This image is just a residue of topoisomerase II (PDB 1BJT). This is the core that binds to and cleaves the DNA (residues 409-1201). The spaces where DNA fits are apparent in this structure. Because this is only a residue, this is all one chain.
This image is the same topoisomerase residue as above (PDB 1BJT), but here you can see the helices and sheets that make up this residue. Again, this is all one chain and the color represents that.
In this image (PDB 2RGR) we can see the same topoisomerase II residue as before, but now it is bound to the helical DNA (shown in pink and blue). Topoisomerase II helps relax super-coiling and repairs knots in the DNA by cutting through both strands and releasing tension.
This next image (PDB 2RGR) shows the residue that binds to the DNA and the DNA molecule as well. When the colors are sorted by chain, you can see the doubled-stranded helical DNA in pink and blue and the chain in green is the topoisomerase II.
In this final image (PDB 1BJT), we can see the topoisomerase II residue not bound to the DNA.
