Two molecules of the complex cis-[Pd(en)(H2O)(2)](2+) lose aqua ligands and bind to His5 and His9 residues in the nonadecapeptide that is the carboxy-terminal segment of the protein myohemerythrin. The known modes of palladium(II)-histidine coordination are detected by H-1 NMR spectroscopy. Only the [Pd(en)(H2O)](2+) group bound to His5 cleaves the polypeptide backbone; the group bound to His9 does not. Only the amide bond Val3-Pro4 is cleaved. This regioselectivity is attributed to electrostatic repulsion of the [Pd(en)(H2O)](2+) group by cationic lysine residues 6, 7, and 10 and the absence of repulsion by the residues "upstream" from His5. The polypeptide in a partially alpha-helical conformation and the tripeptide AcGly-Gly-His, which adopts many flexible conformations, are both cleaved at the second amide bond "upstream" from the histidine residue bearing the [Pd(en)(H2O)](2+) group. Moreover, the rate constants for the cleavages of these two peptides are virtually the same. Regioselectivity and kinetics of the cleavage of peptides by palladium(II) aqua complexes seems to be affected by the local secondary structure in the vicinity of the scissile bond. This study is a step toward our ultimate goal-design of artificial metallopeptidases.