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金属-核苷酸相互作用：腺苷2'-单磷酸的碱金属（Li+、Na+、K+）和碱土金属（Ca2+、Mg2+）金属配合物的晶体结构

Metal-nucleotide interactions: crystal structures of alkali (Li+, Na+, K+) and alkaline earth (Ca2+, Mg2+) metal complexes of adenosine 2'-monophosphate.

作者信息

Padiyar G S, Seshadri T P

机构信息

Department of Physics, Indian Institute of Science, Bangalore.

出版信息

J Biomol Struct Dyn. 1998 Feb;15(4):803-21. doi: 10.1080/07391102.1998.10508994.

DOI:10.1080/07391102.1998.10508994
PMID:9514255
Abstract

Crystal structures of lithium, sodium, potassium, calcium and magnesium salts of adenosine 2'-monophosphate (2'-AMP) have been obtained at atomic resolution by X-ray crystallographic methods. 2'-AMP.Li belongs to the monoclinic space group P2(1) with a = 7.472(3)A, b = 26.853(6) A, c = 9.184(1)A, b = 113.36(1)A and Z= 4. 2'-AMP.Na and 2'-AMP.K crystallize in the trigonal space groups P3(1) and P3(1)21 with a = 8.762(1)A, c = 34.630(5)A, Z= 6 and a = 8.931(4), Ac = 34.852(9)A and Z= 6 respectively while 2'-AMP.Ca and 2'-AMP.Mg belong to space groups P6(5)22 and P2(1) with cell parameters a = 9.487(2), c = 74.622(13), Z = 12 and a = 4.973(1), b = 10.023(2), c = 16.506(2), beta = 91.1(0) and Z = 2 respectively. All the structures were solved by direct methods and refined by full matrix least-squares to final R factors of 0.033, 0.028, 0.075, 0.069 and 0.030 for 2'-AMP.Li, 2'-AMP.Na, 2'- AMP.K, 2'-AMP.Ca and 2'-AMP.Mg, respectively. The neutral adenine bases in all the structures are in syn conformation stabilized by the O5'-N3 intramolecular hydrogen bond as in free acid and ammonium complex reported earlier. In striking contrast, the adenine base is in the anti geometry (chiCN = -156.4(2)degrees) in 2'-AMP.Mg. Ribose moieties adopt C2'-endo puckering in 2'-AMP.Li and 2'-AMP.Ca, C2'-endo-C3'-exo twist puckering in 2'-AMP.Na and 2'-AMP.K and a C3'-endo-C2'-exo twist puckering in 2'-AMP.Mg structure. The conformation about the exocyclic C4'-C5' bond is the commonly observed gauche-gauche (g+) in all the structures except the gauche- trans (g-) conformation observed in 2'-AMP.Mg structure. Lithium ions coordinate with water, ribose and phosphate oxygens at distances 1.88 to 1.99A. Na+ ions and K+ ions interact with phosphate and ribose oxygens directly and with N7 indirectly through a water oxygen. A distinct feature of 2'-AMP.Na and 2'-AMP.K structures is the involvement of ribose 04' in metal coordination. The calcium ion situated on a two-fold axis coordinates directly with three oxygens OW1, OW2 and O2 and their symmetry mates at distances 2.18 to 2.42A forming an octahedron. A classic example of an exception to the existence of the O5'-N3 intramolecular hydorgen bond is the 2'-AMP.Mg strucure. Magnesium ion forms an octahedral coordination with three water and three phosphate oxygens at distances ranging from 2.02 to 2.11 A. A noteworthy feature of its coordination is the indirect link with N3 through OW3 oxygen resulting in macrochelation between the base and the phosphate group. Greater affnity of metal clays towards 5' compared to 2' and 3' nucleotides (J. Lawless, E. Edelson, and L. Manning, Am. Chem. Soc. Northwest Region Meeting, Seattle. 1978) due to macrochelation infered from solution studies (S. S. Massoud, H. Sigel, Eur J. Biochem. 179, 451-458 (1989)) and interligand hydrogen bonding induced by metals postulated from metal-nucleotide structures in solid state (V. Swaminathan and M. Sundaralingam, CRC. Crit. Rev. Biochem. 6, 245-336 (1979)) are borne out by our structures also. The stacking patterns of adenine bases of both 2'-AMP.Na and 2'-AMP.K structures resemble the 2'-AMP.NH4 structure reported in the previous article. 2'-AMP.Li, 2'-AMP.Ca and 2'-AMP.Mg structures display base-ribose 04' stacking. An overview of interaction of monovalent and divalent cations with 2' and 5'-nucleotides has been presented.

摘要

通过X射线晶体学方法已获得了腺苷2'-单磷酸（2'-AMP）的锂盐、钠盐、钾盐、钙盐和镁盐的原子分辨率晶体结构。2'-AMP·Li属于单斜空间群P2(1)，a = 7.472(3)Å，b = 26.853(6) Å，c = 9.184(1)Å，β = 113.36(1)°且Z = 4。2'-AMP·Na和2'-AMP·K分别结晶于三方空间群P3(1)和P3(1)21，a = 8.762(1)Å，c = 34.630(5)Å，Z = 6以及a = 8.931(4)，c = 34.852(9)Å且Z = 6，而2'-AMP·Ca和2'-AMP·Mg分别属于空间群P6(5)22和P2(1)，晶胞参数分别为a = 9.487(2)，c = 74.622(13)，Z = 12以及a = 4.973(1)，b = 10.023(2)，c = 16.506(2)，β = 91.1(0)且Z = 2。所有结构均通过直接法解析，并通过全矩阵最小二乘法精修，2'-AMP·Li、2'-AMP·Na、2'-AMP·K、2'-AMP·Ca和2'-AMP·Mg的最终R因子分别为0.033、0.028、0.075、0.069和0.030。所有结构中的中性腺嘌呤碱基均处于顺式构象，通过O5'-N3分子内氢键得以稳定，如同先前报道的游离酸和铵络合物中的情况。与之形成显著对比的是，在2'-AMP·Mg中腺嘌呤碱基处于反式构象（χCN = -156.4(2)°）。核糖部分在2'-AMP·Li和2'-AMP·Ca中采用C2'-内式褶皱，在2'-AMP·Na和2'-AMP·K中采用C2'-内式-C3'-外式扭转褶皱，在2'-AMP·Mg结构中采用C3'-内式-C2'-外式扭转褶皱。除了在2'-AMP·Mg结构中观察到的gauche-反式（g-）构象外，所有结构中外环C4'-C5'键的构象均为常见的gauche- gauche（g+）。锂离子与水、核糖和磷酸氧原子配位，距离为1.88至1.99Å。Na+离子和K+离子直接与磷酸和核糖氧原子相互作用，并通过一个水氧原子间接与N7相互作用。2'-AMP·Na和2'-AMP·K结构的一个显著特征是核糖O4'参与金属配位。位于二重轴上的钙离子直接与三个氧原子OW1、OW2和O2及其对称配偶体配位，距离为2.18至2.42Å，形成一个八面体结构。O5'-N3分子内氢键不存在的一个典型例外是2'-AMP·Mg结构。镁离子与三个水分子和三个磷酸氧原子形成八面体配位，距离范围为2.02至2.11 Å。其配位的一个值得注意的特征是通过OW3氧原子与N3间接相连，导致碱基与磷酸基团之间形成大环螯合。与2'和3'核苷酸相比，金属粘土对5'核苷酸具有更高的亲和力（J. Lawless、E. Edelson和L. Manning，美国化学学会西北地区会议，西雅图，1978年），这是基于溶液研究推断出的大环螯合作用（S. S. Massoud、H. Sigel，欧洲生物化学杂志179，451 - 458（1989年））以及固态金属 - 核苷酸结构中推测的金属诱导的配体间氢键作用（V. Swaminathan和M. Sundaralingam，CRC. Crit. Rev. Biochem. 6，245 - 336（1979年）），我们的结构也证实了这一点。2'-AMP·Na和2'-AMP·K结构中腺嘌呤碱基的堆积模式类似于上一篇文章中报道的2'-AMP·NH4结构。2'-AMP·Li、2'-AMP·Ca和2'-AMP·Mg结构显示出碱基 - 核糖O4'堆积。本文概述了单价和二价阳离子与2'和5'-核苷酸的相互作用。

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