The refined structure of ribonuclease-A at 1.45 Å resolution

Abstract

Features of the refined X-ray crystal structure of bovine pancreatic ribonuclease-A at 1.45 Å resolution are described. The positions of the protein atoms have been determined within the range 0.004–0.05 Å, and of solvent atoms, assumed to be oxygens, within the range 0.08–0.13 Å. The present model contains 127 solvent molecules, taken to be water, and a sulfate anion located in the active site. Mean square atomic displacement parameters,U _iso, refined for each atom, give an indication of the mobility of different parts of the structure. Main-chainU _iso values tend to be less than side-chain values, having an average value of 0.15 Ų compared to 0.25 Ų. Both main-chain and side-chain averageU _iso values tend to increase with distance from the center of gravity of the molecule. Side-chain averageU _iso values also tend to increase with the number of atoms in the side-chain, with different distributions for ring and chain type residues. Side-chain conformations have been analyzed and found on the whole to follow commonly observed distributions. A notable exception to this is the active-site residue His-119 which occupies two distinct sites. Apart from two small clusters of eight and seven atoms respectively, the solvent molecules are distributed in quite small numbers on the protein surface. The solvent clusters occur in the active-site region and, together with the sulfate anion, appear to stabilize residues in this region. Sixty-three solvent atoms have only one identified hydrogen bond contact. Of the rest, 36 form two, 22 form three, and 6 form four hydrogen bonds. There is a marked tendency for the mean square displacement parameter,U _iso, for the solvent atoms to be lower for atoms with many hydrogen bond contacts than for those with fewer contacts.