A) Conserved topology of the common core and the most typical architecture of the active site in PD-(D/E)XK nucleases, B) Topological variation of the common fold found in the nuclease XPF (1j24), C) Extension of the common core and migration of the carboxylate residue (e.g. in NgoMIV, 1fiu), D) Different extension of the common core and migration of the lysine residue (e.g. in Tt1018, 1wjd). Helices are shown as circles, strands are shown as triangles (the orientation – up or down indicates the direction and the parallel/antiparallel character). The common core is shown in green/black, the variable elaborations are shown in red/white. The most common catalytic residues (known or putative) are indicated by letters in yellow boxes (E, D, and K), structurally important, semi-conserved P residue is also indicated.