Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents
Anke Gelbin(Czech Academy of Sciences, J. Heyrovský Institute of Physical Chemistry), Bohdan Schneider(Czech Academy of Sciences, J. Heyrovský Institute of Physical Chemistry), Lester Clowney(Rutgers, The State University of New Jersey), Shu-Hsin Hsieh(Rutgers, The State University of New Jersey), Wilma K. Olson(Czech Academy of Sciences, J. Heyrovský Institute of Physical Chemistry), Helen M. Berman(Czech Academy of Sciences, J. Heyrovský Institute of Physical Chemistry)
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Abstract
A statistical survey of the torsion angles, bond angles, and bond lengths in the sugar and phosphate groups of well-refined mononucleoside, mononucleotide, dinucleoside monophosphate, and trinucleoside diphosphate crystal structures contained in the Cambridge Structural Database and the Nucleic Acid Database is reported. The mean values of the geometrical parameters in these structures and their estimated standard deviations are separated according to their chemistry and conformation. These new parameters serve as a basis for a dictionary of standard nucleic acid geometry.
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