Figure 5.

Thermodynamic cycle for calculating the electrostatic free energy difference associated with replacing potassium with nickel in the second metal-binding site. Numbers in circles delineate each structure in the pathway. Red rectangles represent the MBD, black triangles the RHH domains, and parallel green lines the DNA, and K⁺ ions are explicitly shown in purple. The Ni²⁺ ions are shown in either blue or orange, depending on the geometry of the groups that surround the ion. In structure 3, Ni²⁺ is placed in the secondary site; however, the coordinating species in the site are arranged in a manner that is consistent with a bound K⁺ ion (Ni²⁺ colored blue). In structure 4, the coordinating residues have been energy minimized, yielding a rearranged site that has Ni²⁺-preferred geometry and bond distances (Ni²⁺ colored orange).