Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin

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Abstract
The water structure has been analyzed for a model of the protein crambin refined against 0.945-Å x-ray diffraction data. Crystals contain 32% solvent by volume, and 77% of the solvent molecules have been located—i.e., 2 ethanol molecules and 64 water molecules with 10-14 alternate positions. Many water oxygen atoms found form chains between polar groups on the surface of the protein. However, a cluster of pentagonal arrays made up of 16 water molecules sits at a hydrophobic, intermolecular cleft and forms a cap around the methyl group of leucine-18. Several waters in the cluster are hydrogen-bonded directly to the protein. Additional closed circular arrays, which include both protein atoms and other water oxygen atoms, form next to the central cluster. This water array stretches in the b lattice direction between groups of three ionic side chains.