Hydrogen bonding cooperativity of water to nucleotide recognition: Structure of octadecahydrated inosine 5′-monophosphate, 2(C10H12N4O8P)·18H 2O at atomic resolution

Asim K. Bera, Bishnu P. Mukhopadhyay, Asok K. Pal, U. Haldar, S. Bhattacharya, Asok Banerjee

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

The crystal structure of an octadecahydrated complex between two inosine 5′-monophosphate (IMP) has been determined at atomic resolution, which reveals the hydrogen bonding and the coordination cooperativity of water molecules to nucleotide recognition. The crystal belongs to monoclinic space group P21 with cell dimensions a = 8.65(1), b = 21.90(1), c = 12.37(1)Å, and β = 110.38(9)°. The ribose hydroxyls, purine N7, keto(O6) bonded water molecules W1, W2, W5, W6, W8 and the phosphate bridge forming water oxygens of W4, W7, W11 appear to play an invariant role in their hydrogen bonding interactions with the IMPs. The synergistic role of the water molecules W5, W6, W8 in the purine staking domain (N27⋯W5 = 2.583, N17⋯W5 = 2.563, O16⋯W8 = 2.759, O26⋯W6 = 2.723 Å) have been clearly observed for the first time. The complexation of the water molecules through variable hydrogen bonding coordination indicate their functional involvement through extensive cooperative donoracceptor network mechanism. The occurrence of hydrogen-bonded water spines, water bridges and their interplay in the structural association of IMPs could indicate the possible viability of those aquatic centers in the biological situation.

Original languageEnglish (US)
Pages (from-to)509-516
Number of pages8
JournalJournal of Chemical Crystallography
Volume28
Issue number7
DOIs
StatePublished - Jul 1998

Bibliographical note

Funding Information:
We wish to thank C.S.I.R, Government of India their full financial help in this work, Project No.

Keywords

  • Inosine 5′-monophosphate polyhydrated complex
  • Nucleic acid-water interaction
  • Variant and invariant water molecules for nucleotide recognition
  • Water mediated recognition in biology

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