Fig. 4

Structures of APE1 bound to a 3ʹ mismatched base exo product and a matched DNA substrate. a APE1 exo C/T mismatched product complex. 2F_o–F_c map density (1σ) is shown in light blue. Positive (green) and negative (red) omit map densities are shown 4 Å from the 3′-OH at +3 and −3σ, respectively. b APE1 exo C/G match substrate complex. The base pairing interaction for the C/G base pair is shown as dashes. 2F_o–F_c map density (1σ) is shown in light blue. c APE1 exo C/G match substrate complex in surface representation. The 5′-P is highlighted in red. d Overlay of the APE1 substrate complex with a C/T mismatch and C/G match at the 3ʹ end of a nick with DNA in yellow and cyan, respectively. Protein is from the 3′ mismatched structure and is shown in surface representation. The shift in location of the cleavage sites between the mismatched and matched structures is indicated by an arrow. For each structure, waters are shown as blue spheres and key residues, the site of cleavage, and distances (Å) are indicated