Ribonuclease A. Analysis of the hydrogen bond geometry, and spatial accessibility at the active site.
The hydrogen bonding of bovine ribonuclease A derived from the high resolution X-ray structure has been studied in detail. Correlations have been examined for main-chain-main-chain hydrogen bond angles, torsion angles and distances, respectively. Differences are found consistently for correlations associated with alpha-helix and beta-sheet, respectively. Ten of the 124 side-chains have four or more hydrogen bond contacts; two, including Glu-101, have five or more. Three potential C = O---H, three N---X and three potential side-chain H-bonds fail to form. A search for highly inaccessible buried residues resulted in nine outstanding examples, all of which are conserved across 38 known mammalian ribonuclease A sequences, indicating the importance of these residues for structural stability. Of the two histidines in the active site, His-12 has five hydrogen bonds and His-119 three. The conformational space accessible to these two catalytically important residues studied by means of simple non-bonded contact energy calculations confirms the existence of two alternative, interchangeable locations for His-119, while His-12 is locked in a local energy minimum.
D001665:Binding Sites; D003461:Crystallography; D006639:Histidine; D006860:Hydrogen Bonding; D010100:Oxygen; D011487:Protein Conformation; D012259:Ribonuclease, Pancreatic; D014867:Water; D014965:X-Rays
D014867:Water; D006639:Histidine; D012259:Ribonuclease, Pancreatic; D010100:Oxygen