Figure 4.

A snapshot of the active site of the hammerhead ribozyme after 600 ps of total simulation time displaying a NAC. The attack angle and attack distance in this snapshot are 164° and 3.23 Å, respectively. The 2′-hydroxyl and the pro-R phosphate oxygen remained coordinated to the Mg²⁺ ion while the stacking of the bases at the active site were altered somewhat (compare with Fig. 2). Here, the H1 of Wat2447 is 2.01 Å from the 5′-oxygen of residue A_1.1. A sodium counter ion has migrated to this region and is 2.76 Å from the Wat2447 oxygen and 3.98 Å from the leaving group oxygen.