Structural characteristics of protein binding sites for calcium and lanthanide ions

Surveys of X-ray structures of Ca2+-containing and lanthanide ion-containin g proteins and coordination complexes have been performed and structural fe atures of the metal binding sites compared. A total of 515 structures of Ca 2+-containing proteins were considered, although the final data set contain ed only 44 structures and 60 Ca2+ binding sites with a total of 323 ligands . Eighteen protein structures containing lanthanide ions were considered wi th a final data set containing eight structures and 11 metal binding sites. Structural features analysed include coordination numbers of the metal ion s, the identity of their ligands, the denticity of carboxylate ligands, and the type of secondary structure from which the ligands are derived. Three general types of calcium binding site were identified in the final data set : class I sites supply the Ca2+ ligands from a continuous short sequence of amino acids; class II sites have one ligand supplied by a part of the amin o acid sequence far removed from the main binding sequence; and class III s ites are created by amino acids remote from one another in the sequence. Th e abundant EF-hand type of Ca2+ binding site was under-represented in the d ata set of structures analysed as far as its biological distribution is con cerned, but was adequately represented for the chemical survey undertaken. A turn or loop structure was found to provide the bulk of the ligands to Ca 2+, but helix and sheet secondary structures are slightly better providers of bidentate carboxylate ligation than turn or loop structures. The average coordination number for Ca2+ was 6.0, though for EF-hand sites it is 7. Th e average coordination number, of a lanthanide ion in an intrinsic protein Ca2+ site was 7.2, but for the adventitious sites was only 4.4. A survey of the Cambridge Structural Database showed there are small-molecule lanthani de complexes with low coordination numbers but it is likely that water mole cules, which do not appear in the electron density maps, are present for so me lanthanide sites in proteins. A detailed comparison of the well-defined Ca2+ and lanthanide ion binding sites suggests that a reduction of hydrogen bonding associated with the ligating residues of the binding sites contain ing lanthanide ions may be a response to the additional positive charge of the lanthanide ion. Major structural differences between Ca2+ binding sites with weak and strong binding affinities were not obvious, a consequence of long-range electrostatic interactions and metal ion-induced protein confor mational changes modulating affinities.