Iron in the structure of Bovine Heart Cytochrome C Oxidase At the Fully Oxidized State (pdb 2dyr)

The binding sites of Iron atom in the structure of Bovine Heart Cytochrome C Oxidase At the Fully Oxidized State (pdb code 2dyr). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2dyr structure was solved by K.SHINZAWA-ITOH, H.AOYAMA, K.MURAMOTO, T.KURAUCHI, T.MIZUSHIMA, E.YAMASHITA, T.TSUKIHARA, S.YOSHIKAWA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-1.8 Space group P212121 a (A) 182.590 b (A) 205.140 c (A) 178.250 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.2 Rfree (%) 22.7 Iron Binding Sites: Iron binding site 1 out of 4 in 2dyr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2dyr. 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 1.96 Fe ND1 A:His61 4.13 Fe CD2 A:His61 3.02 Fe CE1 A:His61 2.97 Fe CG A:His61 4.17 Fe CE2 A:Phe377 4.97 Fe NE2 A:His378 1.88 Fe ND1 A:His378 3.99 Fe CD2 A:His378 3.06 Fe CE1 A:His378 2.78 Fe CG A:His378 4.14 Fe C2D A:Hea515 4.35 Fe NC A:Hea515 2.00 Fe CHB A:Hea515 3.43 Fe CHC A:Hea515 3.40 Fe C3D A:Hea515 4.34 Fe NA A:Hea515 2.07 Fe CHA A:Hea515 3.49 Fe C2A A:Hea515 4.32 Fe C4B A:Hea515 3.02 Fe C4A A:Hea515 3.08 Fe C1D A:Hea515 3.10 Fe C3A A:Hea515 4.32 Fe C4C A:Hea515 3.04 Fe C2B A:Hea515 4.23 Fe C1C A:Hea515 3.06 Fe C2C A:Hea515 4.31 Fe ND A:Hea515 2.02 Fe CHD A:Hea515 3.45 Fe C1B A:Hea515 3.01 Fe NB A:Hea515 1.95 Fe FE A:Hea515 0.00 Fe C3B A:Hea515 4.26 Fe C3C A:Hea515 4.29 Fe C4D A:Hea515 3.10 Fe C1A A:Hea515 3.11 interactive model: Iron binding site 2 out of 4 in 2dyr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2dyr. 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: Cu517, A: Hea516, conact list: Atom Atom Distance (A) Fe NE2 A:His376 2.07 Fe ND1 A:His376 4.18 Fe CD2 A:His376 3.20 Fe CE1 A:His376 2.97 Fe CG A:His376 4.30 Fe CU A:Cu517 4.96 Fe C2D A:Hea516 4.26 Fe NC A:Hea516 2.07 Fe CHB A:Hea516 3.40 Fe CHC A:Hea516 3.43 Fe C3D A:Hea516 4.21 Fe NA A:Hea516 2.02 Fe CHA A:Hea516 3.41 Fe C2A A:Hea516 4.32 Fe C4B A:Hea516 3.01 Fe C4A A:Hea516 3.06 Fe C1D A:Hea516 3.04 Fe C3A A:Hea516 4.34 Fe C4C A:Hea516 3.12 Fe C2B A:Hea516 4.21 Fe C1C A:Hea516 3.10 Fe C2C A:Hea516 4.37 Fe ND A:Hea516 1.92 Fe CHD A:Hea516 3.47 Fe C1B A:Hea516 2.99 Fe NB A:Hea516 1.93 Fe FE A:Hea516 0.00 Fe C3B A:Hea516 4.26 Fe C3C A:Hea516 4.37 Fe C4D A:Hea516 2.99 Fe C1A A:Hea516 3.07 interactive model: Iron binding site 3 out of 4 in 2dyr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2dyr. 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 1.90 Fe ND1 N:His61 4.06 Fe CD2 N:His61 2.95 Fe CE1 N:His61 2.91 Fe CG N:His61 4.10 Fe CE2 N:Phe377 4.81 Fe NE2 N:His378 1.96 Fe ND1 N:His378 4.08 Fe CD2 N:His378 3.09 Fe CE1 N:His378 2.89 Fe CG N:His378 4.19 Fe C2D N:Hea515 4.33 Fe NC N:Hea515 2.00 Fe CHB N:Hea515 3.42 Fe CHC N:Hea515 3.43 Fe C3D N:Hea515 4.31 Fe NA N:Hea515 2.00 Fe CHA N:Hea515 3.42 Fe C2A N:Hea515 4.29 Fe C4B N:Hea515 3.05 Fe C4A N:Hea515 3.06 Fe C1D N:Hea515 3.06 Fe C3A N:Hea515 4.31 Fe C4C N:Hea515 3.04 Fe C2B N:Hea515 4.26 Fe C1C N:Hea515 3.07 Fe C2C N:Hea515 4.34 Fe ND N:Hea515 2.00 Fe CHD N:Hea515 3.43 Fe C1B N:Hea515 3.03 Fe NB N:Hea515 1.99 Fe FE N:Hea515 0.00 Fe C3B N:Hea515 4.29 Fe C3C N:Hea515 4.31 Fe C4D N:Hea515 3.05 Fe C1A N:Hea515 3.06 interactive model: Iron binding site 4 out of 4 in 2dyr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2dyr. 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: His376, N: Cu517, N: Hea516, conact list: Atom Atom Distance (A) Fe NE2 N:His376 2.16 Fe ND1 N:His376 4.33 Fe CD2 N:His376 3.14 Fe CE1 N:His376 3.20 Fe CG N:His376 4.32 Fe CU N:Cu517 4.99 Fe C2D N:Hea516 4.22 Fe NC N:Hea516 2.02 Fe CHB N:Hea516 3.50 Fe CHC N:Hea516 3.44 Fe C3D N:Hea516 4.19 Fe NA N:Hea516 2.07 Fe CHA N:Hea516 3.43 Fe C2A N:Hea516 4.35 Fe C4B N:Hea516 3.04 Fe C4A N:Hea516 3.15 Fe C1D N:Hea516 2.97 Fe C3A N:Hea516 4.39 Fe C4C N:Hea516 3.07 Fe C2B N:Hea516 4.27 Fe C1C N:Hea516 3.09 Fe C2C N:Hea516 4.35 Fe ND N:Hea516 1.87 Fe CHD N:Hea516 3.42 Fe C1B N:Hea516 3.06 Fe NB N:Hea516 1.98 Fe FE N:Hea516 0.00 Fe C3B N:Hea516 4.29 Fe C3C N:Hea516 4.36 Fe C4D N:Hea516 2.96 Fe C1A N:Hea516 3.11 interactive model: