Iron in the structure of Crystal Structure of Type I Cytochrome C3 From Desulfovibrio Africanus (pdb 2bq4)

The binding sites of Iron atom in the structure of Crystal Structure of Type I Cytochrome C3 From Desulfovibrio Africanus (pdb code 2bq4). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2bq4 structure was solved by M.CZJZEK, L.PIEULLE, X.MORELLI, F.GUERLESQUIN, E.C.HATCHIKIAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 48.2-1.7 Space group C121 a (A) 100.900 b (A) 46.300 c (A) 54.816 alpha (°) 90.00 beta (°) 118.97 gamma (°) 90.00 Rfactor (%) 20 Rfree (%) 24 Iron Binding Sites: Iron binding site 1 out of 8 in 2bq4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2bq4. 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: His27, A: His44, A: Hec1115, conact list: Atom Atom Distance (A) Fe NE2 A:His27 2.17 Fe ND1 A:His27 4.11 Fe CD2 A:His27 3.19 Fe CE1 A:His27 2.99 Fe CG A:His27 4.23 Fe NE2 A:His44 2.03 Fe ND1 A:His44 4.11 Fe CD2 A:His44 3.06 Fe CE1 A:His44 2.99 Fe CG A:His44 4.18 Fe C2D A:Hec1115 4.30 Fe NC A:Hec1115 1.99 Fe CHB A:Hec1115 3.39 Fe CHC A:Hec1115 3.48 Fe C3D A:Hec1115 4.32 Fe NA A:Hec1115 2.04 Fe CHA A:Hec1115 3.49 Fe C2A A:Hec1115 4.29 Fe C1D A:Hec1115 3.05 Fe C4A A:Hec1115 3.04 Fe C4B A:Hec1115 3.08 Fe C3A A:Hec1115 4.27 Fe C4C A:Hec1115 2.99 Fe C2B A:Hec1115 4.26 Fe C1C A:Hec1115 3.07 Fe C2C A:Hec1115 4.27 Fe ND A:Hec1115 2.08 Fe CHD A:Hec1115 3.38 Fe C1B A:Hec1115 3.04 Fe NB A:Hec1115 2.03 Fe FE A:Hec1115 0.00 Fe C3C A:Hec1115 4.22 Fe C3B A:Hec1115 4.29 Fe C4D A:Hec1115 3.11 Fe C1A A:Hec1115 3.09 interactive model: Iron binding site 2 out of 8 in 2bq4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2bq4. 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: His45, A: His62, A: Met88, A: Hec1116, conact list: Atom Atom Distance (A) Fe NE2 A:His45 2.09 Fe ND1 A:His45 4.17 Fe CD2 A:His45 3.11 Fe CE1 A:His45 3.04 Fe CG A:His45 4.24 Fe NE2 A:His62 1.98 Fe ND1 A:His62 4.03 Fe CD2 A:His62 3.07 Fe CE1 A:His62 2.88 Fe CG A:His62 4.15 Fe CE A:Met88 4.99 Fe C2D A:Hec1116 4.29 Fe NC A:Hec1116 2.06 Fe CHB A:Hec1116 3.40 Fe CHC A:Hec1116 3.49 Fe C3D A:Hec1116 4.30 Fe NA A:Hec1116 2.02 Fe CHA A:Hec1116 3.42 Fe C2A A:Hec1116 4.26 Fe C1D A:Hec1116 3.04 Fe C4A A:Hec1116 3.03 Fe C4B A:Hec1116 3.09 Fe C3A A:Hec1116 4.25 Fe C4C A:Hec1116 3.04 Fe C2B A:Hec1116 4.28 Fe C1C A:Hec1116 3.11 Fe C2C A:Hec1116 4.30 Fe ND A:Hec1116 2.05 Fe CHD A:Hec1116 3.39 Fe C1B A:Hec1116 3.05 Fe NB A:Hec1116 2.05 Fe FE A:Hec1116 0.00 Fe C3C A:Hec1116 4.28 Fe C3B A:Hec1116 4.29 Fe C4D A:Hec1116 3.07 Fe C1A A:Hec1116 3.05 interactive model: Iron binding site 3 out of 8 in 2bq4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2bq4. 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: Phe25, A: His30, A: His94, A: Gly105, A: Hec1117, conact list: Atom Atom Distance (A) Fe CE1 A:Phe25 4.99 Fe NE2 A:His30 2.13 Fe ND1 A:His30 4.06 Fe CD2 A:His30 3.13 Fe CE1 A:His30 2.97 Fe CG A:His30 4.17 Fe NE2 A:His94 2.12 Fe ND1 A:His94 4.17 Fe CD2 A:His94 3.19 Fe CE1 A:His94 3.02 Fe CG A:His94 4.29 Fe N A:Gly105 4.84 Fe CA A:Gly105 4.63 Fe C2D A:Hec1117 4.31 Fe NC A:Hec1117 2.01 Fe CHB A:Hec1117 3.49 Fe CHC A:Hec1117 3.36 Fe C3D A:Hec1117 4.29 Fe NA A:Hec1117 2.03 Fe CHA A:Hec1117 3.43 Fe C2A A:Hec1117 4.27 Fe C1D A:Hec1117 3.08 Fe C4A A:Hec1117 3.08 Fe C4B A:Hec1117 3.01 Fe C3A A:Hec1117 4.28 Fe C4C A:Hec1117 3.06 Fe C2B A:Hec1117 4.28 Fe C1C A:Hec1117 3.01 Fe C2C A:Hec1117 4.25 Fe ND A:Hec1117 2.06 Fe CHD A:Hec1117 3.43 Fe C1B A:Hec1117 3.09 Fe NB A:Hec1117 2.03 Fe FE A:Hec1117 0.00 Fe C3C A:Hec1117 4.27 Fe C3B A:Hec1117 4.25 Fe C4D A:Hec1117 3.06 Fe C1A A:Hec1117 3.05 interactive model: Iron binding site 4 out of 8 in 2bq4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2bq4. 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: Tyr21, A: His83, A: His113, A: Hec1118, conact list: Atom Atom Distance (A) Fe CD1 A:Tyr21 4.90 Fe NE2 A:His83 2.03 Fe ND1 A:His83 4.11 Fe CD2 A:His83 3.00 Fe CE1 A:His83 3.02 Fe CG A:His83 4.13 Fe NE2 A:His113 2.09 Fe ND1 A:His113 4.12 Fe CD2 A:His113 3.18 Fe CE1 A:His113 2.95 Fe CG A:His113 4.25 Fe C2D A:Hec1118 4.32 Fe NC A:Hec1118 2.04 Fe CHB A:Hec1118 3.43 Fe CHC A:Hec1118 3.41 Fe C3D A:Hec1118 4.31 Fe NA A:Hec1118 2.02 Fe CHA A:Hec1118 3.42 Fe C2A A:Hec1118 4.27 Fe C1D A:Hec1118 3.09 Fe C4A A:Hec1118 3.06 Fe C4B A:Hec1118 3.05 Fe C3A A:Hec1118 4.28 Fe C4C A:Hec1118 3.07 Fe C2B A:Hec1118 4.27 Fe C1C A:Hec1118 3.06 Fe C2C A:Hec1118 4.28 Fe ND A:Hec1118 2.07 Fe CHD A:Hec1118 3.46 Fe C1B A:Hec1118 3.06 Fe NB A:Hec1118 2.03 Fe FE A:Hec1118 0.00 Fe C3C A:Hec1118 4.30 Fe C3B A:Hec1118 4.27 Fe C4D A:Hec1118 3.07 Fe C1A A:Hec1118 3.04 interactive model: Iron binding site 5 out of 8 in 2bq4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 2bq4. 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: B: His27, B: His44, B: Ile53, B: Hec1116, conact list: Atom Atom Distance (A) Fe NE2 B:His27 2.07 Fe ND1 B:His27 4.13 Fe CD2 B:His27 3.04 Fe CE1 B:His27 3.04 Fe CG B:His27 4.17 Fe NE2 B:His44 2.10 Fe ND1 B:His44 4.08 Fe CD2 B:His44 3.21 Fe CE1 B:His44 2.92 Fe CG B:His44 4.25 Fe CG2 B:Ile53 4.97 Fe C2D B:Hec1116 4.30 Fe NC B:Hec1116 2.02 Fe CHB B:Hec1116 3.43 Fe CHC B:Hec1116 3.44 Fe C3D B:Hec1116 4.30 Fe NA B:Hec1116 2.06 Fe CHA B:Hec1116 3.45 Fe C2A B:Hec1116 4.31 Fe C1D B:Hec1116 3.07 Fe C4A B:Hec1116 3.07 Fe C4B B:Hec1116 3.06 Fe C3A B:Hec1116 4.29 Fe C4C B:Hec1116 3.04 Fe C2B B:Hec1116 4.27 Fe C1C B:Hec1116 3.06 Fe C2C B:Hec1116 4.27 Fe ND B:Hec1116 2.06 Fe CHD B:Hec1116 3.42 Fe C1B B:Hec1116 3.05 Fe NB B:Hec1116 2.02 Fe FE B:Hec1116 0.00 Fe C3C B:Hec1116 4.26 Fe C3B B:Hec1116 4.28 Fe C4D B:Hec1116 3.08 Fe C1A B:Hec1116 3.09 interactive model: Iron binding site 6 out of 8 in 2bq4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 2bq4. 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: B: His45, B: His62, B: Hec1117, conact list: Atom Atom Distance (A) Fe NE2 B:His45 2.13 Fe ND1 B:His45 4.14 Fe CD2 B:His45 3.21 Fe CE1 B:His45 2.98 Fe CG B:His45 4.28 Fe NE2 B:His62 2.04 Fe ND1 B:His62 4.05 Fe CD2 B:His62 3.12 Fe CE1 B:His62 2.90 Fe CG B:His62 4.18 Fe C2D B:Hec1117 4.31 Fe NC B:Hec1117 2.03 Fe CHB B:Hec1117 3.38 Fe CHC B:Hec1117 3.47 Fe C3D B:Hec1117 4.35 Fe NA B:Hec1117 2.02 Fe CHA B:Hec1117 3.48 Fe C2A B:Hec1117 4.27 Fe C1D B:Hec1117 3.05 Fe C4A B:Hec1117 3.03 Fe C4B B:Hec1117 3.08 Fe C3A B:Hec1117 4.26 Fe C4C B:Hec1117 3.02 Fe C2B B:Hec1117 4.25 Fe C1C B:Hec1117 3.07 Fe C2C B:Hec1117 4.26 Fe ND B:Hec1117 2.10 Fe CHD B:Hec1117 3.37 Fe C1B B:Hec1117 3.03 Fe NB B:Hec1117 2.04 Fe FE B:Hec1117 0.00 Fe C3C B:Hec1117 4.24 Fe C3B B:Hec1117 4.29 Fe C4D B:Hec1117 3.14 Fe C1A B:Hec1117 3.08 interactive model: Iron binding site 7 out of 8 in 2bq4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 2bq4. 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: B: Phe25, B: His30, B: His94, B: Gly105, B: Hec1118, conact list: Atom Atom Distance (A) Fe CE1 B:Phe25 5.00 Fe NE2 B:His30 2.06 Fe ND1 B:His30 4.12 Fe CD2 B:His30 3.05 Fe CE1 B:His30 3.02 Fe CG B:His30 4.17 Fe NE2 B:His94 2.08 Fe ND1 B:His94 4.13 Fe CD2 B:His94 3.16 Fe CE1 B:His94 2.98 Fe CG B:His94 4.26 Fe N B:Gly105 4.73 Fe CA B:Gly105 4.58 Fe C2D B:Hec1118 4.27 Fe NC B:Hec1118 2.05 Fe CHB B:Hec1118 3.48 Fe CHC B:Hec1118 3.42 Fe C3D B:Hec1118 4.27 Fe NA B:Hec1118 2.04 Fe CHA B:Hec1118 3.41 Fe C2A B:Hec1118 4.28 Fe C1D B:Hec1118 3.04 Fe C4A B:Hec1118 3.09 Fe C4B B:Hec1118 3.06 Fe C3A B:Hec1118 4.30 Fe C4C B:Hec1118 3.08 Fe C2B B:Hec1118 4.31 Fe C1C B:Hec1118 3.07 Fe C2C B:Hec1118 4.30 Fe ND B:Hec1118 2.03 Fe CHD B:Hec1118 3.43 Fe C1B B:Hec1118 3.10 Fe NB B:Hec1118 2.06 Fe FE B:Hec1118 0.00 Fe C3C B:Hec1118 4.30 Fe C3B B:Hec1118 4.29 Fe C4D B:Hec1118 3.05 Fe C1A B:Hec1118 3.05 interactive model: Iron binding site 8 out of 8 in 2bq4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 2bq4. 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: B: His83, B: His113, B: Hec1119, conact list: Atom Atom Distance (A) Fe NE2 B:His83 2.03 Fe ND1 B:His83 4.09 Fe CD2 B:His83 3.08 Fe CE1 B:His83 2.95 Fe CG B:His83 4.18 Fe NE2 B:His113 2.04 Fe ND1 B:His113 4.09 Fe CD2 B:His113 3.10 Fe CE1 B:His113 2.94 Fe CG B:His113 4.19 Fe C2D B:Hec1119 4.29 Fe NC B:Hec1119 2.04 Fe CHB B:Hec1119 3.43 Fe CHC B:Hec1119 3.42 Fe C3D B:Hec1119 4.25 Fe NA B:Hec1119 2.02 Fe CHA B:Hec1119 3.38 Fe C2A B:Hec1119 4.27 Fe C1D B:Hec1119 3.08 Fe C4A B:Hec1119 3.05 Fe C4B B:Hec1119 3.05 Fe C3A B:Hec1119 4.26 Fe C4C B:Hec1119 3.09 Fe C2B B:Hec1119 4.28 Fe C1C B:Hec1119 3.05 Fe C2C B:Hec1119 4.28 Fe ND B:Hec1119 2.03 Fe CHD B:Hec1119 3.47 Fe C1B B:Hec1119 3.07 Fe NB B:Hec1119 2.03 Fe FE B:Hec1119 0.00 Fe C3C B:Hec1119 4.31 Fe C3B B:Hec1119 4.28 Fe C4D B:Hec1119 3.01 Fe C1A B:Hec1119 3.04 interactive model: