Figure 1. The mechanism of the first splicing step by hydrolysis.

The Oi5eD1-5 ribozyme solved in the presence of K⁺/Ca²⁺ at 3.1 Å resolution (left). The inset shows a magnification into the active site (distances are depicted as black dotted lines and are indicated in angstroms). Two divalent ions (M1 and M2, yellow spheres) and two monovalent ions (K1 and K2, purple spheres) tightly coordinate the nucleotides involved in catalysis (sticks, color coded by atom type). The water molecule W1 (cyan sphere) is in an ideal position to perform a nucleophilic attack on the scissile phosphate (black arrows). Upon hydrolysis, the scissile phosphate swings out of the active site (semitransparent sticks and gray dotted arrow) to form an electrostatic interaction with K2 (gray dotted line). See also Figure S1.