Cobalt is an essential microelements in many biological processes involving enzymatic activity. We found that $Zn^{2+}$ and $Mg^{2+}$, which are in the active site of native calf intestine alkaline phosphatase (CIP), can be replaced by $Co^{2+}$ directly in solution. The effect of $Co^{2+}$ concentration on the substitution reaction was examined at ratios of [$Co^{2+}$]/[CIP] from 0:1 to 8:1. The quantity of $Zn^{2+}$ in CIP decreased progressively as the ratio was increased, but the amount of $Mg^{2+}$ changed in irrregular fashion. A series of active site models of the reaction mechanism of CIP are proposed. Low pH was found to promote the replacement of $Mg^{2+}$ by $Co^{2+}$. To understand how the substitution affects the enzyme, we also solved the secondary structure of CIP after reaction with $Co^{2+}$ in different conditions.