Figure 2 - full size



	Figure 2 - full size

Figure 2.
Figure 2: Stereo views of the APE1 complex with AP-DNA showing double-loop penetration of the DNA helix, plus charge and surface complementarity. a, DNA (top) binding to APE1 (bottom) from the co-crystal structure of APE1 bound to the 11-bp abasic DNA. The complex is viewed from the side that is roughly perpendicular to the kinked DNA helix axis oriented with the AP strand running 5' (left) to 3' (right), and shows the two central, six-stranded APE1 -sheets (orange arrows), - and 3[10] -helices (blue coils), and coils (green tubes). Five APE1 DNA-binding regions (yellow; residues 73-79, 126-129, 174-178, 221-228 and 268-272) contact both the AP-DNA strand (pink carbon polytubes and transparent surface) and the opposing strand (orange polytubes and surface). The position of the divalent metal ion (green sphere) which is 5' of the AP site as derived from the ternary product complex, and the side chains for key residues are shown. b, DNA binding to APE1 viewed looking down on the enzyme-DNA interface, rotated 90^° from the view in a. Arg 177 penetrates the DNA major groove (bottom) and Met 270 inserts through the DNA minor groove (top), capping the DNA-bound APE1 active site. The APE1-bound DNA, which is bent 35^ ° with the helix axis kinked 5Å, complements the positively charged DNA-binding surface of APE1, coloured red (-1.5 kT e^ -1) to blue (+1.5 kT e^-1) according to its electrostatic potential (calculated including the Mn2+ ion), which engulfs the AP-DNA strand (pink) around the flipped-out AP site.