Intermetallic compounds offer unique opportunities for atom-by-atom manipulation of catalytic ensembles through precise stoichiometric control. The [Pd, (M), Zn] γ-brass phase allows for controlled synthesis of Pd-M-Pd catalytic sites (M = Zn, Pd, Cu, Ag and Au) isolated in an inert Zn matrix. These multi-atom heteronuclear active sites are catalytically distinct from Pd single atoms and fully coordinated Pd. We quantify the unexpectedly large effect of active site composition (i.e., identity of M atom in Pd-M-Pd sites) on ethylene selectivity during acetylene semi-hydrogenation. Subtle stoichiometric control demonstrates Pd-Pd-Pd sites are active for ethylene hydrogenation, whereas Pd-Zn-Pd sites show no measurable ethylene to ethane conversion. Agreement between experimental and density functional theory predicted activities and selectivities demonstrates precise control of Pd-M-Pd active site composition. The diversity and well-defined structure of intermetallics can be utilized to design active sites assembled with atomic-level precision.