Iron in the structure of Cytochrome BC1 Complex From Chicken With Fenamidone Bound (pdb 3l75)

The binding sites of Iron atom in the structure of Cytochrome BC1 Complex From Chicken With Fenamidone Bound (pdb code 3l75). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3l75 structure was solved by L.HUANG, E.A.BERRY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 58.8-2.8 Space group P212121 a (A) 172.285 b (A) 182.141 c (A) 241.198 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 24.8 Rfree (%) 27.5 Iron Binding Sites: Iron binding site 1 out of 10 in 3l75 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3l75. 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: Gln45, C: Gly49, C: His84, C: Gly131, C: His183, C: Hem501, conact list: Atom Atom Distance (A) Fe NE2 C:Gln45 4.91 Fe CA C:Gly49 4.96 Fe NE2 C:His84 2.01 Fe ND1 C:His84 4.08 Fe CD2 C:His84 3.07 Fe CE1 C:His84 2.93 Fe CG C:His84 4.18 Fe CA C:Gly131 4.99 Fe NE2 C:His183 2.00 Fe ND1 C:His183 4.02 Fe CD2 C:His183 3.12 Fe CE1 C:His183 2.85 Fe CG C:His183 4.18 Fe C2D C:Hem501 4.27 Fe NC C:Hem501 1.94 Fe CHB C:Hem501 3.38 Fe CHC C:Hem501 3.31 Fe C3D C:Hem501 4.28 Fe NA C:Hem501 1.95 Fe CHA C:Hem501 3.41 Fe C2A C:Hem501 4.24 Fe C1D C:Hem501 3.02 Fe C4A C:Hem501 3.01 Fe C4B C:Hem501 2.95 Fe C3A C:Hem501 4.26 Fe C4C C:Hem501 3.00 Fe C2B C:Hem501 4.27 Fe C1C C:Hem501 2.98 Fe C2C C:Hem501 4.23 Fe ND C:Hem501 1.96 Fe CHD C:Hem501 3.39 Fe C1B C:Hem501 3.01 Fe NB C:Hem501 1.92 Fe FE C:Hem501 0.00 Fe C3C C:Hem501 4.24 Fe C3B C:Hem501 4.20 Fe C4D C:Hem501 3.03 Fe C1A C:Hem501 3.01 interactive model: Iron binding site 2 out of 10 in 3l75 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3l75. 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: His98, C: His197, C: Hem502, conact list: Atom Atom Distance (A) Fe NE2 C:His98 2.02 Fe ND1 C:His98 4.11 Fe CD2 C:His98 3.02 Fe CE1 C:His98 3.00 Fe CG C:His98 4.16 Fe NE2 C:His197 2.00 Fe ND1 C:His197 4.13 Fe CD2 C:His197 2.93 Fe CE1 C:His197 3.05 Fe CG C:His197 4.11 Fe C2D C:Hem502 4.27 Fe NC C:Hem502 1.98 Fe CHB C:Hem502 3.39 Fe CHC C:Hem502 3.35 Fe C3D C:Hem502 4.33 Fe NA C:Hem502 1.93 Fe CHA C:Hem502 3.37 Fe C2A C:Hem502 4.23 Fe C1D C:Hem502 2.99 Fe C4A C:Hem502 3.00 Fe C4B C:Hem502 2.93 Fe C3A C:Hem502 4.23 Fe C4C C:Hem502 3.03 Fe C2B C:Hem502 4.21 Fe C1C C:Hem502 3.03 Fe C2C C:Hem502 4.26 Fe ND C:Hem502 1.94 Fe CHD C:Hem502 3.37 Fe C1B C:Hem502 2.98 Fe NB C:Hem502 1.88 Fe FE C:Hem502 0.00 Fe C3C C:Hem502 4.28 Fe C3B C:Hem502 4.21 Fe C4D C:Hem502 3.02 Fe C1A C:Hem502 3.00 interactive model: Iron binding site 3 out of 10 in 3l75 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3l75. 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: D: His41, D: Met160, D: Hec501, conact list: Atom Atom Distance (A) Fe NE2 D:His41 2.00 Fe ND1 D:His41 4.09 Fe CD2 D:His41 3.01 Fe CE1 D:His41 2.97 Fe CG D:His41 4.14 Fe CB D:Met160 4.25 Fe CE D:Met160 3.42 Fe CG D:Met160 3.55 Fe SD D:Met160 2.18 Fe C2D D:Hec501 4.24 Fe NC D:Hec501 1.95 Fe CHB D:Hec501 3.38 Fe CHC D:Hec501 3.43 Fe C3D D:Hec501 4.29 Fe NA D:Hec501 1.94 Fe CHA D:Hec501 3.36 Fe C2A D:Hec501 4.25 Fe C1D D:Hec501 2.94 Fe C4A D:Hec501 2.99 Fe C4B D:Hec501 3.04 Fe C3A D:Hec501 4.22 Fe C4C D:Hec501 3.00 Fe C2B D:Hec501 4.22 Fe C1C D:Hec501 3.04 Fe C2C D:Hec501 4.29 Fe ND D:Hec501 1.91 Fe CHD D:Hec501 3.31 Fe C1B D:Hec501 3.00 Fe NB D:Hec501 1.96 Fe FE D:Hec501 0.00 Fe C3C D:Hec501 4.26 Fe C3B D:Hec501 4.25 Fe C4D D:Hec501 2.99 Fe C1A D:Hec501 3.00 interactive model: Iron binding site 4 out of 10 in 3l75 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3l75. 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: E: Cys139, E: His141, E: Leu142, E: Cys144, E: Cys158, E: Cys160, E: His161, E: Ser163, E: Fes501, conact list: Atom Atom Distance (A) Fe CB E:Cys139 2.97 Fe SG E:Cys139 2.25 Fe C E:Cys139 4.96 Fe CA E:Cys139 4.44 Fe N E:His141 4.92 Fe CB E:His141 3.87 Fe ND1 E:His141 4.38 Fe CG E:His141 4.62 Fe CA E:His141 4.95 Fe N E:Leu142 4.68 Fe O E:Cys144 4.93 Fe N E:Cys144 4.55 Fe CB E:Cys144 4.32 Fe SG E:Cys144 4.82 Fe CA E:Cys144 4.94 Fe O E:Cys158 4.84 Fe CB E:Cys158 3.10 Fe SG E:Cys158 2.25 Fe C E:Cys158 4.85 Fe CA E:Cys158 4.52 Fe N E:Cys160 4.95 Fe CB E:Cys160 4.33 Fe N E:His161 4.58 Fe ND1 E:His161 4.57 Fe N E:Ser163 4.99 Fe CB E:Ser163 4.30 Fe OG E:Ser163 4.13 Fe S1 E:Fes501 2.24 Fe S2 E:Fes501 2.22 Fe FE1 E:Fes501 0.00 Fe FE2 E:Fes501 2.72 interactive model: Iron binding site 5 out of 10 in 3l75 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 3l75. 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: E: Cys139, E: His141, E: Leu142, E: Cys158, E: Cys160, E: His161, E: Ser163, E: Fes501, conact list: Atom Atom Distance (A) Fe SG E:Cys139 4.31 Fe NE2 E:His141 4.27 Fe CB E:His141 3.32 Fe ND1 E:His141 2.15 Fe CD2 E:His141 4.24 Fe C E:His141 4.84 Fe CE1 E:His141 3.18 Fe CG E:His141 3.08 Fe CA E:His141 4.67 Fe N E:Leu142 4.05 Fe CB E:Leu142 4.38 Fe CD1 E:Leu142 4.87 Fe CG E:Leu142 4.55 Fe CA E:Leu142 4.79 Fe SG E:Cys158 4.55 Fe CB E:Cys160 4.02 Fe C E:Cys160 4.46 Fe CA E:Cys160 4.82 Fe NE2 E:His161 4.25 Fe N E:His161 3.73 Fe CB E:His161 3.29 Fe ND1 E:His161 2.15 Fe CD2 E:His161 4.22 Fe C E:His161 4.84 Fe CE1 E:His161 3.18 Fe CG E:His161 3.06 Fe CA E:His161 4.09 Fe OG E:Ser163 4.67 Fe S1 E:Fes501 2.22 Fe S2 E:Fes501 2.23 Fe FE1 E:Fes501 2.72 Fe FE2 E:Fes501 0.00 interactive model: Iron binding site 6 out of 10 in 3l75 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 3l75. 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: P: Gln45, P: Gly49, P: His84, P: His183, P: Hem501, conact list: Atom Atom Distance (A) Fe NE2 P:Gln45 4.88 Fe CA P:Gly49 4.94 Fe NE2 P:His84 2.00 Fe ND1 P:His84 4.08 Fe CD2 P:His84 3.05 Fe CE1 P:His84 2.94 Fe CG P:His84 4.16 Fe NE2 P:His183 2.00 Fe ND1 P:His183 4.04 Fe CD2 P:His183 3.11 Fe CE1 P:His183 2.87 Fe CG P:His183 4.18 Fe C2D P:Hem501 4.26 Fe NC P:Hem501 1.96 Fe CHB P:Hem501 3.39 Fe CHC P:Hem501 3.33 Fe C3D P:Hem501 4.28 Fe NA P:Hem501 1.93 Fe CHA P:Hem501 3.40 Fe C2A P:Hem501 4.22 Fe C1D P:Hem501 3.02 Fe C4A P:Hem501 3.00 Fe C4B P:Hem501 2.98 Fe C3A P:Hem501 4.25 Fe C4C P:Hem501 3.00 Fe C2B P:Hem501 4.27 Fe C1C P:Hem501 2.99 Fe C2C P:Hem501 4.23 Fe ND P:Hem501 1.96 Fe CHD P:Hem501 3.37 Fe C1B P:Hem501 3.02 Fe NB P:Hem501 1.94 Fe FE P:Hem501 0.00 Fe C3C P:Hem501 4.24 Fe C3B P:Hem501 4.22 Fe C4D P:Hem501 3.03 Fe C1A P:Hem501 2.99 interactive model: Iron binding site 7 out of 10 in 3l75 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 3l75. 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: P: His98, P: His197, P: Hem502, P: Hoh383, conact list: Atom Atom Distance (A) Fe NE2 P:His98 2.01 Fe ND1 P:His98 4.10 Fe CD2 P:His98 3.01 Fe CE1 P:His98 2.98 Fe CG P:His98 4.15 Fe NE2 P:His197 2.01 Fe ND1 P:His197 4.10 Fe CD2 P:His197 3.01 Fe CE1 P:His197 3.00 Fe CG P:His197 4.14 Fe C2D P:Hem502 4.22 Fe NC P:Hem502 1.92 Fe CHB P:Hem502 3.41 Fe CHC P:Hem502 3.31 Fe C3D P:Hem502 4.28 Fe NA P:Hem502 1.99 Fe CHA P:Hem502 3.38 Fe C2A P:Hem502 4.28 Fe C1D P:Hem502 2.97 Fe C4A P:Hem502 3.04 Fe C4B P:Hem502 2.96 Fe C3A P:Hem502 4.29 Fe C4C P:Hem502 2.96 Fe C2B P:Hem502 4.25 Fe C1C P:Hem502 2.96 Fe C2C P:Hem502 4.20 Fe ND P:Hem502 1.93 Fe CHD P:Hem502 3.32 Fe C1B P:Hem502 3.02 Fe NB P:Hem502 1.95 Fe FE P:Hem502 0.00 Fe C3C P:Hem502 4.21 Fe C3B P:Hem502 4.22 Fe C4D P:Hem502 3.00 Fe C1A P:Hem502 3.04 Fe O P:Hoh383 4.94 interactive model: Iron binding site 8 out of 10 in 3l75 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 3l75. 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: Q: His41, Q: Met160, Q: Hec501, conact list: Atom Atom Distance (A) Fe NE2 Q:His41 2.00 Fe ND1 Q:His41 4.10 Fe CD2 Q:His41 2.98 Fe CE1 Q:His41 3.00 Fe CG Q:His41 4.12 Fe CB Q:Met160 4.32 Fe CE Q:Met160 3.50 Fe CG Q:Met160 3.58 Fe SD Q:Met160 2.20 Fe C2D Q:Hec501 4.22 Fe NC Q:Hec501 1.93 Fe CHB Q:Hec501 3.39 Fe CHC Q:Hec501 3.35 Fe C3D Q:Hec501 4.27 Fe NA Q:Hec501 2.01 Fe CHA Q:Hec501 3.40 Fe C2A Q:Hec501 4.31 Fe C1D Q:Hec501 2.98 Fe C4A Q:Hec501 3.04 Fe C4B Q:Hec501 2.99 Fe C3A Q:Hec501 4.27 Fe C4C Q:Hec501 2.96 Fe C2B Q:Hec501 4.22 Fe C1C Q:Hec501 2.98 Fe C2C Q:Hec501 4.22 Fe ND Q:Hec501 1.97 Fe CHD Q:Hec501 3.32 Fe C1B Q:Hec501 3.00 Fe NB Q:Hec501 1.96 Fe FE Q:Hec501 0.00 Fe C3C Q:Hec501 4.21 Fe C3B Q:Hec501 4.22 Fe C4D Q:Hec501 3.03 Fe C1A Q:Hec501 3.07 interactive model: Iron binding site 9 out of 10 in 3l75 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Iron in the PDB 3l75. 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: R: Cys139, R: His141, R: Leu142, R: Cys144, R: Cys158, R: Cys160, R: His161, R: Ser163, R: Fes501, conact list: Atom Atom Distance (A) Fe CB R:Cys139 3.04 Fe SG R:Cys139 2.27 Fe CA R:Cys139 4.51 Fe CB R:His141 3.92 Fe ND1 R:His141 4.38 Fe CG R:His141 4.64 Fe N R:Leu142 4.82 Fe N R:Cys144 4.67 Fe CB R:Cys144 4.09 Fe SG R:Cys144 4.79 Fe CA R:Cys144 4.87 Fe O R:Cys158 4.80 Fe CB R:Cys158 3.07 Fe SG R:Cys158 2.25 Fe C R:Cys158 4.80 Fe CA R:Cys158 4.48 Fe N R:Cys160 4.90 Fe CB R:Cys160 4.29 Fe N R:His161 4.53 Fe ND1 R:His161 4.57 Fe N R:Ser163 4.92 Fe CB R:Ser163 4.24 Fe OG R:Ser163 4.02 Fe S1 R:Fes501 2.22 Fe S2 R:Fes501 2.23 Fe FE1 R:Fes501 0.00 Fe FE2 R:Fes501 2.70 interactive model: Iron binding site 10 out of 10 in 3l75 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Iron in the PDB 3l75. 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: R: Cys139, R: His141, R: Leu142, R: Cys158, R: Cys160, R: His161, R: Ser163, R: Fes501, conact list: Atom Atom Distance (A) Fe SG R:Cys139 4.33 Fe NE2 R:His141 4.28 Fe CB R:His141 3.32 Fe ND1 R:His141 2.16 Fe CD2 R:His141 4.26 Fe C R:His141 4.90 Fe CE1 R:His141 3.19 Fe CG R:His141 3.09 Fe CA R:His141 4.69 Fe N R:Leu142 4.13 Fe CB R:Leu142 4.53 Fe CD1 R:Leu142 4.79 Fe CG R:Leu142 4.67 Fe CA R:Leu142 4.91 Fe SG R:Cys158 4.56 Fe CB R:Cys160 4.03 Fe C R:Cys160 4.46 Fe CA R:Cys160 4.82 Fe NE2 R:His161 4.27 Fe N R:His161 3.73 Fe CB R:His161 3.30 Fe ND1 R:His161 2.17 Fe CD2 R:His161 4.24 Fe C R:His161 4.81 Fe CE1 R:His161 3.20 Fe CG R:His161 3.07 Fe CA R:His161 4.08 Fe OG R:Ser163 4.59 Fe S1 R:Fes501 2.23 Fe S2 R:Fes501 2.23 Fe FE1 R:Fes501 2.70 Fe FE2 R:Fes501 0.00 interactive model: