(A) SmYrbA crystal structure. It exhibits an α/β-topology composed of three β-strands and four helices as shown by the cartoon representation. There are two metal-binding sites pointed by spheres, one is filled by lithium and the other occupied by Ni, Co or Cu is referred to as M. Residues involved in metal binding are modeled as sticks: Asp²⁵, Leu²⁶, Asp²⁹ for lithium and His³² and His⁶⁷ for the other metals. (B) Electron density around the cobalt, nickel and copper binding sites (from left to right) in SmYrbA X-ray structures. SmYrbA metal binding site involved His³² and the invariant His⁶⁷ residues (shown as sticks). The metal ion and water molecules are shown as spheres. The maps shown are σ_A-weighted 2mF_o–DF_c maps contoured at 1.2σ (0.62, 0.82 and 1.04 e.Å⁻³, for SmYrbA–Co, SmYrbA–Ni, and SmYrbA–Cu, respectively). (C) X-ray fluorescence spectra of SmYrbA crystals. The energies of the emitted fluorescence for SmYrb–Co, SmYrbA–Ni and SmYrbA–Cu are colored pink, green and orange, respectively. Characteristics Kα and Kβ X-ray emission spectra are observed for copper (8.06 and 8.89 keV), nickel (7.52 and 8.28 keV) and cobalt (6.97 and 7.50 keV) in SmYrbA–Cu, SmYrbA–Ni and SmYrbA–Co X-ray structures, respectively. (D) Jahn–Teller effect. In the octahedral complex, the nickel atom is equidistant from its ligands. In the case of the copper atom, the octahedral complex is distorted. The distortion takes the form of elongating the axial bonds between copper and the water molecules numbered 3 and 4. The other ligands are a little bit closer to the copper atom compared with the nickel coordination.