Fig. 7. Modeling of a DNA fragment onto the Topo domain of NaeI. The NaeI dimer is shown in red and gold ribbons, whereas DNA in the ball-and-stick model is adopted from the CAP–DNA structure. Ser234 and Tyr44 (magenta balls) are two potential candidates to form a covalent phosphoester intermediate for the topoisomerase activity of the L43K mutant. Leu43 is also shown as magenta balls.