Nucleic acid conformation: Crystal and molecular structure of deoxyguanosine (5′) phosphate (disodium salt)—Agauche-trans (gt) conformation about the C(4′)-C(5′) bond and O(1′) puckering of the furanose ring

Abstract

The crystal structure of deoxyguanosine (5′) phosphate, disodium salt, (5′-dGMP Na₂ 4H₂O) has been determined from three dimensional single crystal x-ray data collected by multiple film, equi-inclination, Weissenberg method using CuK_a radiation. The crystal belongs to the monoclinic space groupP2₁ witha=16.002±0.003 Å,b=10.730±0.003 Å,c=5.575±0.005 Å andβ=101.9°. The structure was solved by symbolic addition method using the program Multan, the reliability index being 0.090. The guanine base is in the usualanti conformation about the C (1′)-N (9) bond withx _CN=52.3°. The structure shows two unique conformational features not observed in any nucleotide structure reported so far. The deoxyribose moiety shows O (1′)endo puckering with respect to the best four atom plane defined by C(1′)-C(2′)-C(3′)-C(4′). The conformation about the C(4′)-C(5′) bond isgauche-trans with ø₀₀=62.5° and ø_oc=174.8°. This is the first nucleotide structure where agt conformer similar to that found in the Watson-Crick double helical DNA model has been experimentally observed. These two conformational features have also direct relevance to the concept of ‘a conformationally rigid nucleotide unit’ developed by Sundaralingam. The nine membered guanine ring is essentially planar. Bases of molecules related by a ‘c’ cell translation tend to overlap, the shortest distance being 3.51 Å between the atoms N (3) and C(8). One of the sodium atoms Na(1) has an octahedral coordination with four water oxygens and O(6) and O(3′) atoms occupying the corners at distances ranging from 2.35 Å to 2.55 Å.