In both cases, the metal ion is coordinated by side-chain nitrogen and oxygen atoms of four tetrahedrally arranged residues: His, His, Glu and Asp.
This is similar to the observation in Zn-specific Lbp, the zinc ion is coordinated by the side chains of three histidines and one glutamate in a slightly distorted tetrahedral geometry [28].
For instance, Angkawidjaja and colleagues reported that Ca2+ is coordinated by the side chains of Asp153, Asp157, and Gln120, and the carbonyl oxygens of Thr118 and Ser144 [30]; similarly, Declercq and coworkers show interaction between Ca2+ and the coordinating oxygen atoms of Asp51, Asp53, Ser55, Phe57, Glu59 and Glu62 [31].
We and others have determined high-resolution structures of both metallo- and non-metallo forms of KDO8PS [3], [4], [5], [6], [6], which revealed the features of the active site: in metal dependent KDO8PSs the divalent metal ion (Zn2+, or Fe2+, [7]) is coordinated by the side chains of a cysteine, a histidine, a glutamic acid, and an aspartic acid.
Zinc 2 is coordinated by the side chains of D120, C221 and H263 (Fig. 1).
For example, a shift from 1700 to 1689 cm 1 would be consistent with a Na+ coordinated by a side chain C=O group, e.g., from Asn112 near the Schiff base.
ClAS is coordinated by the side chain atoms of T96, R158, and T153, as well as the backbone atoms of T96 and Y95 and a water molecule.
Both copies of the molecule bind a single Ca2+ ion, coordinated by the side chains of Asp72 (OD1) and Asp140 (OD1 and OD2) and the main-chain carbonyl of Ser141.
The process of sorbitol oxidation by human SDH requires a catalytic zinc atom which is coordinated by the side chains of three amino acids (44C, 69H, 70E, numbering in human SDH) and one water molecular.
The putative fluoride anion is coordinated by the side chains of Aspa27, Hisa114, and Thra72, the backbone NH group of Aspa27, and a water molecule that also contacts the triazole N2 atom and Glub473.
As mentioned briefly above, the bridging site is located between two YjiA protomers on a noncrystallographic 2-fold symmetry axis, with Zn II) coordinated by the side chains of E74 and H114 from both protomers in an approximate tetrahedral geometry.
