a The close-up view of the active site in mAPE1-recessed-dsDNA product complex, including the terminal of the dsDNA product, the RM bridge, and the product pocket. b Structural alignment of Arg176 and Met269 in apo- or DNA bound APE1 structures. The PDB entry of apo-APE1 structures are 1HD7, 4QHD, and 5CGF. c–e The close-up view of a normal cytosine base, an AP site analog, and a damaged 8-oxoG base in the product pocket. The cytosine coordinates are extracted from the hAPE1-mismatched dsDNA substrate complex structure (PDB entry: 5WN5). The AP site analog coordinates are extracted from the hAPE1 AP site analog-containing dsDNA complex structure (PDB entry: 5DFI). The coordinates of the damaged 8-oxoG base are generated by the molecular modeling conducted in this study.