The phenanthroline bridging polyaza ligands L1, L2 and L3 can selectively and strongly bind nucleotides at physiological pH, and hence accelerate the hydrolysis rate of the bound ATP. It is interesting that a phosphoramidate intermediate at 2.88ppm (should be added 5.63ppm when compared with other models) was found in the hydrolysis process of L/ATP. By introduction of metal ions (critical Zn2+ or hard Mg2+, Ca2+) to the L/ATP system, recognition of the anionic substrates by the protonated ligands was greatly promoted. However, due to the different affinities of metal ions to the receptor and the substrate, ATP hydrolysis in Zn2+/L/ATP system and Mg2+ (Ca2+)/L/ATP system occurs through different mechanisms. By comparison with the M/ATP (M=Zn2+, Mg2+, Ca2+) system, the rates of ATP-hydrolysis in the Mg2+Ca2+/L/ATP system and the Zn2+/L/ATP system were enhanced and retarded, respectively. Moreover, the reasons contributing to large rate range of the L/ATP systems and M2+/L/ATP systems were given. The results show that metal ions vertically regulate the recognition and hydrolysis of ATP. On the other hand, water molecule participates in the hydrolysis reactions at different steps with different functions in the L/ATP systems and M (Zn2+, Mg2+, Ca2+) L/ATP systems.