Iron in the structure of Rhodobacter Capsulatus Cytochrome BC1 Complex With Stigmatellin Bound (pdb 1zrt)

The binding sites of Iron atom in the structure of Rhodobacter Capsulatus Cytochrome BC1 Complex With Stigmatellin Bound (pdb code 1zrt). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1zrt structure was solved by E.A.BERRY, L.S.HUANG, L.K.SAECHAO, N.G.PON, M.VALKOVA-VALCHANOV, F.DALDAL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 59.4-3.5 Space group P1211 a (A) 95.633 b (A) 154.360 c (A) 103.057 alpha (°) 90.00 beta (°) 113.57 gamma (°) 90.00 Rfactor (%) 30 Rfree (%) 35.8 Iron Binding Sites: Iron binding site 1 out of 10 in 1zrt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1zrt. 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: His97, C: Gly146, C: His198, C: Hem501, conact list: Atom Atom Distance (A) Fe NE2 C:His97 2.00 Fe ND1 C:His97 3.98 Fe CD2 C:His97 3.12 Fe CE1 C:His97 2.82 Fe CG C:His97 4.16 Fe CA C:Gly146 4.81 Fe NE2 C:His198 2.00 Fe ND1 C:His198 4.07 Fe CD2 C:His198 3.05 Fe CE1 C:His198 2.93 Fe CG C:His198 4.16 Fe C2D C:Hem501 4.35 Fe NC C:Hem501 1.80 Fe CHB C:Hem501 3.26 Fe CHC C:Hem501 3.33 Fe C3D C:Hem501 4.31 Fe NA C:Hem501 1.82 Fe CHA C:Hem501 3.44 Fe C2A C:Hem501 4.25 Fe C1D C:Hem501 3.01 Fe C4A C:Hem501 2.87 Fe C4B C:Hem501 2.94 Fe C3A C:Hem501 4.19 Fe C4C C:Hem501 2.89 Fe C2B C:Hem501 4.18 Fe C1C C:Hem501 2.91 Fe C2C C:Hem501 4.18 Fe ND C:Hem501 1.92 Fe CHD C:Hem501 3.33 Fe C1B C:Hem501 2.89 Fe NB C:Hem501 1.81 Fe FE C:Hem501 0.00 Fe C3C C:Hem501 4.14 Fe C3B C:Hem501 4.21 Fe C4D C:Hem501 3.04 Fe C1A C:Hem501 2.99 interactive model: Iron binding site 2 out of 10 in 1zrt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1zrt. 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: His111, C: His212, C: Hem502, conact list: Atom Atom Distance (A) Fe CA C:Gly48 4.62 Fe NE2 C:His111 2.01 Fe ND1 C:His111 3.86 Fe CD2 C:His111 3.09 Fe CE1 C:His111 2.74 Fe CG C:His111 4.05 Fe NE2 C:His212 2.00 Fe ND1 C:His212 4.08 Fe CD2 C:His212 2.96 Fe CE1 C:His212 2.99 Fe CG C:His212 4.09 Fe C2D C:Hem502 4.17 Fe NC C:Hem502 1.89 Fe CHB C:Hem502 3.39 Fe CHC C:Hem502 3.28 Fe C3D C:Hem502 4.11 Fe NA C:Hem502 1.90 Fe CHA C:Hem502 3.26 Fe C2A C:Hem502 4.18 Fe C1D C:Hem502 2.98 Fe C4A C:Hem502 2.98 Fe C4B C:Hem502 2.94 Fe C3A C:Hem502 4.22 Fe C4C C:Hem502 2.97 Fe C2B C:Hem502 4.25 Fe C1C C:Hem502 2.89 Fe C2C C:Hem502 4.14 Fe ND C:Hem502 1.90 Fe CHD C:Hem502 3.37 Fe C1B C:Hem502 2.98 Fe NB C:Hem502 1.89 Fe FE C:Hem502 0.00 Fe C3C C:Hem502 4.20 Fe C3B C:Hem502 4.21 Fe C4D C:Hem502 2.91 Fe C1A C:Hem502 2.91 Fe O1A C:Hem502 4.43 interactive model: Iron binding site 3 out of 10 in 1zrt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1zrt. 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: His38, D: Met183, D: Hec501, conact list: Atom Atom Distance (A) Fe NE2 D:His38 2.00 Fe ND1 D:His38 4.08 Fe CD2 D:His38 2.94 Fe CE1 D:His38 3.00 Fe CG D:His38 4.08 Fe CB D:Met183 4.28 Fe CE D:Met183 3.35 Fe CG D:Met183 3.51 Fe SD D:Met183 2.09 Fe C2D D:Hec501 4.24 Fe NC D:Hec501 1.95 Fe CHB D:Hec501 3.31 Fe CHC D:Hec501 3.36 Fe C3D D:Hec501 4.25 Fe NA D:Hec501 1.90 Fe CHA D:Hec501 3.36 Fe C2A D:Hec501 4.14 Fe C1D D:Hec501 3.02 Fe C4A D:Hec501 2.91 Fe C4B D:Hec501 3.01 Fe C3A D:Hec501 4.11 Fe C4C D:Hec501 3.00 Fe C2B D:Hec501 4.25 Fe C1C D:Hec501 2.99 Fe C2C D:Hec501 4.22 Fe ND D:Hec501 1.97 Fe CHD D:Hec501 3.37 Fe C1B D:Hec501 3.00 Fe NB D:Hec501 1.97 Fe FE D:Hec501 0.00 Fe C3C D:Hec501 4.23 Fe C3B D:Hec501 4.24 Fe C4D D:Hec501 3.03 Fe C1A D:Hec501 2.94 interactive model: Iron binding site 4 out of 10 in 1zrt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1zrt. 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: Cys133, E: His135, E: Leu136, E: Cys138, E: Cys153, E: Cys155, E: His156, E: Ser158, E: Fes501, conact list: Atom Atom Distance (A) Fe CB E:Cys133 3.09 Fe SG E:Cys133 2.26 Fe CA E:Cys133 4.57 Fe N E:His135 4.75 Fe CB E:His135 3.96 Fe ND1 E:His135 4.33 Fe CG E:His135 4.60 Fe CA E:His135 4.83 Fe N E:Leu136 4.52 Fe N E:Cys138 4.80 Fe CB E:Cys138 4.48 Fe SG E:Cys138 4.89 Fe CB E:Cys153 3.06 Fe SG E:Cys153 2.27 Fe C E:Cys153 4.92 Fe CA E:Cys153 4.48 Fe N E:Cys155 4.90 Fe CB E:Cys155 4.12 Fe CA E:Cys155 4.87 Fe N E:His156 4.38 Fe ND1 E:His156 4.40 Fe CB E:Ser158 4.48 Fe OG E:Ser158 3.20 Fe S1 E:Fes501 2.20 Fe S2 E:Fes501 2.19 Fe FE1 E:Fes501 0.00 Fe FE2 E:Fes501 2.63 interactive model: Iron binding site 5 out of 10 in 1zrt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1zrt. 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: Cys133, E: His135, E: Leu136, E: Cys153, E: Cys155, E: His156, E: Ser158, E: Fes501, conact list: Atom Atom Distance (A) Fe SG E:Cys133 4.36 Fe NE2 E:His135 4.17 Fe CB E:His135 3.33 Fe ND1 E:His135 2.13 Fe CD2 E:His135 4.14 Fe C E:His135 4.39 Fe CE1 E:His135 3.12 Fe CG E:His135 3.02 Fe CA E:His135 4.46 Fe N E:Leu136 4.04 Fe CB E:Leu136 4.09 Fe CD1 E:Leu136 4.86 Fe CG E:Leu136 4.75 Fe CA E:Leu136 4.66 Fe SG E:Cys153 4.34 Fe CB E:Cys155 3.88 Fe C E:Cys155 4.29 Fe CA E:Cys155 4.68 Fe NE2 E:His156 4.20 Fe N E:His156 3.74 Fe CB E:His156 3.26 Fe ND1 E:His156 2.12 Fe CD2 E:His156 4.16 Fe CE1 E:His156 3.14 Fe CG E:His156 3.00 Fe CA E:His156 4.11 Fe OG E:Ser158 4.77 Fe S1 E:Fes501 2.19 Fe S2 E:Fes501 2.18 Fe FE1 E:Fes501 2.63 Fe FE2 E:Fes501 0.00 interactive model: Iron binding site 6 out of 10 in 1zrt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1zrt. 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: His97, P: Gly146, P: His198, P: Hem501, conact list: Atom Atom Distance (A) Fe NE2 P:His97 2.00 Fe ND1 P:His97 4.00 Fe CD2 P:His97 3.11 Fe CE1 P:His97 2.84 Fe CG P:His97 4.16 Fe CA P:Gly146 4.77 Fe NE2 P:His198 2.01 Fe ND1 P:His198 4.07 Fe CD2 P:His198 3.07 Fe CE1 P:His198 2.93 Fe CG P:His198 4.18 Fe C2D P:Hem501 4.40 Fe NC P:Hem501 1.89 Fe CHB P:Hem501 3.17 Fe CHC P:Hem501 3.31 Fe C3D P:Hem501 4.36 Fe NA P:Hem501 1.84 Fe CHA P:Hem501 3.43 Fe C2A P:Hem501 4.23 Fe C1D P:Hem501 3.12 Fe C4A P:Hem501 2.82 Fe C4B P:Hem501 2.94 Fe C3A P:Hem501 4.14 Fe C4C P:Hem501 2.96 Fe C2B P:Hem501 4.13 Fe C1C P:Hem501 2.93 Fe C2C P:Hem501 4.19 Fe ND P:Hem501 2.01 Fe CHD P:Hem501 3.42 Fe C1B P:Hem501 2.85 Fe NB P:Hem501 1.82 Fe FE P:Hem501 0.00 Fe C3C P:Hem501 4.19 Fe C3B P:Hem501 4.19 Fe C4D P:Hem501 3.10 Fe C1A P:Hem501 2.98 interactive model: Iron binding site 7 out of 10 in 1zrt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1zrt. 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: Gly48, P: His111, P: His212, P: Hem502, conact list: Atom Atom Distance (A) Fe CA P:Gly48 4.63 Fe NE2 P:His111 2.00 Fe ND1 P:His111 3.87 Fe CD2 P:His111 3.08 Fe CE1 P:His111 2.74 Fe CG P:His111 4.05 Fe NE2 P:His212 2.00 Fe ND1 P:His212 4.07 Fe CD2 P:His212 2.98 Fe CE1 P:His212 2.98 Fe CG P:His212 4.10 Fe C2D P:Hem502 4.15 Fe NC P:Hem502 1.91 Fe CHB P:Hem502 3.40 Fe CHC P:Hem502 3.29 Fe C3D P:Hem502 4.09 Fe NA P:Hem502 1.91 Fe CHA P:Hem502 3.25 Fe C2A P:Hem502 4.18 Fe C1D P:Hem502 2.97 Fe C4A P:Hem502 3.00 Fe C4B P:Hem502 2.98 Fe C3A P:Hem502 4.22 Fe C4C P:Hem502 2.97 Fe C2B P:Hem502 4.28 Fe C1C P:Hem502 2.90 Fe C2C P:Hem502 4.14 Fe ND P:Hem502 1.89 Fe CHD P:Hem502 3.34 Fe C1B P:Hem502 3.02 Fe NB P:Hem502 1.93 Fe FE P:Hem502 0.00 Fe C3C P:Hem502 4.19 Fe C3B P:Hem502 4.23 Fe C4D P:Hem502 2.91 Fe C1A P:Hem502 2.91 Fe O1A P:Hem502 4.43 interactive model: Iron binding site 8 out of 10 in 1zrt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 1zrt. 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: His38, Q: Met183, Q: Hec501, conact list: Atom Atom Distance (A) Fe NE2 Q:His38 2.00 Fe ND1 Q:His38 4.07 Fe CD2 Q:His38 2.94 Fe CE1 Q:His38 3.00 Fe CG Q:His38 4.07 Fe CB Q:Met183 4.27 Fe CE Q:Met183 3.33 Fe CG Q:Met183 3.51 Fe SD Q:Met183 2.10 Fe C2D Q:Hec501 4.23 Fe NC Q:Hec501 1.93 Fe CHB Q:Hec501 3.32 Fe CHC Q:Hec501 3.34 Fe C3D Q:Hec501 4.25 Fe NA Q:Hec501 1.93 Fe CHA Q:Hec501 3.37 Fe C2A Q:Hec501 4.16 Fe C1D Q:Hec501 3.01 Fe C4A Q:Hec501 2.94 Fe C4B Q:Hec501 3.01 Fe C3A Q:Hec501 4.14 Fe C4C Q:Hec501 2.98 Fe C2B Q:Hec501 4.25 Fe C1C Q:Hec501 2.97 Fe C2C Q:Hec501 4.21 Fe ND Q:Hec501 1.98 Fe CHD Q:Hec501 3.35 Fe C1B Q:Hec501 3.00 Fe NB Q:Hec501 1.97 Fe FE Q:Hec501 0.00 Fe C3C Q:Hec501 4.21 Fe C3B Q:Hec501 4.24 Fe C4D Q:Hec501 3.04 Fe C1A Q:Hec501 2.96 interactive model: Iron binding site 9 out of 10 in 1zrt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Iron in the PDB 1zrt. 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: Cys133, R: His135, R: Leu136, R: Cys138, R: Cys153, R: Cys155, R: His156, R: Ser158, R: Tyr160, R: Fes501, conact list: Atom Atom Distance (A) Fe CB R:Cys133 3.11 Fe SG R:Cys133 2.27 Fe CA R:Cys133 4.59 Fe N R:His135 4.79 Fe CB R:His135 3.99 Fe ND1 R:His135 4.36 Fe CG R:His135 4.63 Fe CA R:His135 4.87 Fe N R:Leu136 4.58 Fe N R:Cys138 4.84 Fe CB R:Cys138 4.51 Fe SG R:Cys138 4.93 Fe CB R:Cys153 3.03 Fe SG R:Cys153 2.23 Fe C R:Cys153 4.89 Fe CA R:Cys153 4.45 Fe N R:Cys155 4.89 Fe CB R:Cys155 4.13 Fe CA R:Cys155 4.87 Fe N R:His156 4.37 Fe ND1 R:His156 4.40 Fe CB R:Ser158 4.45 Fe OG R:Ser158 3.16 Fe OH R:Tyr160 5.00 Fe S1 R:Fes501 2.20 Fe S2 R:Fes501 2.20 Fe FE1 R:Fes501 0.00 Fe FE2 R:Fes501 2.64 interactive model: Iron binding site 10 out of 10 in 1zrt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Iron in the PDB 1zrt. 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: Cys133, R: His135, R: Leu136, R: Cys153, R: Cys155, R: His156, R: Ser158, R: Fes501, conact list: Atom Atom Distance (A) Fe SG R:Cys133 4.38 Fe NE2 R:His135 4.17 Fe CB R:His135 3.32 Fe ND1 R:His135 2.12 Fe CD2 R:His135 4.14 Fe C R:His135 4.41 Fe CE1 R:His135 3.12 Fe CG R:His135 3.01 Fe CA R:His135 4.46 Fe N R:Leu136 4.07 Fe CB R:Leu136 4.13 Fe CD1 R:Leu136 4.88 Fe CG R:Leu136 4.77 Fe CA R:Leu136 4.69 Fe SG R:Cys153 4.35 Fe O R:Cys155 4.99 Fe CB R:Cys155 3.90 Fe C R:Cys155 4.30 Fe CA R:Cys155 4.69 Fe NE2 R:His156 4.21 Fe N R:His156 3.75 Fe CB R:His156 3.27 Fe ND1 R:His156 2.12 Fe CD2 R:His156 4.17 Fe CE1 R:His156 3.15 Fe CG R:His156 3.02 Fe CA R:His156 4.11 Fe OG R:Ser158 4.74 Fe S1 R:Fes501 2.19 Fe S2 R:Fes501 2.20 Fe FE1 R:Fes501 2.64 Fe FE2 R:Fes501 0.00 interactive model: