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The crystal structure of the mesophile Bacillus subtilis adenylate kinase (AKsub) with bound Mg²⁺Ap5A has been solved to resolution of 1.9 Å, and compared with that of the thermophilic Bacillus stearothermophilus adenylate kinase (AKste, PDB code: 1ZIO). The structures of the enzymes are very similar to each other except for the position of the LID domain which is fully closed in AKsub but is partially open in AKste. Both enzymes have a structural zinc ion in their LID domains, and the zinc ion in AKsub is ligated to three Cys and one Asp, which is a novel zinc coordination. The AKsub structure shows six coordinate octahedral geometry for bound Mg²⁺ with four water and two phosphate oxygen ligands. Despite possessing 74% sequence identity, AKsub and AKste exhibit significantly different thermal stabilities. To study the determinants of thermostability, several structural features including ion pairs, hydrogen bonds, packing density, surface to volume ratio and buried surface area are compared between the enzymes. From their difference in ion pairs, electrostatic interaction is proposed to be primarily responsible for the disparate thermostabilities. The thermophilic AKste has additional attractive ion pairs bridging two distant regions of polypeptide while the mesophilic AKsub has repulsive ion pairs destabilizing the structure at high temperature.