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FIG. 1. Metal binding to ArsR and CadC produces derepression by different mechanisms. Derepression in ArsR is the result of a conformational change in the DNA binding domain by binding arsenic, while in CadC the DNA binding domain is shielded by the N terminus as a result of metal binding. (A) Least-squares overlap between models of the ${alpha}$ 3 helix of apo-ArsR and arsenic-bound ArsR based on the ${alpha}$ 3 helix of SmtB. The arsenic-bound model was made by adjusting the phi/psi angles of residues 32, 34, and 37 in a suitable position to bind arsenic with the bond distances of the S3 complex determined by X-ray absorption spectroscopy. The models predict that binding of arsenic would substantially distort the ${alpha}$ 3 helix such that it might not be able to bind to DNA. (B) Least-squares overlap between the crystal structure of apo-CadC (cyan) in which residue 11 was made a cysteine and a model with bound zinc (purple sphere) made by adjusting the phi/psi angles of the N-terminal residues to place Cys-7 and Cys-11 in a suitable position to bind zinc with Cys-58 and Cys-60 of the ${alpha}$ 4 helix according to the bond distances determined by X-ray absorption spectroscopy. The model was placed in a 9.8-nm box and solvated (simple point charge water model; solute-wall distance, 0.9 nm). The model was then energy minimized by steepest descents and subjected to a 20-ps relaxation "soak" with positional restraints (particle mesh Ewald electrostatics, Berendsen temperature/pressure coupling, Gromos 43A1 force field). This was followed by a 100-ps molecular-dynamics simulation in a completely free system. The model predicts that the conformation of the ${alpha}$ 4 helix is not substantially changed. On the other hand, there is a large difference in the buried area between the N terminus and the helix-turn-helix motif before (416 Å²) and after (675 Å²) zinc binding. The model suggests that ${alpha}$ 4 is shielded and may not be able to bind to DNA.

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