Iron in the structure of Bovine Heart Cytochrome C Oxidase Re-Refined With Molecular Oxygen (pdb 2y69)

The binding sites of Iron atom in the structure of Bovine Heart Cytochrome C Oxidase Re-Refined With Molecular Oxygen (pdb code 2y69). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2y69 structure was solved by V.R.I.KAILA, E.OKSANEN, A.GOLDMAN, M.I.VERKHOVSKY, D.SUNDHOLM, M.WIKSTROM, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 64.2-1.9 Space group P212121 a (A) 183.697 b (A) 206.991 c (A) 178.251 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.062 Rfree (%) 24.546 Iron Binding Sites: Iron binding site 1 out of 4 in 2y69 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2y69. 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: His61, A: Phe377, A: His378, A: Hea515, conact list: Atom Atom Distance (A) Fe NE2 A:His61 1.95 Fe ND1 A:His61 4.01 Fe CD2 A:His61 3.03 Fe CE1 A:His61 2.86 Fe CG A:His61 4.13 Fe CE1 A:Phe377 4.96 Fe NE2 A:His378 1.92 Fe ND1 A:His378 4.01 Fe CD2 A:His378 2.95 Fe CE1 A:His378 2.89 Fe CG A:His378 4.07 Fe C2D A:Hea515 4.29 Fe NC A:Hea515 2.01 Fe CHB A:Hea515 3.39 Fe CHC A:Hea515 3.42 Fe C3D A:Hea515 4.32 Fe NA A:Hea515 2.00 Fe CHA A:Hea515 3.45 Fe C2A A:Hea515 4.37 Fe C4B A:Hea515 3.06 Fe C4A A:Hea515 3.00 Fe C1D A:Hea515 3.02 Fe C3A A:Hea515 4.27 Fe C4C A:Hea515 3.02 Fe C2B A:Hea515 4.33 Fe C1C A:Hea515 3.05 Fe C2C A:Hea515 4.34 Fe ND A:Hea515 1.98 Fe CHD A:Hea515 3.39 Fe C1B A:Hea515 3.03 Fe NB A:Hea515 1.99 Fe FE A:Hea515 0.00 Fe C3B A:Hea515 4.36 Fe C3C A:Hea515 4.31 Fe C4D A:Hea515 3.02 Fe C1A A:Hea515 3.06 interactive model: Iron binding site 2 out of 4 in 2y69 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2y69. 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: His376, A: Hea516, A: Cu517, A: Oxy1515, conact list: Atom Atom Distance (A) Fe NE2 A:His376 2.00 Fe ND1 A:His376 4.08 Fe CD2 A:His376 3.05 Fe CE1 A:His376 2.95 Fe CG A:His376 4.17 Fe C2D A:Hea516 4.29 Fe NC A:Hea516 2.01 Fe CHB A:Hea516 3.45 Fe CHC A:Hea516 3.40 Fe C3D A:Hea516 4.30 Fe NA A:Hea516 1.98 Fe CHA A:Hea516 3.38 Fe C2A A:Hea516 4.30 Fe C4B A:Hea516 3.03 Fe C4A A:Hea516 3.00 Fe C1D A:Hea516 3.04 Fe C3A A:Hea516 4.23 Fe C4C A:Hea516 3.05 Fe C2B A:Hea516 4.33 Fe C1C A:Hea516 3.03 Fe C2C A:Hea516 4.34 Fe ND A:Hea516 1.96 Fe CHD A:Hea516 3.48 Fe C1B A:Hea516 3.05 Fe NB A:Hea516 1.99 Fe FE A:Hea516 0.00 Fe C3B A:Hea516 4.32 Fe C3C A:Hea516 4.34 Fe C4D A:Hea516 2.99 Fe C1A A:Hea516 3.00 Fe CU A:Cu517 4.89 Fe O1 A:Oxy1515 3.06 Fe O2 A:Oxy1515 2.24 interactive model: Iron binding site 3 out of 4 in 2y69 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2y69. 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: N: His61, N: Phe377, N: His378, N: Hea515, conact list: Atom Atom Distance (A) Fe NE2 N:His61 1.96 Fe ND1 N:His61 4.07 Fe CD2 N:His61 2.93 Fe CE1 N:His61 2.98 Fe CG N:His61 4.08 Fe CE1 N:Phe377 4.97 Fe NE2 N:His378 1.91 Fe ND1 N:His378 4.02 Fe CD2 N:His378 2.88 Fe CE1 N:His378 2.93 Fe CG N:His378 4.03 Fe C2D N:Hea515 4.37 Fe NC N:Hea515 1.96 Fe CHB N:Hea515 3.36 Fe CHC N:Hea515 3.45 Fe C3D N:Hea515 4.41 Fe NA N:Hea515 1.96 Fe CHA N:Hea515 3.46 Fe C2A N:Hea515 4.33 Fe C4B N:Hea515 3.07 Fe C4A N:Hea515 2.97 Fe C1D N:Hea515 3.05 Fe C3A N:Hea515 4.23 Fe C4C N:Hea515 2.96 Fe C2B N:Hea515 4.32 Fe C1C N:Hea515 3.05 Fe C2C N:Hea515 4.32 Fe ND N:Hea515 2.03 Fe CHD N:Hea515 3.37 Fe C1B N:Hea515 3.01 Fe NB N:Hea515 2.01 Fe FE N:Hea515 0.00 Fe C3B N:Hea515 4.37 Fe C3C N:Hea515 4.24 Fe C4D N:Hea515 3.07 Fe C1A N:Hea515 3.03 interactive model: Iron binding site 4 out of 4 in 2y69 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2y69. 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: N: Val243, N: His376, N: Hea516, N: Cu517, N: Oxy1515, conact list: Atom Atom Distance (A) Fe CG2 N:Val243 4.91 Fe NE2 N:His376 2.01 Fe ND1 N:His376 4.08 Fe CD2 N:His376 3.08 Fe CE1 N:His376 2.93 Fe CG N:His376 4.19 Fe C2D N:Hea516 4.30 Fe NC N:Hea516 1.98 Fe CHB N:Hea516 3.42 Fe CHC N:Hea516 3.41 Fe C3D N:Hea516 4.31 Fe NA N:Hea516 1.98 Fe CHA N:Hea516 3.39 Fe C2A N:Hea516 4.32 Fe C4B N:Hea516 3.03 Fe C4A N:Hea516 3.01 Fe C1D N:Hea516 3.04 Fe C3A N:Hea516 4.26 Fe C4C N:Hea516 3.02 Fe C2B N:Hea516 4.30 Fe C1C N:Hea516 3.00 Fe C2C N:Hea516 4.29 Fe ND N:Hea516 1.98 Fe CHD N:Hea516 3.46 Fe C1B N:Hea516 3.02 Fe NB N:Hea516 1.98 Fe FE N:Hea516 0.00 Fe C3B N:Hea516 4.31 Fe C3C N:Hea516 4.29 Fe C4D N:Hea516 2.99 Fe C1A N:Hea516 3.01 Fe CU N:Cu517 4.85 Fe O1 N:Oxy1515 2.36 Fe O2 N:Oxy1515 3.01 interactive model: