Proton transfer to calcium channels results in rapid fluctuations between two non-zero conductance levels when the current is carried by monovalent cations. A combination of site-directed mutagenesis and single-channel recording techniques were used to identify the unique proton acceptor site as Glu-1086, a conserved glutamate residue located in the S5-S6 linker of motif III of calcium channels. Glu-1086 is part of an array of four glutamate residues in the pore-lining region of the channel conferring the high selectivity of calcium channels. Titration of Glu-1086 yielded a pKa value of 7.91 which is different from that expected for a free glutamic acid side-chain carboxyl. Proposed electrostatic interactions between charged nearby residues can account only in part for this phenomenon since individual elimination of the other three glutamate residues only slightly decreased the pKa of Glu-1086. These data, in addition to identifying the proton acceptor site, provide evidence for the influence of the microenvironment in forming the asymmetry of the conducting pathway of calcium channels.