The H V 1 voltage-gated proton (H V 1) channel is a key component of the cellular proton extrusion machinery and is pivotal for charge compensation during the respiratory burst of phagocytes. The best-described physiological inhibitor of H V 1 is Zn 2+. Externally applied ZnCl 2 drastically reduces proton currents reportedly recorded in Homo sapiens, Rattus norvegicus, Mus musculus, Oryctolagus cuniculus, Rana esculenta, Helix aspersa, Ciona intestinalis, Coccolithus pelagicus, Emiliania huxleyi, Danio rerio, Helisoma trivolvis, and Lingulodinium polyedrum, but with considerable species variability. Here, we report the effects of Zn 2+ and Cd 2+ on H V 1 from Nicoletia phytophila, NpH V 1. We introduced mutations at potential Zn 2+ coordination sites and measured Zn 2+ inhibition in different extracellular pH, with Zn 2+ concentrations up to 1000 lM. Zn 2+ inhibition in NpH V 1 was quantified by the slowing of the activation time constant and a positive shift of the conductance-voltage curve. Replacing aspartate in the S3-S4 loop with histidine (D145H) enhanced both the slowing of activation kinetics and the shift in the voltage-conductance curve, such that Zn 2+ inhibition closely resembled that of the human channel. Histidine is much more effective than aspartate in coordinating Zn 2+ in the S3-S4 linker. A simple Hodgkin Huxley model of NpH V 1 suggests a decrease in the opening rate if it is inhibited by zinc or cadmium. Limiting slope measurements and high-resolution clear native gel electrophoresis (hrCNE) confirmed that NpH V 1 functions as a dimer. The data support the hypothesis that zinc is coordinated in between the dimer instead of the monomer. Zinc coordination sites may be potential targets for drug development. Abbreviations Asp145, aspartate at position 145; g H,max , maximal proton conductance; g H,max /10, 10% of the maximal proton conductance; g H-V, proton conductance-voltage relationship; hH V 1, human voltage-gated proton channel; H V 1, voltage-gated proton channel 1; NpH V 1, Nicoletia phytophila voltage-gated proton channel 1; pH i , pH inside the cell; pH o , pH outside the cell; TM, transmembrane domain; TMA, tetramethylammonium; TSA, Transcriptome Shotgun Assembly; V rev , reversal potential; V threshold , threshold potential.