Fig. 5. The structure at the cleavage site of the PK hammerhead ribozyme, and comparison with the corresponding structure in the pistol ribozyme.

A The PK hammerhead structure. The red broken line indicates the direction of attack by the O2’ nucleophile. G12 is well placed to act as general base to remove the proton from the nucleophile, while G8 is positioned to act as general acid using its O2’ to protonate the O5’ leaving group, at a distance of 2.9 Å. The electron density is shown as the 2F_o-F_c map contoured at 2.5 σ. B The pistol ribozyme structure. G32 is reoriented such that the O2’ - O5’ distance is 4.7 Å.