Iron in the structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State At 280 K (pdb 3ag1)

The binding sites of Iron atom in the structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State At 280 K (pdb code 3ag1). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3ag1 structure was solved by K.MURAMOTO, K.OHTA, K.SHINZAWA-ITOH, K.KANDA, M.TANIGUCHI, H.NABEKURA, E.YAMASHITA, T.TSUKIHARA, S.YOSHIKAWA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-2.2 Space group P212121 a (A) 189.493 b (A) 210.887 c (A) 178.301 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.2 Rfree (%) 19.2 Iron Binding Sites: Iron binding site 1 out of 4 in 3ag1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3ag1. 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 1.98 Fe ND1 A:His61 4.09 Fe CD2 A:His61 3.00 Fe CE1 A:His61 2.96 Fe CG A:His61 4.14 Fe CE2 A:Phe377 4.96 Fe NE2 A:His378 2.03 Fe ND1 A:His378 4.08 Fe CD2 A:His378 3.12 Fe CE1 A:His378 2.91 Fe CG A:His378 4.20 Fe C2D A:Hea515 4.28 Fe NC A:Hea515 2.10 Fe CHB A:Hea515 3.36 Fe CHC A:Hea515 3.44 Fe C3D A:Hea515 4.30 Fe NA A:Hea515 2.11 Fe CHA A:Hea515 3.59 Fe C2A A:Hea515 4.31 Fe C4B A:Hea515 3.02 Fe C4A A:Hea515 3.03 Fe C1D A:Hea515 3.03 Fe C3A A:Hea515 4.26 Fe C4C A:Hea515 3.11 Fe C2B A:Hea515 4.32 Fe C1C A:Hea515 3.13 Fe C2C A:Hea515 4.35 Fe ND A:Hea515 2.05 Fe CHD A:Hea515 3.49 Fe C1B A:Hea515 3.04 Fe NB A:Hea515 2.00 Fe FE A:Hea515 0.00 Fe C3B A:Hea515 4.26 Fe C3C A:Hea515 4.33 Fe C4D A:Hea515 3.09 Fe C1A A:Hea515 3.14 interactive model: Iron binding site 2 out of 4 in 3ag1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3ag1. 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: Cmo520, conact list: Atom Atom Distance (A) Fe NE2 A:His376 2.08 Fe ND1 A:His376 4.16 Fe CD2 A:His376 3.09 Fe CE1 A:His376 3.06 Fe CG A:His376 4.22 Fe C2D A:Hea516 4.22 Fe NC A:Hea516 2.09 Fe CHB A:Hea516 3.48 Fe CHC A:Hea516 3.49 Fe C3D A:Hea516 4.20 Fe NA A:Hea516 2.17 Fe CHA A:Hea516 3.51 Fe C2A A:Hea516 4.39 Fe C4B A:Hea516 3.01 Fe C4A A:Hea516 3.13 Fe C1D A:Hea516 3.02 Fe C3A A:Hea516 4.33 Fe C4C A:Hea516 3.09 Fe C2B A:Hea516 4.17 Fe C1C A:Hea516 3.11 Fe C2C A:Hea516 4.32 Fe ND A:Hea516 2.00 Fe CHD A:Hea516 3.47 Fe C1B A:Hea516 2.97 Fe NB A:Hea516 1.99 Fe FE A:Hea516 0.00 Fe C3B A:Hea516 4.19 Fe C3C A:Hea516 4.30 Fe C4D A:Hea516 3.01 Fe C1A A:Hea516 3.17 Fe O A:Cmo520 2.95 Fe C A:Cmo520 1.85 interactive model: Iron binding site 3 out of 4 in 3ag1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3ag1. 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 1.95 Fe ND1 N:His61 4.09 Fe CD2 N:His61 2.83 Fe CE1 N:His61 3.04 Fe CG N:His61 4.03 Fe CE2 N:Phe377 4.88 Fe NE2 N:His378 2.13 Fe ND1 N:His378 4.19 Fe CD2 N:His378 3.20 Fe CE1 N:His378 3.03 Fe CG N:His378 4.30 Fe C2D N:Hea515 4.35 Fe NC N:Hea515 1.99 Fe CHB N:Hea515 3.37 Fe CHC N:Hea515 3.56 Fe C3D N:Hea515 4.37 Fe NA N:Hea515 2.06 Fe CHA N:Hea515 3.60 Fe C2A N:Hea515 4.30 Fe C4B N:Hea515 3.09 Fe C4A N:Hea515 3.01 Fe C1D N:Hea515 3.10 Fe C3A N:Hea515 4.23 Fe C4C N:Hea515 2.92 Fe C2B N:Hea515 4.25 Fe C1C N:Hea515 3.05 Fe C2C N:Hea515 4.23 Fe ND N:Hea515 2.14 Fe CHD N:Hea515 3.35 Fe C1B N:Hea515 3.02 Fe NB N:Hea515 2.03 Fe FE N:Hea515 0.00 Fe C3B N:Hea515 4.27 Fe C3C N:Hea515 4.14 Fe C4D N:Hea515 3.19 Fe C1A N:Hea515 3.14 interactive model: Iron binding site 4 out of 4 in 3ag1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3ag1. 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: Hea516, N: Cmo520, conact list: Atom Atom Distance (A) Fe NE2 N:His376 2.13 Fe ND1 N:His376 4.27 Fe CD2 N:His376 3.04 Fe CE1 N:His376 3.18 Fe CG N:His376 4.23 Fe C2D N:Hea516 4.23 Fe NC N:Hea516 2.03 Fe CHB N:Hea516 3.49 Fe CHC N:Hea516 3.57 Fe C3D N:Hea516 4.18 Fe NA N:Hea516 2.10 Fe CHA N:Hea516 3.43 Fe C2A N:Hea516 4.34 Fe C4B N:Hea516 3.05 Fe C4A N:Hea516 3.12 Fe C1D N:Hea516 3.01 Fe C3A N:Hea516 4.33 Fe C4C N:Hea516 2.99 Fe C2B N:Hea516 4.19 Fe C1C N:Hea516 3.10 Fe C2C N:Hea516 4.28 Fe ND N:Hea516 2.02 Fe CHD N:Hea516 3.35 Fe C1B N:Hea516 2.97 Fe NB N:Hea516 2.00 Fe FE N:Hea516 0.00 Fe C3B N:Hea516 4.23 Fe C3C N:Hea516 4.21 Fe C4D N:Hea516 2.98 Fe C1A N:Hea516 3.09 Fe O N:Cmo520 2.78 Fe C N:Cmo520 1.67 interactive model: