Class A beta-lactamases are enzymes that hydrolyse beta-lactam antibiotics such as penicillins and cephalosporins. They also hydrolyse substrate analogues such as oxacillin and cloxacillin, with a biphasic kinetic as it has been reported for Bacillus cereus beta-lactamase. A molecular model of Bacillus cereus beta-lactamase was built and the conformational changes that the substrates benzylpenicillin and cloxacilline produced in the conformation of selected regions of the protein were analyzed. This study was performed using the docking of the substrates, their tetrahedral intermediates and the corresponding acids on the active site, followed by molecular dynamic and subsequent optimisation procedures. The most important changes were produced on Tyr105 and Tyr273, when the tetrahedral intermediate of cloxacillin was docked at the active site, these amino acids are partially responsible for the stabilisation of the substrates at the active site. These changes may explain the kinetic differences observed during the hydrolysis of substrates type S and type A by beta-lactamases class A.