To resolve this apparent discrepancy, we measured equilibrium binding and hydrolysis of MgTNP-ATP under identical conditions, using Y331W mutant Escherichia coli F 1 -ATPase, in which the genetically engineered tryptophan provides a direct fluorescent probe of catalytic site occupancy. We found that MgTNP-ATP hydrolysis at V max rate did require filling of all three catalytic sites, but in contrast to the situation with MgATP, "bisite hydrolysis" of MgTNP-ATP amounted to a substantial fraction (ϳ40%) of V max .Binding of MgTNP-ATP to the three catalytic sites showed strong binding cooperativity (K d1 < 1 nM, K d2 ؍ 23 nM, K d3 ؍ 1.4 M). Free TNP-ATP (i.e. in presence of EDTA) bound to all three catalytic sites with lower affinity but was not hydrolyzed. These data emphasize that the presence of Mg 2؉ is critical for cooperativity of substrate binding, formation of the very high affinity first catalytic site, and hydrolytic activity in F 1 -ATPases and that these three properties are strongly correlated.