Cavities and Atomic Packing in Protein Structures and Interfaces
Figure 12
Some examples of cavities with water molecules, cation and ligand.
The largest interface cavity (containing 56 water molecules, with a total volume of 2341 Å3 and Rvs of 0.5), in the homodimeric structure of 1oac is displayed in (A). Cavities with a large water content are also observed in dimeric interfaces: 1mor (46, 2202 Å3 and 0.5), 1chm (58, 1798 Å3, 0.3). PDB codes for cavities containing 10–20 water molecules are Ter_str (1cmb); Inter_H (1ade, 1b8j, 1bis, 1chm, 1mkb (2 cases), 1mor, 1oac, 1sox, 1utg and 5rub); Inter_C (1kz7). (B) shows a Ca2+ ion and a water (red) molecule in a cavity (volume: 17.2 Å3 and Rvs: 0.96) of 2scp. (C) shows α-d-glucose-6-phosphate and nine water molecules in a cavity (565.1 Å3 and 0.69) of 1mor.