Iron in the structure of The 1.5 A Resolution Crystal Structure of [FE3S4]- Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus (pdb 1sj1)

The binding sites of Iron atom in the structure of The 1.5 A Resolution Crystal Structure of [FE3S4]- Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus (pdb code 1sj1). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1sj1 structure was solved by M.S.NIELSEN, P.HARRIS, B.L.OOI, H.E.CHRISTENSEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.6-1.5 Space group P1211 a (A) 31.230 b (A) 47.511 c (A) 52.029 alpha (°) 90.00 beta (°) 103.86 gamma (°) 90.00 Rfactor (%) 19.4 Rfree (%) 22.3 Iron Binding Sites: Iron binding site 1 out of 6 in 1sj1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1sj1. 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: Val6, A: Cys11, A: Ile12, A: Gly13, A: Asp14, A: Ala15, A: Cys17, A: Ala33, A: Cys56, A: Ala60, A: F3s70, A: Hoh145, conact list: Atom Atom Distance (A) Fe CG1 A:Val6 4.76 Fe CB A:Cys11 3.34 Fe SG A:Cys11 2.28 Fe C A:Cys11 4.31 Fe CA A:Cys11 3.81 Fe N A:Ile12 4.09 Fe C A:Ile12 4.85 Fe N A:Gly13 3.78 Fe C A:Gly13 4.69 Fe CA A:Gly13 4.12 Fe N A:Asp14 4.24 Fe N A:Ala15 4.80 Fe SG A:Cys17 4.76 Fe N A:Ala33 4.40 Fe CB A:Ala33 4.30 Fe CA A:Ala33 4.99 Fe SG A:Cys56 4.66 Fe CB A:Ala60 4.69 Fe S1 A:F3s70 2.17 Fe FE1 A:F3s70 0.00 Fe FE3 A:F3s70 2.65 Fe S4 A:F3s70 3.83 Fe S2 A:F3s70 2.32 Fe FE4 A:F3s70 2.71 Fe S3 A:F3s70 2.33 Fe O A:Hoh145 3.81 interactive model: Iron binding site 2 out of 6 in 1sj1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1sj1. 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: Cys11, A: Ala15, A: Ile16, A: Cys17, A: Ala33, A: Cys56, A: Ile61, A: F3s70, A: Hoh145, conact list: Atom Atom Distance (A) Fe SG A:Cys11 4.66 Fe N A:Ala15 4.08 Fe C A:Ala15 4.69 Fe CA A:Ala15 4.29 Fe N A:Ile16 4.67 Fe N A:Cys17 4.06 Fe CB A:Cys17 3.38 Fe SG A:Cys17 2.32 Fe CA A:Cys17 4.37 Fe CB A:Ala33 3.82 Fe SG A:Cys56 4.79 Fe CD1 A:Ile61 4.43 Fe S1 A:F3s70 2.25 Fe FE1 A:F3s70 2.65 Fe FE3 A:F3s70 0.00 Fe S4 A:F3s70 2.26 Fe S2 A:F3s70 3.96 Fe FE4 A:F3s70 2.75 Fe S3 A:F3s70 2.31 Fe O A:Hoh145 2.90 interactive model: Iron binding site 3 out of 6 in 1sj1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1sj1. 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: Cys11, A: Asp14, A: Cys17, A: Cys56, A: Pro57, A: Val58, A: Ala60, A: Ile61, A: F3s70, A: Hoh145, conact list: Atom Atom Distance (A) Fe SG A:Cys11 4.81 Fe CB A:Asp14 4.72 Fe SG A:Cys17 4.88 Fe CB A:Cys56 3.20 Fe SG A:Cys56 2.23 Fe C A:Cys56 4.62 Fe CA A:Cys56 3.93 Fe N A:Pro57 4.71 Fe CD A:Pro57 4.32 Fe CG2 A:Val58 4.56 Fe N A:Ala60 5.00 Fe CB A:Ala60 4.29 Fe CD1 A:Ile61 4.56 Fe CG1 A:Ile61 4.86 Fe S1 A:F3s70 3.91 Fe FE1 A:F3s70 2.71 Fe FE3 A:F3s70 2.75 Fe S4 A:F3s70 2.24 Fe S2 A:F3s70 2.34 Fe FE4 A:F3s70 0.00 Fe S3 A:F3s70 2.38 Fe O A:Hoh145 2.59 interactive model: Iron binding site 4 out of 6 in 1sj1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1sj1. 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: Val6, B: Cys11, B: Ile12, B: Gly13, B: Asp14, B: Ala15, B: Cys17, B: Ala33, B: Cys56, B: Ala60, B: F3s70, B: Hoh77, conact list: Atom Atom Distance (A) Fe CG1 B:Val6 4.83 Fe CB B:Cys11 3.39 Fe SG B:Cys11 2.27 Fe C B:Cys11 4.30 Fe CA B:Cys11 3.81 Fe N B:Ile12 4.10 Fe C B:Ile12 4.84 Fe N B:Gly13 3.76 Fe C B:Gly13 4.70 Fe CA B:Gly13 4.13 Fe N B:Asp14 4.30 Fe N B:Ala15 4.85 Fe SG B:Cys17 4.76 Fe N B:Ala33 4.38 Fe CB B:Ala33 4.39 Fe SG B:Cys56 4.70 Fe CB B:Ala60 4.72 Fe S1 B:F3s70 2.23 Fe FE1 B:F3s70 0.00 Fe FE3 B:F3s70 2.69 Fe S4 B:F3s70 3.87 Fe S2 B:F3s70 2.32 Fe FE4 B:F3s70 2.68 Fe S3 B:F3s70 2.35 Fe O B:Hoh77 2.89 interactive model: Iron binding site 5 out of 6 in 1sj1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1sj1. 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: Cys11, B: Ala15, B: Ile16, B: Cys17, B: Ala33, B: Cys56, B: Ile61, B: F3s70, B: Hoh77, conact list: Atom Atom Distance (A) Fe SG B:Cys11 4.70 Fe N B:Ala15 4.11 Fe C B:Ala15 4.64 Fe CA B:Ala15 4.30 Fe N B:Ile16 4.58 Fe N B:Cys17 4.02 Fe CB B:Cys17 3.34 Fe SG B:Cys17 2.32 Fe CA B:Cys17 4.32 Fe CB B:Ala33 3.94 Fe SG B:Cys56 4.79 Fe CD1 B:Ile61 4.44 Fe S1 B:F3s70 2.33 Fe FE1 B:F3s70 2.69 Fe FE3 B:F3s70 0.00 Fe S4 B:F3s70 2.23 Fe S2 B:F3s70 3.93 Fe FE4 B:F3s70 2.72 Fe S3 B:F3s70 2.36 Fe O B:Hoh77 2.64 interactive model: Iron binding site 6 out of 6 in 1sj1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1sj1. 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: Cys11, B: Asp14, B: Cys17, B: Cys56, B: Pro57, B: Val58, B: Ala60, B: Ile61, B: F3s70, B: Hoh77, conact list: Atom Atom Distance (A) Fe SG B:Cys11 4.78 Fe CB B:Asp14 4.73 Fe SG B:Cys17 4.87 Fe CB B:Cys56 3.32 Fe SG B:Cys56 2.28 Fe C B:Cys56 4.70 Fe CA B:Cys56 3.97 Fe N B:Pro57 4.73 Fe CD B:Pro57 4.29 Fe CG2 B:Val58 4.44 Fe CB B:Ala60 4.33 Fe CD1 B:Ile61 4.58 Fe CG1 B:Ile61 4.90 Fe S1 B:F3s70 3.94 Fe FE1 B:F3s70 2.68 Fe FE3 B:F3s70 2.72 Fe S4 B:F3s70 2.32 Fe S2 B:F3s70 2.32 Fe FE4 B:F3s70 0.00 Fe S3 B:F3s70 2.31 Fe O B:Hoh77 2.54 interactive model: