Iron in the structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides With D132A Mutation (pdb 3omi)

The binding sites of Iron atom in the structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides With D132A Mutation (pdb code 3omi). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3omi structure was solved by J.LIU, L.QIN, S.FERGUSON-MILLER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 35.8-2.1 Space group P212121 a (A) 125.064 b (A) 131.519 c (A) 175.674 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.2 Rfree (%) 21.5 Iron Binding Sites: Iron binding site 1 out of 4 in 3omi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3omi. 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: Thr48, A: His102, A: Phe420, A: His421, A: Hea1, conact list: Atom Atom Distance (A) Fe CG2 A:Thr48 4.55 Fe NE2 A:His102 2.03 Fe ND1 A:His102 4.11 Fe CD2 A:His102 3.06 Fe CE1 A:His102 2.99 Fe CG A:His102 4.18 Fe CE1 A:Phe420 4.89 Fe NE2 A:His421 2.05 Fe ND1 A:His421 4.10 Fe CD2 A:His421 3.12 Fe CE1 A:His421 2.95 Fe CG A:His421 4.22 Fe C2D A:Hea1 4.28 Fe NC A:Hea1 2.05 Fe CHB A:Hea1 3.45 Fe CHC A:Hea1 3.42 Fe C3D A:Hea1 4.30 Fe NA A:Hea1 2.09 Fe CHA A:Hea1 3.46 Fe C2A A:Hea1 4.29 Fe C4B A:Hea1 3.06 Fe C4A A:Hea1 3.09 Fe C1D A:Hea1 3.06 Fe C3A A:Hea1 4.29 Fe C4C A:Hea1 3.05 Fe C2B A:Hea1 4.31 Fe C1C A:Hea1 3.06 Fe C2C A:Hea1 4.27 Fe ND A:Hea1 2.07 Fe CHD A:Hea1 3.41 Fe C1B A:Hea1 3.10 Fe NB A:Hea1 2.07 Fe FE A:Hea1 0.00 Fe C3B A:Hea1 4.28 Fe C3C A:Hea1 4.27 Fe C4D A:Hea1 3.10 Fe C1A A:Hea1 3.09 interactive model: Iron binding site 2 out of 4 in 3omi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3omi. 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: His419, A: Val423, A: Oh741, A: Hea2, A: Cu5, A: Hoh742, conact list: Atom Atom Distance (A) Fe NE2 A:His419 2.12 Fe ND1 A:His419 4.21 Fe CD2 A:His419 3.11 Fe CE1 A:His419 3.09 Fe CG A:His419 4.25 Fe CG2 A:Val423 4.96 Fe O A:Oh741 3.84 Fe C2D A:Hea2 4.28 Fe NC A:Hea2 2.09 Fe CHB A:Hea2 3.47 Fe CHC A:Hea2 3.44 Fe C3D A:Hea2 4.28 Fe NA A:Hea2 2.13 Fe CHA A:Hea2 3.44 Fe C2A A:Hea2 4.33 Fe C4B A:Hea2 3.09 Fe C4A A:Hea2 3.14 Fe C1D A:Hea2 3.07 Fe C3A A:Hea2 4.34 Fe C4C A:Hea2 3.10 Fe C2B A:Hea2 4.30 Fe C1C A:Hea2 3.10 Fe C2C A:Hea2 4.34 Fe ND A:Hea2 2.04 Fe CHD A:Hea2 3.44 Fe C1B A:Hea2 3.11 Fe NB A:Hea2 2.09 Fe FE A:Hea2 0.00 Fe C3B A:Hea2 4.30 Fe C3C A:Hea2 4.34 Fe C4D A:Hea2 3.06 Fe C1A A:Hea2 3.11 Fe CU A:Cu5 4.78 Fe O A:Hoh742 2.15 interactive model: Iron binding site 3 out of 4 in 3omi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3omi. 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: C: Thr48, C: His102, C: Phe420, C: His421, C: Hea552, conact list: Atom Atom Distance (A) Fe CG2 C:Thr48 4.61 Fe NE2 C:His102 2.05 Fe ND1 C:His102 4.14 Fe CD2 C:His102 3.08 Fe CE1 C:His102 3.01 Fe CG C:His102 4.20 Fe CE1 C:Phe420 4.85 Fe NE2 C:His421 2.08 Fe ND1 C:His421 4.15 Fe CD2 C:His421 3.10 Fe CE1 C:His421 3.03 Fe CG C:His421 4.22 Fe C2D C:Hea552 4.27 Fe NC C:Hea552 2.09 Fe CHB C:Hea552 3.46 Fe CHC C:Hea552 3.34 Fe C3D C:Hea552 4.26 Fe NA C:Hea552 2.13 Fe CHA C:Hea552 3.42 Fe C2A C:Hea552 4.31 Fe C4B C:Hea552 2.96 Fe C4A C:Hea552 3.13 Fe C1D C:Hea552 3.07 Fe C3A C:Hea552 4.33 Fe C4C C:Hea552 3.13 Fe C2B C:Hea552 4.22 Fe C1C C:Hea552 3.03 Fe C2C C:Hea552 4.28 Fe ND C:Hea552 2.02 Fe CHD C:Hea552 3.49 Fe C1B C:Hea552 3.03 Fe NB C:Hea552 1.95 Fe C3B C:Hea552 4.19 Fe C3C C:Hea552 4.32 Fe C4D C:Hea552 3.04 Fe C1A C:Hea552 3.09 interactive model: Iron binding site 4 out of 4 in 3omi Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3omi. 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: C: His419, C: Oh741, C: Hea2, C: Cu554, C: Hoh743, conact list: Atom Atom Distance (A) Fe NE2 C:His419 2.15 Fe ND1 C:His419 4.25 Fe CD2 C:His419 3.12 Fe CE1 C:His419 3.14 Fe CG C:His419 4.27 Fe O C:Oh741 3.66 Fe C2D C:Hea2 4.31 Fe NC C:Hea2 2.15 Fe CHB C:Hea2 3.47 Fe CHC C:Hea2 3.43 Fe C3D C:Hea2 4.28 Fe NA C:Hea2 2.10 Fe CHA C:Hea2 3.39 Fe C2A C:Hea2 4.30 Fe C4B C:Hea2 3.07 Fe C4A C:Hea2 3.12 Fe C1D C:Hea2 3.12 Fe C3A C:Hea2 4.32 Fe C4C C:Hea2 3.18 Fe C2B C:Hea2 4.30 Fe C1C C:Hea2 3.12 Fe C2C C:Hea2 4.37 Fe ND C:Hea2 2.07 Fe CHD C:Hea2 3.51 Fe C1B C:Hea2 3.09 Fe NB C:Hea2 2.06 Fe FE C:Hea2 0.00 Fe C3B C:Hea2 4.30 Fe C3C C:Hea2 4.40 Fe C4D C:Hea2 3.05 Fe C1A C:Hea2 3.07 Fe CU C:Cu554 4.76 Fe O C:Hoh743 2.11 interactive model: