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5-Nitrouridine-monohydrate: crystal structure and conformation

E Egert, H J Lindner, W Hillen

    Nucleic Acids Research
    |April 1, 1977
    PubMed
    Summary

    The crystal structure of 5-nitrouridine reveals a shallow boat conformation of the pyrimidine ring and a C3'-endo ribose. Hydrogen bonding and water interactions stabilize its conformation, with minimal base stacking.

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    Area of Science:

    • Crystallography
    • Molecular Biology
    • Biochemistry

    Background:

    • Uridine derivatives are crucial in biological systems.
    • Understanding the structural nuances of modified nucleosides like 5-nitrouridine is key to their function.
    • Previous studies have explored related compounds, necessitating a detailed analysis of 5-nitrouridine.

    Purpose of the Study:

    • To elucidate the three-dimensional crystal structure of 5-nitrouridine.
    • To analyze the conformational aspects of the pyrimidine ring and ribose moiety.
    • To investigate the role of hydrogen bonding and intermolecular interactions in the crystal lattice.

    Main Methods:

    • X-ray diffraction analysis was employed to determine the crystal structure.
    • Detailed crystallographic analysis was performed to identify bond lengths, angles, and conformations.
    • Intermolecular interactions, including hydrogen bonds and stacking, were characterized.

    Main Results:

    • 5-nitrouridine exhibits a slightly non-planar pyrimidine ring in a shallow boat conformation.
    • The ribose moiety adopts a C3 -endo conformation with the base in an anti orientation.
    • Hydrogen bonding, particularly involving a water molecule, significantly influences the crystal packing and stabilization, with negligible base stacking.

    Conclusions:

    • The crystal structure of 5-nitrouridine provides insights into its molecular conformation and intermolecular interactions.
    • The observed hydrogen bonding network, including water mediation, is critical for stabilizing the structure.
    • Comparison with related compounds highlights unique structural features of 5-nitrouridine.

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