Fig. 5.

Mechanism of catalysis. (A) The distances among the proposed catalytic residues are optimal for potential shuttling of the protons. (B) Proposed mechanism of religation involving residues E9, D111, and H365. (C) The side chains of D111 and D113 are about 5 Å away from the scissile phosphate and +1 position phosphate, respectively. The distances can accommodate two magnesium ions. (D) Proposed function of magnesium ions. The two magnesium ions coordinate with phosphates as well as the 3′-hydroxy group (after cleavage) to hold the DNA chains in position for catalysis.