We reported recently that a lead ribozyme with modified bases cleaved at an additional site at high Pb2+ concentrations (> 0.1 mM), and that the cleavage at a canonical site was enhanced nearly fourfold at the optimum combination of Pb2+ and Mg2+ concentrations [Kim, M. H., Katahira, M., Sugiyama, T. & Uesugi, S. (1997) J. Biochem. (Tokyo) 122, 1062-1067]. Here we have identified two metal-binding sites (sites 1 and 2) of the lead ribozyme at the residue level by NMR. Both sites are located in an asymmetric internal loop of the lead ribozyme. Site 1 is composed of residues of an enzyme strand and site 2 of residues of a substrate strand. The two sites are bound to competitively by Pb2+ and Mg2+. It was revealed that at certain Pb2+ and Mg2+ concentrations, site 1 is occupied by Pb2+ and site 2 is occupied by Mg2+. The dependency of the cleavage at the canonical and other sites on the Pb2+ and Mg2+ concentrations is interpreted by considering the species of metal ions bound to the two sites. It is suggested that the addition of the two metal ions produces similar and different effects on the structure of the lead ribozyme, and the two metal ions have a synergistic effect on the structure.