Zinc(II)-beta-lactamases are among the latest generation of antibiotic-resistant enzymes developed by bacteria against beta-lactams. Here we have used density functional theory to provide the full structure of the catalytic site from Bacillus cereus mononuclear beta-lactamase II. Calculations are carried out on relative large models built on the X-ray structure of the free enzyme at the highest available resolution (1.7 A, PDB entry 3BC2). The most stable conformation emerging from our calculations consists of a Zn(II)-bound hydroxide, which acts as nucleophilic agent in the enzymatic reaction, highly stabilized by a complex hydrogen-bond network, in which the protonation state of Asp90 plays a major role. The pattern differs from that previously proposed on the basis of smaller models. Furthermore, the calculations confirm that Arg91 contributes to determine the orientation and the protonation state of Asp90, as recently suggested by mutagenesis experiments.