Cavities in proteins: structure of a metmyoglobin-xenon complex solved to 1.9 A

X-ray crystallographic data to 1.9-A resolution were collected on sperm whale metmyoglobin equilibrated with 7 atm of xenon gas. The results indicate four xenon sites of occupancy from 0.45 to 1.0. These sites are located in interior spaces or packing defects of the myoglobin molecule. The effects of the bound xenon on the protein structure are minor, and we observe a small overall reduction in refined isotropic atomic protein temperature factors. We interpret the results as a confirmation that, on a time-averaged basis, cavities exist within the myoglobin molecule and suggest that the binding of small ligands in these cavities affects the internal motions and conformational substrates of the protein.