Fig. 5: Asymmetry of compound binding correlates with an asymmetry of catalytic pocket configuration. | Nature Communications

Fig. 5: Asymmetry of compound binding correlates with an asymmetry of catalytic pocket configuration.

From: Potent DNA gyrase inhibitors bind asymmetrically to their target using symmetrical bifurcated halogen bonds

Fig. 5

a Superimposition of the two 5′ DNA strands with the tower domain and the WHD domain as references. For clarity only, the phosphate and ribose backbone is shown. This shows the two configurations (A and B) adopted by the metal (see inset). On one side, the A metal contacts the scissile phosphate. On the other side, the scissile phosphate is away from the metal, which is in the B configuration. The superimposition also shows the shifting of the phosphate from nucleotide +1 (scissile phosphate) to +4, around the compound (red arrows). b The shifting of the phosphate position correlates with a rotation of the bases around the double-helix axis observed only for two nucleotides on each side of the compound. One DNA strand is coloured in green, the complementary strand in tan, while O, N, and P are colour coded by element.

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