Figure 2.

A snapshot of the active site of the hammerhead ribozyme in a NAC that developed after 100 ps of total simulation time. In this snapshot, the attack angle is 172° and the attack distance is 3.17 Å. The arrow shows the bond that is cleaved during the reaction. The Mg²⁺ ion was coordinated to the pro-R phosphate oxygen and the attacking 2′-oxygen. Notice the outer sphere water molecule (Wat3701) that is poised to donate a proton to the 5′-leaving group (Wat3701 H1 to A_1.1 O5′ distance is 2.32 Å). The H1 proton of the additional water molecule near the leaving group shown in this figure, Wat2821, is 2.27 Å from the 5′-oxygen but is not associated with a magnesium or counter ion.