Figure 2
Metal and niacin-binding sites in Bacillus halodurans NiaR. (a) The metal-binding site of apo BhNiaR. Coordination with the zinc ion (green) and distances between the zinc and the residues (blue) of metal-binding sites are shown in yellow. In addition, a water molecule (red) coordinates with the zinc ion and forms a tetrahedral geometry. In contrast to TmNiaR, the His83 is too distant to coordinate with the zinc ion. The distance between the zinc and His83 is shown in gray. (b) The metal-binding site of niacin-bound BhNiaR. The residues are shown in cyan. The niacin (orange) coordinates with the zinc ion instead of the water molecule and interacts with the His83 residue. (c) The metal-binding site of apo TmNiaR. Residues of the metal-binding site are shown in yellow. His79 coordinates with the nickel ion (light blue) and forms an octahedral geometry. (d) Electrostatic surface diagram of BhNiaR. The blue areas represent positive electrostatic regions and red areas represent negative electrostatic regions. Niacin is bound to the C-terminal domain of BhNiaR. (e) Niacin is surrounded by well-conserved hydrophobic residues (cyan) in the C-terminal domain of BhNiaR. The hydrophobic residues make a hydrophobic pocket and van der Waals attractions with niacin (Met88, Leu92, Phe130, Met134, Leu141, Leu142, and Tyr112′). The symmetry-related Tyr112 is colored gray. The figure was generated using the computer program PyMol (Version 2.3.2, Schrödinger, LLC, https://www.pymol.org).
