MβLs and some of their substrates. A.

<p>Zinc binding sites of B1 (CcrA), B2 (CphA with carbonate), B3 (L1) β-lactamases. Structural models are from PDB entries 1A7T, 1X8I, 2AIO. <b>B.</b> Two typical carbapenems: Imipenem (left), Biapenem (right). An asterisk marks the carbon atom that replaces the sulfur of penicillins. <b>C.</b> Active site of CphA in complex with a bicyclic form of hydrolyzed biapenem (PDB entry 1X8I). Zn²⁺ coordination and hydrogen bonds are shown as thin yellow lines and dashed blue lines. The two bonds formed during the rearrangement are shown as thin green lines. Biapenem numbering is in red with the exception of the hydrogen transferred from O62 to C2 during the rearrangement. Red and blue arrows indicate the dynamic constraints applied during QM/MM geometry optimization to reverse the rearrangement and generate the open-ring form shown in panel D. <b>D.</b> QM/MM optimized model of the CphA active site in complex with hydrolyzed biapenem: in this state both N4 and the C6 carboxylate are protonated (atoms HN4 and HO7). A water molecule hydrogen bonded to Asp120 and loosely coordinated to Zn²⁺ (2.9 Å, dashed yellow bond) is labeled Wat2 because it is near the Zn2 site (Panel A) and to distinguish it from a second water molecule (Wat1) that might be involved in the reaction. Zn²⁺ has only five strong ligands, in agreement with spectroscopic data <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055136#pone.0055136-Sharma1" target="_blank">[22]</a>.