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Role of water molecules in protein-nucleic acid interactions: visualization of a model highly hydrated complex structure of Inosine 5′-monophosphate and L-Serine (2C10H13N4O8P·C3H7NO3·12H2O) at atomic resolution

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Abstract

The crystal structure of a dodecahydrated co-complex between two Inosine 5′-monophosphate (IMP) and one L-serine, the first of its kind reported, has been determined at atomic resolution by X-ray crystallographic methods. The crystal belongs to a monoclinic space group, P21, with the cell dimensionsa=8.695(7),b=21.898(6),c=12.374(3)Å, β=110.59(3)°. This structure reveals the recognition mechanism of serine to the nucleotides through direct and water-mediated hydrogen bonds. The phosphate oxygen (O22) seems to prefer the nonspecific interaction with the functional sites of serine (N...O22=2.735, OG...O22=2.970, O1...O22 =3.121 Å), whereas the bases prefer specific (N17...N=3.199, N23...O2=2.784 Å) bondings. The solvent-mediated hydrogen bonds N17...W3...N27 endow extra stabilization to the stacked bases. The presence of hydrogen-bonded water spines and their interplay in the specific and nonspecific bindings with potential ligands indicate the functional involvement of solvent molecules through cooperative donor-acceptor network and could act as viable centers of intricate interactions in protein-DNA complexation processes.

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Authors and Affiliations

  1. Biophysics Division, Bose Institute, P 1/12 C.I.T. Scheme VIIM, 700 054, Calcutta, India

    B. P. Mukhopadhyay, S. Ghosh & Asok Banerjee

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  1. B. P. Mukhopadhyay
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  2. S. Ghosh
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  3. Asok Banerjee
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Mukhopadhyay, B.P., Ghosh, S. & Banerjee, A. Role of water molecules in protein-nucleic acid interactions: visualization of a model highly hydrated complex structure of Inosine 5′-monophosphate and L-Serine (2C10H13N4O8P·C3H7NO3·12H2O) at atomic resolution. J Chem Crystallogr 25, 477–485 (1995). https://doi.org/10.1007/BF01665704

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  • DOI: https://doi.org/10.1007/BF01665704

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