a, Prenyltransferase AmbP3. b, Human cytomegalovirus pUL50–pUL53 complex. For both examples, the overall structure is shown in cartoon representation in the top panel, highlighting the Lys–Cys linkage and providing the PDB code56,57. In the corresponding middle panels, the structure of the lysine–cysteine pair as deposited in the PDB is shown enlarged, including the calculated 2mFo − DFc (in blue, contour level 1σ) and mFo − DFc difference (in green, contour level 3σ) electron density maps. There is a pronounced positive difference peak in the electron density maps in between the lysine nitrogen atoms and the cysteine sulfur atoms, indicating the presence of a covalent bridge. In the bottom panels, the refined structural models that include the covalent lysine–cysteine NOS bridges are shown with the corresponding 2mF − DFc electron density maps. The mFo − DFc difference electron density maps are shown in green and are contoured at 3σ. The calculated occupancies of the NOS bridges amount to 62% (a) and 76% (b). The NOS bridge is prominently located at either the substrate binding site or the protein–protein binding interface.