Iron in the structure of Bovine Heart Cytochrome C Oxidase Modified By Dccd (pdb 2dys)

The binding sites of Iron atom in the structure of Bovine Heart Cytochrome C Oxidase Modified By Dccd (pdb code 2dys). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2dys 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) 40.0-2.2 Space group P212121 a (A) 184.130 b (A) 207.232 c (A) 178.242 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.7 Rfree (%) 24.2 Iron Binding Sites: Iron binding site 1 out of 4 in 2dys Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2dys. 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 1.94 Fe ND1 A:His61 4.08 Fe CD2 A:His61 3.01 Fe CE1 A:His61 2.93 Fe CG A:His61 4.15 Fe CE2 A:Phe377 4.82 Fe NE2 A:His378 1.85 Fe ND1 A:His378 3.92 Fe CD2 A:His378 3.05 Fe CE1 A:His378 2.70 Fe CG A:His378 4.10 Fe C2D A:Hea515 4.22 Fe NC A:Hea515 2.09 Fe CHB A:Hea515 3.44 Fe CHC A:Hea515 3.41 Fe C3D A:Hea515 4.20 Fe NA A:Hea515 2.06 Fe CHA A:Hea515 3.39 Fe C2A A:Hea515 4.25 Fe C4B A:Hea515 3.03 Fe C4A A:Hea515 3.10 Fe C1D A:Hea515 3.01 Fe C3A A:Hea515 4.30 Fe C4C A:Hea515 3.12 Fe C2B A:Hea515 4.26 Fe C1C A:Hea515 3.11 Fe C2C A:Hea515 4.38 Fe ND A:Hea515 1.93 Fe CHD A:Hea515 3.43 Fe C1B A:Hea515 3.02 Fe NB A:Hea515 1.96 Fe FE A:Hea515 0.00 Fe C3B A:Hea515 4.27 Fe C3C A:Hea515 4.36 Fe C4D A:Hea515 2.98 Fe C1A A:Hea515 3.05 interactive model: Iron binding site 2 out of 4 in 2dys Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2dys. 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: Val243, A: His376, A: Cu517, A: Hea516, conact list: Atom Atom Distance (A) Fe CG2 A:Val243 4.97 Fe NE2 A:His376 2.09 Fe ND1 A:His376 4.20 Fe CD2 A:His376 3.28 Fe CE1 A:His376 2.97 Fe CG A:His376 4.36 Fe CU A:Cu517 4.59 Fe C2D A:Hea516 4.20 Fe NC A:Hea516 2.13 Fe CHB A:Hea516 3.36 Fe CHC A:Hea516 3.38 Fe C3D A:Hea516 4.14 Fe NA A:Hea516 1.95 Fe CHA A:Hea516 3.36 Fe C2A A:Hea516 4.22 Fe C4B A:Hea516 2.93 Fe C4A A:Hea516 3.00 Fe C1D A:Hea516 2.98 Fe C3A A:Hea516 4.24 Fe C4C A:Hea516 3.16 Fe C2B A:Hea516 4.19 Fe C1C A:Hea516 3.12 Fe C2C A:Hea516 4.40 Fe ND A:Hea516 1.86 Fe CHD A:Hea516 3.47 Fe C1B A:Hea516 2.95 Fe NB A:Hea516 1.86 Fe FE A:Hea516 0.00 Fe C3B A:Hea516 4.20 Fe C3C A:Hea516 4.45 Fe C4D A:Hea516 2.93 Fe C1A A:Hea516 2.99 interactive model: Iron binding site 3 out of 4 in 2dys Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2dys. 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 1.94 Fe ND1 N:His61 4.12 Fe CD2 N:His61 2.94 Fe CE1 N:His61 2.99 Fe CG N:His61 4.12 Fe CE2 N:Phe377 4.84 Fe NE2 N:His378 1.97 Fe ND1 N:His378 4.02 Fe CD2 N:His378 3.17 Fe CE1 N:His378 2.79 Fe CG N:His378 4.21 Fe C2D N:Hea515 4.23 Fe NC N:Hea515 2.08 Fe CHB N:Hea515 3.46 Fe CHC N:Hea515 3.45 Fe C3D N:Hea515 4.19 Fe NA N:Hea515 1.97 Fe CHA N:Hea515 3.33 Fe C2A N:Hea515 4.21 Fe C4B N:Hea515 3.06 Fe C4A N:Hea515 3.06 Fe C1D N:Hea515 2.99 Fe C3A N:Hea515 4.26 Fe C4C N:Hea515 3.12 Fe C2B N:Hea515 4.27 Fe C1C N:Hea515 3.14 Fe C2C N:Hea515 4.42 Fe ND N:Hea515 1.87 Fe CHD N:Hea515 3.45 Fe C1B N:Hea515 3.03 Fe NB N:Hea515 1.98 Fe FE N:Hea515 0.00 Fe C3B N:Hea515 4.31 Fe C3C N:Hea515 4.38 Fe C4D N:Hea515 2.92 Fe C1A N:Hea515 2.99 interactive model: Iron binding site 4 out of 4 in 2dys Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2dys. 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: Cu517, N: Hea516, conact list: Atom Atom Distance (A) Fe CG2 N:Val243 4.98 Fe NE2 N:His376 2.16 Fe ND1 N:His376 4.33 Fe CD2 N:His376 3.17 Fe CE1 N:His376 3.18 Fe CG N:His376 4.34 Fe CU N:Cu517 4.58 Fe C2D N:Hea516 4.14 Fe NC N:Hea516 2.08 Fe CHB N:Hea516 3.40 Fe CHC N:Hea516 3.40 Fe C3D N:Hea516 4.09 Fe NA N:Hea516 1.96 Fe CHA N:Hea516 3.33 Fe C2A N:Hea516 4.22 Fe C4B N:Hea516 2.98 Fe C4A N:Hea516 3.04 Fe C1D N:Hea516 2.93 Fe C3A N:Hea516 4.26 Fe C4C N:Hea516 3.14 Fe C2B N:Hea516 4.23 Fe C1C N:Hea516 3.10 Fe C2C N:Hea516 4.38 Fe ND N:Hea516 1.81 Fe CHD N:Hea516 3.44 Fe C1B N:Hea516 2.99 Fe NB N:Hea516 1.92 Fe FE N:Hea516 0.00 Fe C3B N:Hea516 4.23 Fe C3C N:Hea516 4.43 Fe C4D N:Hea516 2.87 Fe C1A N:Hea516 2.99 interactive model: