Fig. 5.

Structure of APE1 poised to remove a 3ʹ-PG. a Schematic showing the structure of PG at the 3ʹ end of a DNA nick at neutral pH. b APE1 exo 3ʹ-PG substrate complex. 2F_o–F_c map density (1σ) is shown in light blue. The two 3ʹ-PG conformations are shown. c A close-up of the APE1 3ʹ-PG substrate complex active site. The protein side chains are shown in magenta and DNA residues in gray. Waters are shown as blue spheres and key residues, the site of cleavage, and distances (Å) are indicated. d An overlay of the 3ʹ-PG (magenta) substrate complex with the 3ʹ mismatched (yellow) substrate complex