Iron in the structure of Crystal Structure of Mitochondrial Cytochrome BC1 in Complex With Antimycin A1 (pdb 1ntk)

The binding sites of Iron atom in the structure of Crystal Structure of Mitochondrial Cytochrome BC1 in Complex With Antimycin A1 (pdb code 1ntk). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1ntk structure was solved by X.GAO, X.WEN, L.ESSER, B.QUINN, L.YU, C.-A.YU, D.XIA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-2.6 Space group I4122 a (A) 153.785 b (A) 153.785 c (A) 592.498 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 23.3 Rfree (%) 27 Iron Binding Sites: Iron binding site 1 out of 5 in 1ntk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1ntk. 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: Gln44, C: Gly48, C: His83, C: Gly130, C: His182, C: Hem381, conact list: Atom Atom Distance (A) Fe OE1 C:Gln44 4.99 Fe CA C:Gly48 4.77 Fe NE2 C:His83 2.07 Fe ND1 C:His83 4.09 Fe CD2 C:His83 3.18 Fe CE1 C:His83 2.91 Fe CG C:His83 4.24 Fe CA C:Gly130 4.93 Fe NE2 C:His182 2.00 Fe ND1 C:His182 4.04 Fe CD2 C:His182 3.09 Fe CE1 C:His182 2.88 Fe CG C:His182 4.16 Fe C2D C:Hem381 4.08 Fe NC C:Hem381 1.99 Fe CHB C:Hem381 3.62 Fe CHC C:Hem381 3.66 Fe C3D C:Hem381 4.07 Fe NA C:Hem381 2.13 Fe CHA C:Hem381 3.57 Fe C2A C:Hem381 4.38 Fe C1D C:Hem381 3.00 Fe C4A C:Hem381 3.11 Fe C4B C:Hem381 3.09 Fe C3A C:Hem381 4.39 Fe C4C C:Hem381 3.03 Fe C2B C:Hem381 4.18 Fe C1C C:Hem381 3.09 Fe C2C C:Hem381 4.15 Fe ND C:Hem381 1.96 Fe CHD C:Hem381 3.57 Fe C1B C:Hem381 3.07 Fe NB C:Hem381 1.99 Fe FE C:Hem381 0.00 Fe C3C C:Hem381 4.11 Fe C3B C:Hem381 4.17 Fe C4D C:Hem381 3.00 Fe C1A C:Hem381 3.10 interactive model: Iron binding site 2 out of 5 in 1ntk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1ntk. 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: His196, C: Hem382, conact list: Atom Atom Distance (A) Fe NE2 C:His97 2.33 Fe ND1 C:His97 4.44 Fe CD2 C:His97 3.05 Fe CE1 C:His97 3.45 Fe CG C:His97 4.30 Fe NE2 C:His196 2.17 Fe ND1 C:His196 4.12 Fe CD2 C:His196 3.20 Fe CE1 C:His196 3.00 Fe CG C:His196 4.25 Fe C2D C:Hem382 4.16 Fe NC C:Hem382 2.00 Fe CHB C:Hem382 3.58 Fe CHC C:Hem382 3.58 Fe C3D C:Hem382 4.15 Fe NA C:Hem382 2.12 Fe CHA C:Hem382 3.56 Fe C2A C:Hem382 4.34 Fe C1D C:Hem382 3.06 Fe C4A C:Hem382 3.07 Fe C4B C:Hem382 3.07 Fe C3A C:Hem382 4.34 Fe C4C C:Hem382 3.00 Fe C2B C:Hem382 4.17 Fe C1C C:Hem382 3.00 Fe C2C C:Hem382 4.05 Fe ND C:Hem382 1.97 Fe CHD C:Hem382 3.57 Fe C1B C:Hem382 3.07 Fe NB C:Hem382 1.99 Fe FE C:Hem382 0.00 Fe C3C C:Hem382 4.03 Fe C3B C:Hem382 4.17 Fe C4D C:Hem382 3.04 Fe C1A C:Hem382 3.08 interactive model: Iron binding site 3 out of 5 in 1ntk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1ntk. 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: Pro110, D: Met160, D: Hem242, conact list: Atom Atom Distance (A) Fe NE2 D:His41 2.25 Fe ND1 D:His41 4.31 Fe CD2 D:His41 3.27 Fe CE1 D:His41 3.17 Fe CG D:His41 4.40 Fe CB D:Pro110 4.61 Fe CB D:Met160 4.24 Fe CE D:Met160 3.62 Fe CG D:Met160 3.35 Fe SD D:Met160 2.96 Fe C2D D:Hem242 4.08 Fe NC D:Hem242 1.98 Fe CHB D:Hem242 3.62 Fe CHC D:Hem242 3.64 Fe C3D D:Hem242 4.09 Fe NA D:Hem242 2.15 Fe CHA D:Hem242 3.61 Fe C2A D:Hem242 4.41 Fe C1D D:Hem242 3.01 Fe C4A D:Hem242 3.12 Fe C4B D:Hem242 3.10 Fe C3A D:Hem242 4.39 Fe C4C D:Hem242 3.04 Fe C2B D:Hem242 4.18 Fe C1C D:Hem242 3.06 Fe C2C D:Hem242 4.14 Fe ND D:Hem242 1.98 Fe CHD D:Hem242 3.58 Fe C1B D:Hem242 3.08 Fe NB D:Hem242 2.00 Fe FE D:Hem242 0.00 Fe C3C D:Hem242 4.14 Fe C3B D:Hem242 4.20 Fe C4D D:Hem242 3.03 Fe C1A D:Hem242 3.12 interactive model: Iron binding site 4 out of 5 in 1ntk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1ntk. 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: Fes197, conact list: Atom Atom Distance (A) Fe CB E:Cys139 3.52 Fe SG E:Cys139 2.81 Fe CA E:Cys139 4.99 Fe CB E:His141 4.34 Fe ND1 E:His141 4.75 Fe N E:Leu142 4.61 Fe N E:Cys144 4.59 Fe CB E:Cys144 3.91 Fe SG E:Cys144 4.64 Fe CA E:Cys144 4.79 Fe O E:Cys158 4.65 Fe CB E:Cys158 3.32 Fe SG E:Cys158 2.14 Fe C E:Cys158 4.68 Fe CA E:Cys158 4.56 Fe N E:Cys160 4.61 Fe CB E:Cys160 4.04 Fe SG E:Cys160 4.81 Fe CA E:Cys160 4.73 Fe N E:His161 4.38 Fe ND1 E:His161 4.26 Fe CB E:Ser163 4.73 Fe OG E:Ser163 4.47 Fe S1 E:Fes197 2.20 Fe S2 E:Fes197 2.20 Fe FE1 E:Fes197 0.00 Fe FE2 E:Fes197 2.73 interactive model: Iron binding site 5 out of 5 in 1ntk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1ntk. 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: Pro175, E: Fes197, conact list: Atom Atom Distance (A) Fe SG E:Cys139 4.59 Fe NE2 E:His141 4.53 Fe CB E:His141 3.48 Fe ND1 E:His141 2.43 Fe CD2 E:His141 4.50 Fe C E:His141 4.74 Fe CE1 E:His141 3.44 Fe CG E:His141 3.32 Fe CA E:His141 4.71 Fe N E:Leu142 4.09 Fe CB E:Leu142 4.22 Fe CD1 E:Leu142 4.46 Fe CG E:Leu142 4.26 Fe CA E:Leu142 4.73 Fe SG E:Cys158 4.73 Fe CB E:Cys160 4.16 Fe C E:Cys160 4.36 Fe CA E:Cys160 4.80 Fe NE2 E:His161 4.10 Fe N E:His161 3.70 Fe CB E:His161 3.23 Fe ND1 E:His161 2.04 Fe CD2 E:His161 4.08 Fe C E:His161 4.82 Fe CE1 E:His161 3.04 Fe CG E:His161 2.94 Fe CA E:His161 4.01 Fe OG E:Ser163 4.86 Fe CG E:Pro175 4.55 Fe S1 E:Fes197 2.21 Fe S2 E:Fes197 2.20 Fe FE1 E:Fes197 2.73 Fe FE2 E:Fes197 0.00 interactive model: