Interaction of metal ions with 2′-deoxyribonucleotides. Crystal and molecular structure of a cobalt(II) complex with 2′-deoxyinosine 5′-monophosphate

Abstract

The crystal structure of the cobalt(II) complex with 2′-deoxyinosine 5′-monophosphate (5′-dlMP), [Co(5′-dlMP)(H₂O)₅]·2H₂O, has been analysed by X-ray diffraction. The complex crystallizes in the space group P2₁2₁2₁ with a= 6.877(3), b= 10.904(2), c= 25.421(6)Å, and Z= 4. The structure was solved by the heavy-atom method and refined to an R value of 0.043 using 1 776 unique reflections. The cobalt ion binds only to the 6-oxopurine base of the nucleotide at the N(7) position, the octahedral co-ordination of the metal being completed by five water oxygens. The phosphate oxygens are involved in hydrogen bonding with the co-ordinated water molecules. The structure is closely similar to that of the corresponding ribonucleotide complex. The nucleotide has the energetically preferred conformation: an anti base, a C(3′)-endo sugar pucker, and a gauche–gauche conformation about the C(4′)–C(5′) bond. The significance of sugar puckering in the monomeric complexes of general formula [M(5′-nucleotide)(H₂O)₅] is explained in terms of the structural requirements for metal–water–phosphate bridging interactions.