The binding mechanism of Mg 2+ at the M3 site of human placental alkaline phosphatase was found to be a slow-binding process with a low binding affinity (K Mg(app.) ס 3.32 mM). Quenching of the intrinsic fluorescence of the Mg 2+ -free and Mg 2+ -containing enzymes by acrylamide showed almost identical dynamic quenching constant (K sv ס 4.44 ± 0.09 M −1 ), indicating that there is no gross conformational difference between the M3-free and the M3-Mg 2+ enzymes. However, Zn 2+ was found to have a high affinity with the M3 site (K Zn(app.) ס 0.11 mM) and was observed as a time-dependent inhibitor of the enzyme. The dependence of the observed transition rate from higher activity to lower activity (k obs ) at different zinc concentrations resulted in a hyperbolic curve suggesting that zinc ion induces a slow conformational change of the enzyme, which locks the enzyme in a conformation (M3Ј-Zn) having an extremely high affinity for the Zn 2+ (K* Zn(app.) ס 0.33 M). The conformation of the M3Ј-Zn enzyme, however, is unfavorable for the catalysis by the enzyme. Both Mg 2+ activation and Zn 2+ inhibition of the enzyme are reversible processes. Structural information indicates that the M3 site, which is octahedrally coordinated to Mg 2+ , has been converted to a distorted tetrahedral coordination when zinc ion substitutes for magnesium ion at the M3 site. This conformation of the enzyme has a small dynamic quenching constant for acrylamide (K sv ס 3.86 ± 0.04 M −1 ), suggesting a conformational change. Both Mg 2+ and phosphate prevent the enzyme from reaching this inactive structure. GTP plays an important role in reactivating the Zn-inhibited enzyme activity. We propose that, under physiological conditions, magnesium ion may play an important modulatory role in the cell for protecting the enzyme by retaining a favorable geometry of the active site needed for catalysis.Keywords: Slow binding; magnesium ion; zinc ion; enzyme regulation; alkaline phosphatase Alkaline phosphatase (EC 3.1.3.1) is a substrate nonspecific phosphomonoesterase, which exists in almost all living forms, from bacteria to human (McComb et al. 1979). It is an enzyme well known for its clinical and diagnostic applications (McComb et al. 1979). However, the physiological role of the enzyme has not been fully elucidated. The crystal structure of the Escherichia coli alkaline phosphatase was first solved by Sowadski et al. (1985) and has been refined Reprint requests to: Dr. Hui-Chih Hung, Department of Biochemistry, National Defense Medical Center, P.O. Box 90048-501 (Neihu), Taipei 114, Taiwan, Republic of China; e-mail: ibio33@ndmctsgh.edu.tw; fax: 886-2-2933-9996.Abbreviations: GdmCl, guanidinium chloride; M3-Mg enzyme (M1,M2-Zn/M3-Mg), native human placental alkaline phosphatase with the M1 and M2 metal sites occupied by Zn 2+ and M3 site by Mg 2+ ; M3-free enzyme (M1,M2-Zn/M3-free), the enzyme with the M1 and M2 metal sites occupied by Zn 2+ but M3 site is free; M3Ј-Zn enzyme (M1,M2,M3Ј-Zn), inactive enzyme with all metal sites oc...