Iron in the structure of Crystal Structure of the Cytochrome B6F Complex With 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus (pdb 2e75)

The binding sites of Iron atom in the structure of Crystal Structure of the Cytochrome B6F Complex With 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus (pdb code 2e75). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2e75 structure was solved by W.A.CRAMER, E.YAMASHITA, H.ZHANG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 49.9-3.5 Space group P6122 a (A) 159.164 b (A) 159.164 c (A) 362.269 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 20.1 Rfree (%) 26.7 Iron Binding Sites: Iron binding site 1 out of 6 in 2e75 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2e75. 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: His86, A: His187, A: Hem301, conact list: Atom Atom Distance (A) Fe NE2 A:His86 1.89 Fe ND1 A:His86 3.93 Fe CD2 A:His86 3.02 Fe CE1 A:His86 2.75 Fe CG A:His86 4.09 Fe NE2 A:His187 1.91 Fe ND1 A:His187 3.93 Fe CD2 A:His187 3.08 Fe CE1 A:His187 2.72 Fe CG A:His187 4.14 Fe C2D A:Hem301 4.20 Fe NC A:Hem301 2.06 Fe CHB A:Hem301 3.09 Fe CHC A:Hem301 3.43 Fe C3D A:Hem301 4.31 Fe NA A:Hem301 1.82 Fe CHA A:Hem301 3.56 Fe C2A A:Hem301 4.18 Fe C1D A:Hem301 2.92 Fe C4A A:Hem301 2.72 Fe C4B A:Hem301 2.91 Fe C3A A:Hem301 4.01 Fe C4C A:Hem301 2.97 Fe C2B A:Hem301 4.11 Fe C1C A:Hem301 3.17 Fe C2C A:Hem301 4.44 Fe ND A:Hem301 2.02 Fe CHD A:Hem301 3.22 Fe C1B A:Hem301 2.81 Fe NB A:Hem301 1.81 Fe FE A:Hem301 0.00 Fe C3C A:Hem301 4.24 Fe C3B A:Hem301 4.06 Fe C4D A:Hem301 3.13 Fe C1A A:Hem301 3.03 interactive model: Iron binding site 2 out of 6 in 2e75 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2e75. 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: His100, A: His202, A: Hem302, conact list: Atom Atom Distance (A) Fe NE2 A:His100 2.05 Fe ND1 A:His100 3.77 Fe CD2 A:His100 3.33 Fe CE1 A:His100 2.51 Fe CG A:His100 4.21 Fe NE2 A:His202 1.88 Fe ND1 A:His202 3.87 Fe CD2 A:His202 2.96 Fe CE1 A:His202 2.73 Fe CG A:His202 4.02 Fe C2D A:Hem302 4.12 Fe NC A:Hem302 1.93 Fe CHB A:Hem302 3.46 Fe CHC A:Hem302 3.29 Fe C3D A:Hem302 4.26 Fe NA A:Hem302 1.97 Fe CHA A:Hem302 3.37 Fe C2A A:Hem302 4.20 Fe C1D A:Hem302 2.83 Fe C4A A:Hem302 3.06 Fe C4B A:Hem302 2.88 Fe C3A A:Hem302 4.25 Fe C4C A:Hem302 2.84 Fe C2B A:Hem302 4.20 Fe C1C A:Hem302 3.03 Fe C2C A:Hem302 4.29 Fe ND A:Hem302 1.94 Fe CHD A:Hem302 3.14 Fe C1B A:Hem302 3.01 Fe NB A:Hem302 1.91 Fe FE A:Hem302 0.00 Fe C3C A:Hem302 4.10 Fe C3B A:Hem302 4.13 Fe C4D A:Hem302 3.06 Fe C1A A:Hem302 2.96 interactive model: Iron binding site 3 out of 6 in 2e75 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2e75. 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: Tyr34, B: Phe40, A: Hem302, A: Hem303, A: Qno501, A: Hoh1107, conact list: Atom Atom Distance (A) Fe O A:Tyr34 4.75 Fe CE2 B:Phe40 3.15 Fe CD2 B:Phe40 4.55 Fe CZ B:Phe40 3.22 Fe CE1 B:Phe40 4.59 Fe O2A A:Hem302 4.96 Fe C2D A:Hem303 4.28 Fe NC A:Hem303 2.08 Fe CHB A:Hem303 3.37 Fe CHC A:Hem303 3.45 Fe C3D A:Hem303 4.44 Fe NA A:Hem303 2.03 Fe CHA A:Hem303 3.58 Fe C2A A:Hem303 4.25 Fe C1D A:Hem303 3.04 Fe C4A A:Hem303 2.93 Fe C4B A:Hem303 3.13 Fe C3A A:Hem303 4.14 Fe C4C A:Hem303 3.02 Fe C2B A:Hem303 4.28 Fe C1C A:Hem303 3.03 Fe C2C A:Hem303 4.15 Fe ND A:Hem303 2.20 Fe CHD A:Hem303 3.34 Fe C1B A:Hem303 3.08 Fe NB A:Hem303 2.13 Fe FE A:Hem303 0.00 Fe C3C A:Hem303 4.15 Fe C3B A:Hem303 4.31 Fe C4D A:Hem303 3.26 Fe C1A A:Hem303 3.11 Fe C61 A:Qno501 3.50 Fe OH A:Qno501 2.18 Fe C62 A:Qno501 4.62 Fe C2 A:Qno501 4.61 Fe N1 A:Qno501 3.45 Fe C6 A:Qno501 3.97 Fe O A:Hoh1107 2.25 interactive model: Iron binding site 4 out of 6 in 2e75 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2e75. 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: Tyr1, C: Pro2, C: Trp4, C: His26, C: Asn154, C: Hem301, conact list: Atom Atom Distance (A) Fe O C:Tyr1 4.00 Fe N C:Tyr1 1.99 Fe CB C:Tyr1 4.24 Fe C C:Tyr1 3.60 Fe CG C:Tyr1 4.73 Fe CA C:Tyr1 2.86 Fe N C:Pro2 4.45 Fe CD C:Pro2 4.73 Fe CE3 C:Trp4 4.67 Fe CZ3 C:Trp4 4.93 Fe NE2 C:His26 2.07 Fe ND1 C:His26 4.22 Fe CD2 C:His26 2.75 Fe CE1 C:His26 3.25 Fe CG C:His26 4.02 Fe OD1 C:Asn154 4.92 Fe C2D C:Hem301 4.33 Fe NC C:Hem301 1.91 Fe CHB C:Hem301 3.30 Fe CHC C:Hem301 3.49 Fe C3D C:Hem301 4.22 Fe NA C:Hem301 1.81 Fe CHA C:Hem301 3.15 Fe C2A C:Hem301 4.06 Fe C1D C:Hem301 3.11 Fe C4A C:Hem301 2.89 Fe C4B C:Hem301 3.20 Fe C3A C:Hem301 4.10 Fe C4C C:Hem301 2.93 Fe C2B C:Hem301 4.34 Fe C1C C:Hem301 2.97 Fe C2C C:Hem301 4.15 Fe ND C:Hem301 1.99 Fe CHD C:Hem301 3.47 Fe C1B C:Hem301 3.04 Fe NB C:Hem301 2.09 Fe FE C:Hem301 0.00 Fe C3C C:Hem301 4.11 Fe C3B C:Hem301 4.42 Fe C4D C:Hem301 2.91 Fe C1A C:Hem301 2.80 interactive model: Iron binding site 5 out of 6 in 2e75 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 2e75. 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: Cys108, D: Thr109, D: His110, D: Leu111, D: Cys126, D: His129, D: Ser131, D: Tyr133, D: Ala144, D: Fes200, conact list: Atom Atom Distance (A) Fe CB D:Cys108 3.06 Fe SG D:Cys108 1.32 Fe C D:Cys108 4.52 Fe CA D:Cys108 4.28 Fe N D:Thr109 4.26 Fe N D:His110 4.27 Fe CB D:His110 3.72 Fe ND1 D:His110 4.51 Fe C D:His110 4.91 Fe CG D:His110 4.58 Fe CA D:His110 4.61 Fe N D:Leu111 4.44 Fe CB D:Cys126 3.31 Fe SG D:Cys126 2.42 Fe CA D:Cys126 4.80 Fe CB D:His129 4.99 Fe N D:Ser131 4.96 Fe CB D:Ser131 4.32 Fe OG D:Ser131 2.97 Fe OH D:Tyr133 4.21 Fe CB D:Ala144 4.28 Fe S1 D:Fes200 2.23 Fe S2 D:Fes200 2.23 Fe FE1 D:Fes200 0.00 Fe FE2 D:Fes200 3.19 interactive model: Iron binding site 6 out of 6 in 2e75 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 2e75. 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: Cys108, D: His110, D: Leu111, D: Cys113, D: Cys126, D: Cys128, D: His129, D: Pro143, D: Fes200, conact list: Atom Atom Distance (A) Fe SG D:Cys108 4.10 Fe NE2 D:His110 4.74 Fe CB D:His110 4.02 Fe ND1 D:His110 2.76 Fe CD2 D:His110 4.85 Fe CE1 D:His110 3.59 Fe CG D:His110 3.78 Fe N D:Leu111 4.07 Fe CB D:Leu111 4.35 Fe CG D:Leu111 4.86 Fe CA D:Leu111 4.75 Fe SG D:Cys113 4.88 Fe SG D:Cys126 4.10 Fe CB D:Cys128 4.15 Fe C D:Cys128 4.56 Fe CA D:Cys128 4.97 Fe NE2 D:His129 4.33 Fe N D:His129 3.96 Fe CB D:His129 2.71 Fe ND1 D:His129 2.24 Fe CD2 D:His129 4.05 Fe C D:His129 4.72 Fe CE1 D:His129 3.44 Fe CG D:His129 2.79 Fe CA D:His129 3.89 Fe CG D:Pro143 4.64 Fe S1 D:Fes200 2.25 Fe S2 D:Fes200 2.23 Fe FE1 D:Fes200 3.19 Fe FE2 D:Fes200 0.00 interactive model: