( A ) RMSD between Cα atoms of WHD in the simulation with reference to the crystal of drug-bound complex (hTopIIβ-t.c.; 3QX3), the non-covalent complex of IIα isozyme (hTopII... 003b1;; 4FM9), topoisomerase IV with the ‘resealed’ DNA (sTopIV; 3KSB), and the cleavage complex of yeast enzyme (yTopII-c.c.
(C) conformations of the gate-DNA in the representative snapshot from simulation UD1 (hTopIIβ-cc), the crystal of drug-bound topoisomerase II (hTopIIβ-tc; PDB code 3QX3), the pre-cleavage complex of yeast topoisomerase II (yTopII-pcc; PDB code 2RGR), and topoisomerase IV with the ‘resealed’ DNA (sTopIV; PDB code 3KSB).