Iron in the structure of Cytochrome BC1 Complex From Bovine (pdb 1bgy)

The binding sites of Iron atom in the structure of Cytochrome BC1 Complex From Bovine (pdb code 1bgy). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1bgy structure was solved by S.IWATA, J.W.LEE, K.OKADA, J.K.LEE, M.IWATA, S.RAMASWAMY, B.K.JAP, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-3.0 Space group P65 a (A) 130.110 b (A) 130.110 c (A) 720.940 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 32 Rfree (%) 36 Iron Binding Sites: Iron binding site 1 out of 8 in 1bgy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1bgy. 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: Gly48, C: His83, C: His182, C: Hem380, conact list: Atom Atom Distance (A) Fe CA C:Gly48 4.98 Fe NE2 C:His83 2.05 Fe ND1 C:His83 3.89 Fe CD2 C:His83 3.32 Fe CE1 C:His83 2.64 Fe CG C:His83 4.24 Fe NE2 C:His182 2.07 Fe ND1 C:His182 4.00 Fe CD2 C:His182 3.28 Fe CE1 C:His182 2.78 Fe CG C:His182 4.29 Fe C2D C:Hem380 4.32 Fe NC C:Hem380 2.01 Fe CHB C:Hem380 3.44 Fe CHC C:Hem380 3.45 Fe C3D C:Hem380 4.30 Fe NA C:Hem380 1.99 Fe CHA C:Hem380 3.37 Fe C2A C:Hem380 4.25 Fe C1D C:Hem380 3.07 Fe C4A C:Hem380 3.03 Fe C4B C:Hem380 3.07 Fe C3A C:Hem380 4.24 Fe C4C C:Hem380 3.03 Fe C2B C:Hem380 4.32 Fe C1C C:Hem380 3.03 Fe C2C C:Hem380 4.24 Fe ND C:Hem380 2.02 Fe CHD C:Hem380 3.43 Fe C1B C:Hem380 3.07 Fe NB C:Hem380 2.04 Fe FE C:Hem380 0.00 Fe C3C C:Hem380 4.26 Fe C3B C:Hem380 4.29 Fe C4D C:Hem380 3.06 Fe C1A C:Hem380 3.02 interactive model: Iron binding site 2 out of 8 in 1bgy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1bgy. 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: Leu37, C: His97, C: His196, C: Hem381, conact list: Atom Atom Distance (A) Fe CD1 C:Leu37 4.62 Fe NE2 C:His97 2.05 Fe ND1 C:His97 4.23 Fe CD2 C:His97 2.89 Fe CE1 C:His97 3.23 Fe CG C:His97 4.15 Fe NE2 C:His196 2.18 Fe ND1 C:His196 4.13 Fe CD2 C:His196 3.32 Fe CE1 C:His196 2.95 Fe CG C:His196 4.36 Fe C2D C:Hem381 4.23 Fe NC C:Hem381 2.02 Fe CHB C:Hem381 3.29 Fe CHC C:Hem381 3.41 Fe C3D C:Hem381 4.25 Fe NA C:Hem381 1.98 Fe CHA C:Hem381 3.38 Fe C2A C:Hem381 4.20 Fe C1D C:Hem381 3.02 Fe C4A C:Hem381 3.01 Fe C4B C:Hem381 3.07 Fe C3A C:Hem381 4.20 Fe C4C C:Hem381 3.08 Fe C2B C:Hem381 4.27 Fe C1C C:Hem381 3.10 Fe C2C C:Hem381 4.39 Fe ND C:Hem381 2.01 Fe CHD C:Hem381 3.42 Fe C1B C:Hem381 3.04 Fe NB C:Hem381 2.01 Fe FE C:Hem381 0.00 Fe C3C C:Hem381 4.34 Fe C3B C:Hem381 4.29 Fe C4D C:Hem381 3.04 Fe C1A C:Hem381 3.00 interactive model: Iron binding site 3 out of 8 in 1bgy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1bgy. 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: Hec242, conact list: Atom Atom Distance (A) Fe NE2 D:His41 1.92 Fe ND1 D:His41 3.78 Fe CD2 D:His41 3.15 Fe CE1 D:His41 2.53 Fe CG D:His41 4.09 Fe CB D:Met160 4.93 Fe CE D:Met160 3.59 Fe CG D:Met160 3.80 Fe SD D:Met160 2.36 Fe C2D D:Hec242 4.26 Fe NC D:Hec242 2.00 Fe CHB D:Hec242 3.40 Fe CHC D:Hec242 3.39 Fe C3D D:Hec242 4.26 Fe NA D:Hec242 2.01 Fe CHA D:Hec242 3.41 Fe C2A D:Hec242 4.21 Fe C1D D:Hec242 3.04 Fe C4A D:Hec242 3.03 Fe C4B D:Hec242 3.03 Fe C3A D:Hec242 4.23 Fe C4C D:Hec242 3.03 Fe C2B D:Hec242 4.25 Fe C1C D:Hec242 3.03 Fe C2C D:Hec242 4.24 Fe ND D:Hec242 2.01 Fe CHD D:Hec242 3.40 Fe C1B D:Hec242 3.03 Fe NB D:Hec242 2.00 Fe FE D:Hec242 0.00 Fe C3C D:Hec242 4.23 Fe C3B D:Hec242 4.25 Fe C4D D:Hec242 3.04 Fe C1A D:Hec242 3.02 interactive model: Iron binding site 4 out of 8 in 1bgy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1bgy. 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: O: Gly48, O: His83, O: His182, O: Hem380, conact list: Atom Atom Distance (A) Fe CA O:Gly48 5.00 Fe NE2 O:His83 2.12 Fe ND1 O:His83 4.01 Fe CD2 O:His83 3.39 Fe CE1 O:His83 2.76 Fe CG O:His83 4.36 Fe NE2 O:His182 2.03 Fe ND1 O:His182 3.89 Fe CD2 O:His182 3.24 Fe CE1 O:His182 2.69 Fe CG O:His182 4.19 Fe C2D O:Hem380 4.28 Fe NC O:Hem380 1.99 Fe CHB O:Hem380 3.39 Fe CHC O:Hem380 3.44 Fe C3D O:Hem380 4.31 Fe NA O:Hem380 2.02 Fe CHA O:Hem380 3.41 Fe C2A O:Hem380 4.34 Fe C1D O:Hem380 3.02 Fe C4A O:Hem380 3.03 Fe C4B O:Hem380 3.11 Fe C3A O:Hem380 4.28 Fe C4C O:Hem380 3.00 Fe C2B O:Hem380 4.41 Fe C1C O:Hem380 3.06 Fe C2C O:Hem380 4.23 Fe ND O:Hem380 2.00 Fe CHD O:Hem380 3.35 Fe C1B O:Hem380 3.11 Fe NB O:Hem380 2.04 Fe FE O:Hem380 0.00 Fe C3C O:Hem380 4.23 Fe C3B O:Hem380 4.34 Fe C4D O:Hem380 3.09 Fe C1A O:Hem380 3.09 interactive model: Iron binding site 5 out of 8 in 1bgy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1bgy. 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: O: Leu37, O: His97, O: His196, O: Hem381, conact list: Atom Atom Distance (A) Fe CD1 O:Leu37 4.61 Fe NE2 O:His97 2.06 Fe ND1 O:His97 4.21 Fe CD2 O:His97 2.83 Fe CE1 O:His97 3.20 Fe CG O:His97 4.08 Fe NE2 O:His196 2.10 Fe ND1 O:His196 4.18 Fe CD2 O:His196 3.25 Fe CE1 O:His196 3.00 Fe CG O:His196 4.34 Fe C2D O:Hem381 4.24 Fe NC O:Hem381 2.06 Fe CHB O:Hem381 3.35 Fe CHC O:Hem381 3.44 Fe C3D O:Hem381 4.25 Fe NA O:Hem381 2.06 Fe CHA O:Hem381 3.39 Fe C2A O:Hem381 4.27 Fe C1D O:Hem381 3.01 Fe C4A O:Hem381 3.03 Fe C4B O:Hem381 3.02 Fe C3A O:Hem381 4.23 Fe C4C O:Hem381 3.06 Fe C2B O:Hem381 4.25 Fe C1C O:Hem381 3.07 Fe C2C O:Hem381 4.28 Fe ND O:Hem381 1.97 Fe CHD O:Hem381 3.39 Fe C1B O:Hem381 3.07 Fe NB O:Hem381 2.02 Fe FE O:Hem381 0.00 Fe C3C O:Hem381 4.26 Fe C3B O:Hem381 4.27 Fe C4D O:Hem381 3.03 Fe C1A O:Hem381 3.12 interactive model: Iron binding site 6 out of 8 in 1bgy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1bgy. 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: His41, P: Met160, P: Hec242, conact list: Atom Atom Distance (A) Fe NE2 P:His41 1.96 Fe ND1 P:His41 3.89 Fe CD2 P:His41 3.15 Fe CE1 P:His41 2.67 Fe CG P:His41 4.14 Fe CB P:Met160 4.93 Fe CE P:Met160 3.80 Fe CG P:Met160 3.68 Fe SD P:Met160 2.35 Fe C2D P:Hec242 4.28 Fe NC P:Hec242 2.01 Fe CHB P:Hec242 3.37 Fe CHC P:Hec242 3.39 Fe C3D P:Hec242 4.28 Fe NA P:Hec242 1.98 Fe CHA P:Hec242 3.39 Fe C2A P:Hec242 4.19 Fe C1D P:Hec242 3.06 Fe C4A P:Hec242 2.99 Fe C4B P:Hec242 3.02 Fe C3A P:Hec242 4.19 Fe C4C P:Hec242 3.03 Fe C2B P:Hec242 4.23 Fe C1C P:Hec242 3.04 Fe C2C P:Hec242 4.26 Fe ND P:Hec242 2.02 Fe CHD P:Hec242 3.42 Fe C1B P:Hec242 3.01 Fe NB P:Hec242 1.98 Fe FE P:Hec242 0.00 Fe C3C P:Hec242 4.24 Fe C3B P:Hec242 4.24 Fe C4D P:Hec242 3.04 Fe C1A P:Hec242 3.00 interactive model: Iron binding site 7 out of 8 in 1bgy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1bgy. 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: Cys139, Q: His141, Q: Leu142, Q: Gly143, Q: Cys144, Q: Cys158, Q: Cys160, Q: His161, Q: Ser163, Q: Fes197, conact list: Atom Atom Distance (A) Fe CB Q:Cys139 3.41 Fe SG Q:Cys139 2.29 Fe CA Q:Cys139 4.75 Fe CB Q:His141 3.97 Fe ND1 Q:His141 4.35 Fe CG Q:His141 4.65 Fe N Q:Leu142 4.68 Fe N Q:Gly143 4.75 Fe O Q:Cys144 4.18 Fe N Q:Cys144 4.81 Fe SG Q:Cys144 4.98 Fe O Q:Cys158 4.36 Fe CB Q:Cys158 3.22 Fe SG Q:Cys158 2.18 Fe C Q:Cys158 4.72 Fe CA Q:Cys158 4.57 Fe CB Q:Cys160 4.09 Fe CA Q:Cys160 4.89 Fe N Q:His161 4.68 Fe ND1 Q:His161 4.58 Fe CB Q:Ser163 4.86 Fe OG Q:Ser163 4.98 Fe S1 Q:Fes197 2.33 Fe S2 Q:Fes197 2.35 Fe FE1 Q:Fes197 0.00 Fe FE2 Q:Fes197 2.71 interactive model: Iron binding site 8 out of 8 in 1bgy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 1bgy. 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: Cys139, Q: His141, Q: Leu142, Q: Cys158, Q: Cys160, Q: His161, Q: Ser163, Q: Fes197, conact list: Atom Atom Distance (A) Fe SG Q:Cys139 4.11 Fe NE2 Q:His141 4.29 Fe CB Q:His141 3.34 Fe ND1 Q:His141 2.17 Fe CD2 Q:His141 4.26 Fe C Q:His141 4.95 Fe CE1 Q:His141 3.21 Fe CG Q:His141 3.10 Fe CA Q:His141 4.77 Fe N Q:Leu142 4.18 Fe CB Q:Leu142 4.67 Fe CG Q:Leu142 4.89 Fe CA Q:Leu142 4.99 Fe SG Q:Cys158 4.10 Fe O Q:Cys160 4.70 Fe CB Q:Cys160 4.23 Fe C Q:Cys160 4.31 Fe CA Q:Cys160 4.86 Fe NE2 Q:His161 4.23 Fe N Q:His161 3.91 Fe CB Q:His161 3.14 Fe ND1 Q:His161 2.14 Fe CD2 Q:His161 4.18 Fe C Q:His161 4.95 Fe CE1 Q:His161 3.19 Fe CG Q:His161 3.00 Fe CA Q:His161 4.11 Fe OG Q:Ser163 4.86 Fe S1 Q:Fes197 2.25 Fe S2 Q:Fes197 2.32 Fe FE1 Q:Fes197 2.71 Fe FE2 Q:Fes197 0.00 interactive model: