Figure 5.

Proposed catalytic mechanism for bottom and top strand cleavage in the major catalytic pathway by I-SceI in which the bottom strand is cleaved first (based on the uncleaved DNA structure) followed by top strand cleavage (based on the nicked bottom strand structure). The metals are depicted by unfilled spheres and labeled 1–4. Ligated waters are depicted as black spheres. The putative nucleophilic water molecules are labeled as W25 (bottom strand cleavage) and W60 (top strand cleavage).