index of 0.034 (Rw=0.046). The D-ribofuranosyl ring is in the T2twist conformation (P=13.1(2)°, τm=36.7(2)°) and the conformation about the C(1′)-N(1) glycosyl bond isanti(XCN=8.3(2)°). The four P-O bond lengths are significantly shorter than those of the nonalkylated nucleotides. The three sets of phosphodiester linkages, (ω,, and (ω, take the (g ,t), (t,g ) and (g ,t) conformations, respectively. Three is no base-base or alkyl-base stacking, however, a novel intermolecular stacking is found between the ribosyl 0(2′) hydroxyl oxygen atom and a neighboring pyrimidine ring. This hydroxyl-base stacking interaction way have implications in the stabilization of the tertiary and quarternary structure of ribonucleic acids and nucleic acid-protein complexes.