The structure of the methyl-alpha-D-mannopyranoside-LOL I complex has been solved by the molecular replacement method using the refined saccharide-free LOL I coordinates as starting model. The methyl-alpha-D-mannopyranoside-LOL I complex was refined by simulated annealing using the program X-PLOR. The final R-factor value is 0.182 [Fo greater than 1 sigma(Fo)]. The isostructural methyl-alpha-D-glucopyranoside-LOL I complex was refined by X-Ray coupled energy minimization using the methyl-alpha-D-mannopyranoside-LOL I structure as a starting model to an R factor of 0.179 (all data). In both crystal forms, each dimer binds two molecules of sugar in pockets found near the calcium ions. The two saccharide moieties, which are in the C1 chair conformation, establish the same hydrogen bond pattern with the lectin. However, the van der Waals contacts are different between the O2, C2, C6, and O6 atoms of the two molecules and the backbone atoms of residues 208-211. Mannose, due to its axial C2 conformation, encloses the backbone atoms of the protein in a clamplike way. Van der Waals energy calculations suggest that this better complementarity of the mannoside molecule with the lectin could explain its higher affinity for isolectin I.

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The relationships between the molecular packing and the morphology of rubredoxin crystals, a metalloprotein, have been studied in detail through the periodic bond chains (PBC) method of Hartman and Perdok (1955). To carry out the PBC analysis the authors considered that the crystallizing particle consisted of the protein molecule plus a tightly bound layer of solvent molecules. Molecular interactions such as hydrogen bonds, van der Waals contacts, ion pairs and hydrophobic free energy have been systematically analysed. In every case, they involved direct protein-protein and protein-solvent-protein contacts. The structure of the respective growth layers (slices) and of the PBCS has been determined with the help of molecular graphics. To get a quantitative insight into crystal packing forces they have estimated, for different faces, the interaction energy of the crystallizing particle with its nearest neighbours in the respective underlying growth layers. There is an inverse correlation between this energy and the morphological importance of the faces. The role of hydrogen bonding is also discussed.