Zn2+ caused a noninhibitory binding of IF1 to mitochondrial membranes in both rabbit heart SMP and intact rabbit heart mitochondria. This Zn(2+)-induced IF1 binding required the presence of at least trace amounts of MgATP and was essentially independent of pH between 6.2 and 8.2. Addition of Zn2+ after the formation of fully inhibited IF1-ATPase complexes very slowly reversed IF1-mediated ATPase inhibition without causing significant IF1 release from the membranes. When Zn2+ was added during the state 4 energization of ischemic mitochondria in which IF1 was already functionally bound, it slowed somewhat energy-driven ATPase activation. This slowing was probably due to the fairly large depressing effect Zn2+ had upon membrane potential development, but Zn2+ did not decrease the degree of ATPase activation eventually reached at 20 min of state 4 incubation. Zn2+ also preempted normal IF1 release from the membranes, causing what little inhibitor that was released to rebind to the enzyme in noninhibitory IF1-ATPase complexes. The data suggest that IF1 can interact with the ATPase in two ways of through two kinds of sites: (a) a noninhibitory interaction involving a non-inhibitory IF1 conformation and/or an IF1 docking site on the enzyme and (b) an inhibitory interaction involving an inhibitory IF1 conformation and/or a distinct ATPase activity regulatory site. Zn2+ appears to have the dual effect of stabilizing the noninhibitory IF1-ATPase interaction and possibly a noninhibitory IF1 conformation while concomitantly preventing the formation of an inhibitory IF1-ATPase interaction and possibly an inhibitory IF1 conformation, regardless of pH. While the data do not rule out direct effects of Zn2+ on either free IF1 or the free enzyme, they suggest that Zn2+ cannot interact readily with either the inhibitor or the enzyme once functional IF1-ATPase complexes are formed.