Nickel ions are the key element of metabolism in numerous lower organisms. They are required for the activity of nine enzymes, e.g. [NiFe] hydrogenase, which catalyzes the reversible oxidation of molecular hydrogen for energy production. Nickel homeostasis and nickel transport into the cell are strictly controlled. HupE is a transmembrane nickel transporter in Rhizobium leguminosarum hydrogenase system which has a conserved, periplasmic, N-terminal domain responsible for nickel binding. This work focuses on the interactions of this region with native Ni2+ and two other metal ions (Cu2+ and Zn2+), which might interfere with nickel binding to the HupE fragment. Metal coordination sites are assigned and thermodynamic parameters are discussed in detail in order to evaluate the potential effectiveness of different soil concentrations of Cu2+ and Zn2+ to displace Ni2+ from its binding site. At physiological pH, the coordination sphere of all three metal complexes consists of the imidazole and amine nitrogens of His1 (a histamine-like binding) and of the imidazole of His5. Cu2+ is able to displace Ni2+ from its binding site, while Zn2+ cannot, neither at equimolar concentrations, nor at soil metal concentrations at which Rhizobium leguminosarum numbers are expected to decrease by several orders of magnitude. (C) 2016 Elsevier B.V. All rights reserved.