Figure 3. Metal binding and putative carbohydrate binding sites.

A) Ca²⁺ site (green sphere) superimposed with an anomalous difference density map (3σ contour level) calculated with in-house diffraction data (CuKα radiation). Metal-ligand interactions are indicated with distances in units of Å. B) σ_A-weighted F_o−F_c difference density map (3σ contour level) of the Ara(1→5)Ara-O-C8 binding site calculated with phases and calculated amplitudes F_c of the model coordinates prior to incorporation of the ligand. Two symmetry-related molecules are shown (yellow and pink sticks, respectively). Primed residue numbers refer to the symmetry mate. C) Identification of putative carbohydrate binding sites in subdomain II by superimposing EmbC^CT with carbohydrate–bound structural homologues. Ligands (shown as stick models) were drawn according to the DALI-alignment with the Cα-traces of structural neighbours. Ligand structures shown in this diagram encompass PDB entries 1ux7, 1w9t, 1o8s, 1w9w, 1uy2, 1od3, 2vzq, 2w47, 2w87, 2cdp, 2cdo, 1uyy, 1uy0, representing the top 10 matches of the DALI search against the PDB90 subset (chains that are less than 90% identical in sequence to each other; Z-scores 6.9–6.3, RMSD 3.0–3.6 Å).