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The properties of the mitochondrial F1FO‐ATPase catalytic site, which can bind Mg2+, Mn2+, or Ca2+ and hydrolyze ATP, were explored by inhibition kinetic analyses to cast light on the Ca2+‐activated F1FO‐ATPase connection with the permeability transition pore (PTP) that initiates cascade events leading to cell death. While the natural cofactor Mg2+ activates the F1FO‐ATPase in competition with Mn2+, Ca2+ is a noncompetitive inhibitor in the presence of Mg2+. Selective F1 inhibitors (Is‐F1), namely NBD‐Cl, piceatannol, resveratrol, and quercetin, exerted different mechanisms (mixed and uncompetitive inhibition) on either Ca2+‐ or Mg2+‐activated F1FO‐ATPase, consistent with the conclusion that the catalytic mechanism changes when Mg2+ is replaced by Ca2+. In a partially purified F1 domain preparation, Ca2+‐activated F1‐ATPase maintained Is‐F1 sensitivity, and enzyme inhibition was accompanied by the maintenance of the mitochondrial calcium retention capacity and membrane potential. The data strengthen the structural relationship between Ca2+‐activated F1FO‐ATPase and the PTP, and, in turn, on consequences, such as physiopathological cellular changes.

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