Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase
Figure 6
Comparison of the Channel 3 region in cNOR (A) and the periplasmic cavity in cbb3 oxidase (B).
Crystal structures of cNOR from Ps. aeruginosa and cbb3 oxidase from Ps. stutzeri (PDB ID: 3MK7) [56] were aligned on hemes b and b3. The transparent blue surfaces indicate the positions of hydrophilic cavities. The central residues, which form the hydrophilic cavity (namely Glu135, Glu138, Arg57 in cNOR and Glu122, Glu125, Arg57 in cbb3 oxidase), are identical and highly conserved in the HCO superfamily. A calcium ion is located in a similar position between hemes.