Phosphoryl transfer is a fundamental reaction in cellular signaling and metabolism that requires Mg as an essential cofactor. While the primary function of Mg is electrostatic activation of substrates, such as ATP, the full spectrum of catalytic mechanisms exerted by Mg is not known. In this study, we integrate structural biology methods, molecular dynamic (MD) simulations, phylogeny, and enzymology assays to provide molecular insights into Mg-dependent structural reorganization in the active site of the metabolic enzyme adenylate kinase. Our results demonstrate that Mg induces a conformational rearrangement of the substrates (ATP and ADP), resulting in a 30° adjustment of the angle essential for reversible phosphoryl transfer, thereby optimizing it for catalysis. MD simulations revealed transitions between conformational substates that link the fluctuation of the angle to large-scale enzyme dynamics. The findings contribute detailed insight into Mg activation of enzymes and may be relevant for reversible and irreversible phosphoryl transfer reactions.