Fig. 3

The APE1 exo substrate complex active site. a Focused view of the APE1 exo active site showing key residues, cleavage site, and nucleophilic water with distances (Å) indicated. b An alternative angle highlighting the nucleophilic water in position for attack of the phosphorus atom with the distance indicated. c The complete APE1 active site after soaking in MnCl₂, with key residues indicated. 2F_o–F_c map density (1σ) for mismatched C and the flanking base are shown in light blue. Anomalous map density (3σ) is shown for the MnCl₂ in purple. The protein side chains are shown in yellow and DNA residues in gray. Water molecules and Mn²⁺ are shown as blue and purple spheres, respectively