Figure 4. The proposed structure of the active site of the pistol ribozyme.

This is derived from the crystal structure of the ribozyme ⁵¹. G40 acts as a general base, accepting a proton at N1 from the O2′ nucleophile. The green sphere is a Mg ²⁺ ion that is directly bound to N7 of the guanine nucleobase. The red spheres are inner-sphere water molecules, the positions of which have been modeled to maximize interactions with the RNA. The water molecule apical with N7 is well positioned to act as a general acid, protonating the O5′ leaving group.