Calcium Ion Coordination:  A Comparison with That of Beryllium, Magnesium, and Zinc

Abstract

The coordination geometry of divalent calcium ions has been investigated by analyses of the crystal structures of small molecules containing this cation that are found in the Cambridge Structural Database, protein crystal structures in the Protein Databank, and by ab initio molecular orbital calculations on hydrated structures of the form Ca‚mH 2 O, in which there are n water molecules in the first coordination shell and m water molecules in the second coordination shell (hydrogen bonded to water molecules in the first shell). Calcium ions in crystal structures generally bind to oxygen atoms in ligands (rather than any other element), and their preferred coordination numbers range from 6 to 8. In protein crystal structures the tendency of calcium to bind water molecules is less than for magnesium (1.5 versus 2.2 water molecules on the average per metal ion site, respectively). The ratio of bidentate to monodentate binding of calcium ions to carboxylate groups is similar for small molecules and protein structures in that no bidentate binding occurs if the coordination number of Ca 2+ is 6, but its occurrence rises to near 20% for coordination numbers 7 and 8. Complexes of the form Ca[H 2 O] 5 2+ ‚H 2 O and Ca[H 2 O] 4 2+ ‚2H 2 O were found (by ab initio molecular orbital calculations in Vacuo) to be significantly higher in energy than Ca[H 2 O] 6 2+ (by 8.2 and 15.0 kcal/mol, respectively). For Ca 2+ surrounded by seven or eight water molecules, the differences in energy between Ca[H 2 O] 6 2+ ‚H 2 O and Ca[H 2 O] 7 2+ and among Ca[H 2 O] 6 2+ ‚2H 2 O, Ca[H 2 O] 7 2+ ‚H 2 O, and Ca[H 2 O] 8 2+are extremely small when diffuse functions are included in the basis set. Thus, the net energy penalty for changing the number of water molecules in the first coordination shell between 6 and 8 is small. Molecular orbital calculations also indicate that the effect of a calcium ion on the H-O-H angle to bound water is less (at normal coordination numbers) than that of magnesium, zinc, or beryllium.

Integrin Activation Dynamics between the RGD-binding Site and the Headpiece Hinge

“…Bidentate coordination is known to be a characteristic feature of Ca 2ϩ ions, relative to Mg 2ϩ (25), and this distinction was consistently displayed in all of our MD and SMD simulations (17). While the preferred number of atoms coordinating Mn 2ϩ or Mg 2ϩ in integrin crystal structures is six, the preferred coordination number of the Ca 2ϩ ion occupying the ADMIDAS is seven (11,12).…”

Crystal structure of calcium dodecin (Rv0379), from Mycobacterium tuberculosis with a unique calcium‐binding site

“…2(b)]. [18][19][20][21] The angle (O-Ca-O) between two Ca-O bonds in Glu18 carboxylate, 49.6 to 52.2 , supports the reported value of $50.0 for bidentate binding. 18,21 Also, the angles of Ca-OE 1,2 -C c , 87-98 , in the Glu18 carboxylate are closer to the values known in other small molecule calcium chelating complexes (80 -100 ), and are unlike the values for monodentate ligands which range between 110 -140 .…”

The Crystal Structure of the Lipid II-degrading Bacteriocin Syringacin M Suggests Unexpected Evolutionary Relationships between Colicin M-like Bacteriocins

“…Finally, the metal ion has a coordination number of 8. This coordination is common for Ca 2ϩ but is not favored by Mg 2ϩ , which rarely has a coordination number higher than 6 (44,45). The presence of this active site metal ion, which is absent in the colicin M structure, probably orientates the side chain of Asp-232 close to the side chains of the other putative active site residues.…”