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Protein Science, Vol 3, Issue 7 1031-1039, Copyright © 1994 by Cold Spring Harbor Laboratory Press

ARTICLE

Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme

X. J. ZHANG and B. W. MATTHEWS
Institute of Molecular Biology, Howard Hughes Medical Institute and Department of Physics, University of Oregon, Eugene, Oregon 97403

Solvent-binding sites were compared in 10 different crystal forms of phage T4 lysozyme that were refined using data from 2.6 A to 1.7 A resolution. The sample included 18 crystallographically independent lysozyme molecules. Despite different crystallization conditions, variable crystal contacts, changes due to mutation, and varying attention to solvent during crystallographic refinement, 62% of the 20 most frequently occupied sites were conserved. Allowing for potential steric interference from neighboring molecules in the crystal lattice, this fraction increased to 79% of the sites. There was, however, no solvent-binding site that was occupied in all 18 lysozyme molecules. A buried double site was occupied in 17 instances and 2 other internal sites were occupied 15 times. Apart from these buried sites, the most frequently occupied sites were often at the amino-termini of {alpha}-helices. Solvent molecules at the most conserved sites tended to have crystallographic thermal factors lower than average, but atoms with low B-factors were not restricted to these sites. Although superficial inspection may suggest that only 50-60% (or less) of solvent-binding sites are conserved in different crystal forms of a protein, it appears that many sites appear to be empty either because of steric interference or because the apparent occupancy of a given site can vary from crystal to crystal. The X-ray method of identifying sites is somewhat subjective and tends to result in specification only of those solvent molecules that are well ordered and bound with high occupancy, even though there is clear evidence for solvent bound at many additional sites. Because similar sites are occupied under a variety of crystallization conditions, it seems likely that binding of solvent to such sites will be maintained in solution under physiological conditions.
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