Iron in the structure of Structure of CAA3-Type Cytochrome Oxidase (pdb 2yev)

The binding sites of Iron atom in the structure of Structure of CAA3-Type Cytochrome Oxidase (pdb code 2yev). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2yev structure was solved by J.A.LYONS, D.ARAGAO, T.SOULIMANE, M.CAFFREY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 77.2-2.4 Space group I121 a (A) 127.250 b (A) 76.030 c (A) 300.267 alpha (°) 90.00 beta (°) 92.21 gamma (°) 90.00 Rfactor (%) 17.12 Rfree (%) 21.83 Iron Binding Sites: Iron binding site 1 out of 6 in 2yev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2yev. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His73, A: His387, A: Has1015, conact list: Atom Atom Distance (A) Fe NE2 A:His73 2.04 Fe ND1 A:His73 4.15 Fe CD2 A:His73 2.96 Fe CE1 A:His73 3.08 Fe CG A:His73 4.14 Fe NE2 A:His387 2.06 Fe ND1 A:His387 4.18 Fe CD2 A:His387 2.97 Fe CE1 A:His387 3.11 Fe CG A:His387 4.15 Fe C2D A:Has1015 4.28 Fe NA A:Has1015 2.11 Fe CHA A:Has1015 3.42 Fe C2A A:Has1015 4.41 Fe C4B A:Has1015 3.15 Fe C4A A:Has1015 3.09 Fe C1D A:Has1015 3.05 Fe C3A A:Has1015 4.38 Fe C1C A:Has1015 3.08 Fe C2C A:Has1015 4.34 Fe NB A:Has1015 2.18 Fe FE A:Has1015 0.00 Fe C3B A:Has1015 4.45 Fe C4D A:Has1015 3.02 Fe NC A:Has1015 2.06 Fe CHB A:Has1015 3.47 Fe CHC A:Has1015 3.46 Fe C3D A:Has1015 4.33 Fe C4C A:Has1015 3.01 Fe C2B A:Has1015 4.45 Fe CHD A:Has1015 3.39 Fe ND A:Has1015 2.05 Fe C1B A:Has1015 3.16 Fe C3C A:Has1015 4.28 Fe C1A A:Has1015 3.10 interactive model: Iron binding site 2 out of 6 in 2yev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2yev. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His385, A: Has1016, A: Cu1017, A: Hoh2076, A: Hoh2077, conact list: Atom Atom Distance (A) Fe NE2 A:His385 2.26 Fe ND1 A:His385 4.36 Fe CD2 A:His385 3.22 Fe CE1 A:His385 3.24 Fe CG A:His385 4.38 Fe C2D A:Has1016 4.32 Fe NA A:Has1016 2.11 Fe CHA A:Has1016 3.44 Fe C2A A:Has1016 4.39 Fe C4B A:Has1016 3.17 Fe C4A A:Has1016 3.10 Fe C1D A:Has1016 3.07 Fe C3A A:Has1016 4.38 Fe C1C A:Has1016 3.13 Fe C2C A:Has1016 4.41 Fe NB A:Has1016 2.16 Fe FE A:Has1016 0.00 Fe C3B A:Has1016 4.46 Fe C4D A:Has1016 3.09 Fe NC A:Has1016 2.14 Fe CHB A:Has1016 3.44 Fe CHC A:Has1016 3.49 Fe C3D A:Has1016 4.39 Fe C4C A:Has1016 3.11 Fe C2B A:Has1016 4.44 Fe CHD A:Has1016 3.45 Fe ND A:Has1016 2.11 Fe C1B A:Has1016 3.14 Fe C3C A:Has1016 4.38 Fe C1A A:Has1016 3.09 Fe CU A:Cu1017 4.85 Fe O A:Hoh2076 4.34 Fe O A:Hoh2077 2.24 interactive model: Iron binding site 3 out of 6 in 2yev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2yev. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: His251, B: Trp290, B: Met303, B: Hec587, conact list: Atom Atom Distance (A) Fe NE2 B:His251 2.05 Fe ND1 B:His251 4.14 Fe CD2 B:His251 3.00 Fe CE1 B:His251 3.05 Fe CG B:His251 4.15 Fe NE1 B:Trp290 4.95 Fe CB B:Met303 4.22 Fe CE B:Met303 3.50 Fe CG B:Met303 3.47 Fe SD B:Met303 2.38 Fe C2D B:Hec587 4.30 Fe NC B:Hec587 2.02 Fe CHB B:Hec587 3.49 Fe CHC B:Hec587 3.43 Fe C3D B:Hec587 4.26 Fe NA B:Hec587 2.02 Fe CHA B:Hec587 3.36 Fe C2A B:Hec587 4.25 Fe C1D B:Hec587 3.08 Fe C4A B:Hec587 3.08 Fe C4B B:Hec587 3.06 Fe C3A B:Hec587 4.28 Fe C4C B:Hec587 3.06 Fe C2B B:Hec587 4.30 Fe C1C B:Hec587 3.05 Fe C2C B:Hec587 4.26 Fe ND B:Hec587 2.03 Fe CHD B:Hec587 3.45 Fe C1B B:Hec587 3.09 Fe NB B:Hec587 2.04 Fe FE B:Hec587 0.00 Fe C3C B:Hec587 4.27 Fe C3B B:Hec587 4.28 Fe C4D B:Hec587 3.01 Fe C1A B:Hec587 3.01 interactive model: Iron binding site 4 out of 6 in 2yev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2yev. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: His73, D: His387, D: Has1015, conact list: Atom Atom Distance (A) Fe NE2 D:His73 2.10 Fe ND1 D:His73 4.22 Fe CD2 D:His73 2.99 Fe CE1 D:His73 3.16 Fe CG D:His73 4.18 Fe NE2 D:His387 2.01 Fe ND1 D:His387 4.14 Fe CD2 D:His387 2.91 Fe CE1 D:His387 3.08 Fe CG D:His387 4.10 Fe C2D D:Has1015 4.36 Fe NA D:Has1015 2.12 Fe CHA D:Has1015 3.44 Fe C2A D:Has1015 4.40 Fe C4B D:Has1015 3.18 Fe C4A D:Has1015 3.08 Fe C1D D:Has1015 3.09 Fe C3A D:Has1015 4.37 Fe C1C D:Has1015 3.10 Fe C2C D:Has1015 4.36 Fe NB D:Has1015 2.18 Fe FE D:Has1015 0.00 Fe C3B D:Has1015 4.46 Fe C4D D:Has1015 3.11 Fe NC D:Has1015 2.09 Fe CHB D:Has1015 3.44 Fe CHC D:Has1015 3.48 Fe C3D D:Has1015 4.43 Fe C4C D:Has1015 3.03 Fe C2B D:Has1015 4.43 Fe CHD D:Has1015 3.38 Fe ND D:Has1015 2.13 Fe C1B D:Has1015 3.14 Fe C3C D:Has1015 4.31 Fe C1A D:Has1015 3.10 interactive model: Iron binding site 5 out of 6 in 2yev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 2yev. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: His385, D: Has1016, D: Cu1017, D: Hoh2053, D: Hoh2054, conact list: Atom Atom Distance (A) Fe NE2 D:His385 2.25 Fe ND1 D:His385 4.33 Fe CD2 D:His385 3.26 Fe CE1 D:His385 3.19 Fe CG D:His385 4.39 Fe C2D D:Has1016 4.30 Fe NA D:Has1016 2.11 Fe CHA D:Has1016 3.45 Fe C2A D:Has1016 4.41 Fe C4B D:Has1016 3.14 Fe C4A D:Has1016 3.10 Fe C1D D:Has1016 3.04 Fe C3A D:Has1016 4.38 Fe C1C D:Has1016 3.04 Fe C2C D:Has1016 4.32 Fe NB D:Has1016 2.14 Fe FE D:Has1016 0.00 Fe C3B D:Has1016 4.42 Fe C4D D:Has1016 3.10 Fe NC D:Has1016 2.06 Fe CHB D:Has1016 3.43 Fe CHC D:Has1016 3.44 Fe C3D D:Has1016 4.40 Fe C4C D:Has1016 3.05 Fe C2B D:Has1016 4.40 Fe CHD D:Has1016 3.43 Fe ND D:Has1016 2.08 Fe C1B D:Has1016 3.11 Fe C3C D:Has1016 4.31 Fe C1A D:Has1016 3.10 Fe CU D:Cu1017 4.83 Fe O D:Hoh2053 4.91 Fe O D:Hoh2054 2.73 interactive model: Iron binding site 6 out of 6 in 2yev Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 2yev. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: E: His251, E: Met303, E: Hec587, conact list: Atom Atom Distance (A) Fe NE2 E:His251 2.06 Fe ND1 E:His251 4.16 Fe CD2 E:His251 2.95 Fe CE1 E:His251 3.10 Fe CG E:His251 4.13 Fe CB E:Met303 4.21 Fe CE E:Met303 3.47 Fe CG E:Met303 3.46 Fe SD E:Met303 2.37 Fe C2D E:Hec587 4.28 Fe NC E:Hec587 2.02 Fe CHB E:Hec587 3.44 Fe CHC E:Hec587 3.49 Fe C3D E:Hec587 4.32 Fe NA E:Hec587 2.07 Fe CHA E:Hec587 3.50 Fe C2A E:Hec587 4.32 Fe C1D E:Hec587 3.02 Fe C4A E:Hec587 3.08 Fe C4B E:Hec587 3.10 Fe C3A E:Hec587 4.30 Fe C4C E:Hec587 3.00 Fe C2B E:Hec587 4.32 Fe C1C E:Hec587 3.09 Fe C2C E:Hec587 4.28 Fe ND E:Hec587 2.06 Fe CHD E:Hec587 3.34 Fe C1B E:Hec587 3.09 Fe NB E:Hec587 2.08 Fe FE E:Hec587 0.00 Fe C3C E:Hec587 4.24 Fe C3B E:Hec587 4.31 Fe C4D E:Hec587 3.11 Fe C1A E:Hec587 3.11 interactive model: