Figure 2:

Associative transphosphorylation mechanism catalyzed by the hammerhead ribozyme and the three reaction coordinates used to represent progression of the general base (ξ_GB), phosphoryl transfer (ξ_PT), and general acid (ξ_GA) steps. Atoms in QM and MM regions are shown as black and gray, respectively. Although not shown in the scheme to avoid crowding, the QM region additionally includes the sugar of G12, and four waters three of which coordinate the Mg²⁺.