The geometry of metal–ligand interactions relevant to proteins

Abstract

Geometrical data which could be of relevance in the structure determination, structure re®nement, assessment or understanding of metalloproteins have been extracted from the Cambridge Structural Database (CSD). The CSD contains crystallographic data from`small-molecule' structures determined by X-ray or neutron diffraction to an accuracy much better than that of most current protein structure determinations. The structures selected have a crystallographic R factor 0.065 and contain Ca, Mg, Mn, Fe, Cu or Zn interacting with ligands which are analogues of the amino-acid side chains commonly found in proteins; they include carboxylate groups, alcohols, phenolates, thiolates, imidazole groups and also water molecules. For each pair, the mean metal±donor-atom distance, the sample standard deviation and the range of observed values are tabulated, using $4500 observations in all. Where practicable, subsets with different coordination numbers and/or oxidation states are given. Also included are inter-bond angles at the ligand donor atom, the orientation of carboxylate and imidazole groups with respect to the metal± donor-atom bond and some other aspects of ligand geometry. Thus, for example, target distances and their standard deviations could be easily looked up for the validation of a metalloprotein structure or for use in restrained re®nement with low-resolution data.

The X-ray Structure of Human Mannan-binding Lectin-associated Protein 19 (MAp19) and Its Interaction Site with Mannan-binding Lectin and L-ficolin

“…3). The bond distances are in average 2.4 Å, consistent with the value determined for known Ca 2ϩ -binding sites (32). The coordination involves the same protein ligands in molecule B, but the water molecule is missing.…”

Altered Active Site Flexibility and a Structural Metal-binding Site in Eukaryotic dUTPase

“…6A) (25). In this niche, the metal ion coordinates to aspartate residues and to structural water molecules that provide six ligands in the metal coordination sphere in the hexagonal geometry that is generally preferred for divalent metal ions in proteins (64). In the structure of dUTPase from equine infectious anemia virus, a close lentiviral relative of FIV lentivirus, however, no such Mg 2ϩ binding is observed.…”

Data mining of metal ion environments present in protein structures

“…It is easier to generalize coordination properties of the imidazole and sulfur classes of metal ions in metalloproteins (Mn, Co, Fe, Ni, Zn, Cu) especially if the oxidation and spin states of the metal ion are taken into account. The coordination geometry preferences for some of these metal ions have been described previously [6,21].…”

“…Alkaline earth cations such as calcium and magnesium are relatively easy to identify in electron density as the geometrical parameters (e.g. bond lengths and coordination number) of their binding sites are very well characterized [5][6][7][8]. Alkali metal ions such as sodium and potassium, however, are more difficult to identify because their coordination spheres are not as regular as those of alkaline earth metal ions [9].…”

“…Studies describing the geometry of metal ion-binding sites within proteins and in small molecule structures were recently extensively discussed in a series of papers by Harding [5][6][7][8][9]11]. Here, in contrast, our objective is to analyze the properties of metal ion binding sites in protein structures as a function of structure resolution and crystallographic methodology.…”