The reaction center (RC) from Rhodobacter sphaeroides couples light-driven electron transfer to protonation of a bound quinone acceptor molecule, Q(B), within the RC. The binding of Cd(2+) or Zn(2+) has been previously shown to inhibit the rate of reduction and protonation of Q(B). We report here on the metal binding site, determined by x-ray diffraction at 2.5-A resolution, obtained from RC crystals that were soaked in the presence of the metal. The structures were refined to R factors of 23% and 24% for the Cd(2+) and Zn(2+) complexes, respectively. Both metals bind to the same location, coordinating to Asp-H124, His-H126, and His-H128. The rate of electron transfer from Q(A)(-) to Q(B) was measured in the Cd(2+)-soaked crystal and found to be the same as in solution in the presence of Cd(2+). In addition to the changes in the kinetics, a structural effect of Cd(2+) on Glu-H173 was observed. This residue was well resolved in the x-ray structure-i.e., ordered-with Cd(2+) bound to the RC, in contrast to its disordered state in the absence of Cd(2+), which suggests that the mobility of Glu-H173 plays an important role in the rate of reduction of Q(B). The position of the Cd(2+) and Zn(2+) localizes the proton entry into the RC near Asp-H124, His-H126, and His-H128. Based on the location of the metal, likely pathways of proton transfer from the aqueous surface to Q(B) are proposed.