Hexacoordinate

About: Hexacoordinate is a research topic. Over the lifetime, 947 publications have been published within this topic receiving 24541 citations.

Crystal structure of substrate-free Pseudomonas putida cytochrome P-450.

Abstract: The crystal structure of Pseudomonas putida cytochrome P-450cam in the substrate-free form has been refined at 2.20-A resolution and compared to the substrate-bound form of the enzyme. In the absence of the substrate camphor, the P-450cam heme iron atom is hexacoordinate with the sulfur atom of Cys-357 providing one axial heme ligand and a water molecule or hydroxide ion providing the other axial ligand. A network of hydrogen-bonded solvent molecules occupies the substrate pocket in addition to the iron-linked aqua ligand. When a camphor molecule binds, the active site waters including the aqua ligand are displaced, resulting in a pentacoordinate high-spin heme iron atom. Analysis of the Fno camphor - F camphor difference Fourier and a quantitative comparison of the two refined structures reveal that no detectable conformational change results from camphor binding other than a small repositioning of a phenylalanine side chain that contacts the camphor molecule. However, large decreases in the mean temperature factors of three separate segments of the protein centered on Tyr-96, Thr-185, and Asp-251 result from camphor binding. This indicates that camphor binding decreases the flexibility in these three regions of the P-450cam molecule without altering the mean position of the atoms involved.

The nitrogenase FeMo-cofactor and P-cluster pair: 2.2 A resolution structures.

Abstract: Structures recently proposed for the FeMo-cofactor and P-cluster pair of the nitrogenase molybdenum-iron (MoFe)-protein from Azotobacter vinelandii have been crystallographically verified at 2.2 angstrom resolution. Significantly, no hexacoordinate sulfur atoms are observed in either type of metal center. Consequently, the six bridged iron atoms in the FeMo-cofactor are trigonally coordinated by nonprotein ligands, although there may be some iron-iron bonding interactions that could provide a fourth coordination interaction for these sites. Two of the cluster sulfurs in the P-cluster pair are very close together (approximately 2.1 angstroms), indicating that they form a disulfide bond. These findings indicate that a cavity exists in the interior of the FeMo-cofactor that could be involved in substrate binding and suggest that redox reactions at the P-cluster pair may be linked to transitions of two cluster-bound sulfurs between disulfide and sulfide oxidation states.

Hydrolysis of ferric ion in water and conformational equilibrium

Abstract: Reported here are results of theoretical calculations on Fe(H2O)63+, Fe(H2O)5(OH)2+, three isomers of Fe(H2O)4(OH)2+, and Fe(H2O)3(OH)2+, which investigate the molecular mechanisms of hydrolysis of ferric ion in water. The combination of density functional electronic structure techniques and a dielectric continuum model for electrostatic solvation applied to the Fe(H2O)63+ complex yields an estimate of −1020 kcal/mol (experimental values −1037 to −1019 kcal/mol) for the absolute free energy of the aqueous ferric ion. The predicted free energy change for the first hydrolysis reaction is surprisingly close to the experimental value (2 kcal/mol predicted compared to 3 kcal/mol experimental). For the second hydrolysis reaction, we found an unexpected low-energy isomer of Fe(H2O)4(OH)2+ with five ligands in the inner sphere and one water outside. The hexacoordinate cis and trans isomers are, respectively, slightly lower and higher in energy. Calculations on the pentacoordinate species Fe(H2O)3(OH)2+ suggest th...