Quinolones are widely studied antibacterial agents that act by forming a ternary complex with DNA and either one of the two essential type II bacterial topoisomerases: DNA gyrase and DNA topoisomerase IV. Inhibition of DNA replication is the resulting consequence. One of the unresolved issues concerning type II topoisomerases is their mode of interaction with quinolones. The aim of this research was to study the quinolones binding mechanism and resistance. For this purpose, two crystallographic structures (PDB codes 3k9f and 2xkk) of DNA-DNA topoisomerase IV complexed with a quinolone (levofloxacin and moxifloxacin respectively), were used. Mutant complexes were modeled to reflect known single mutations, S79A, D83Y, K137N and the double mutation S79A+D83Y. These mutations are known to confer resistance to quinolones. Molecular docking calculations of 15 quinolones (including ciprofloxacin, gatifloxacin, gemifloxacin, clinafloxacin, moxifloxacin, sitafloxacin, ofloxacin, levofloxacin, prulifloxacin, garenoxacin, grepafloxacin, trovafloxacin, sparfloxacin, temafloxacin and tosufloxacin) were performed using the crystal structures and modeled complexes of mutants. Furthermore, to get insight into the binding process, molecular docking calculations were also performed on DNA and protein separately. From the results of the calculations, the binding affinities of quinolones were found to be higher in wild type complexes structures than in modeled mutant complexes, protein or DNA structures. These results are similar to published experimental work that showed quinolones prefer binding to the DNA-protein complex than to DNA or protein. From the docking results we were able to explain interactions between quinolones and key protein residues and explain how mutations in these residues will result in resistance. The residues involved in chromosomal mutations are interacting with the drug moieties (carboxylate and ketone) that are essential for binding and quinolones activity and thus can not be substituted. We have suggested several structural substitutions for new and improved quinolones. Finally, by comparing the different crystal, docked and modeled structures, docking scores and other published studies on quinolone binding model, we were able to provide an insight into the complex formation. We suggest that the binding of DNA to the enzyme generates a structural perturbation that originates the binding site for the quinolones. In turn the quinolones stabilize the DNA-enzyme complex, with a significant increase in the likehood of a double stranded DNA break that is the presumed cytotoxic effect.