Iron in the structure of Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans (pdb 3lxf)

The binding sites of Iron atom in the structure of Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans (pdb code 3lxf). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3lxf structure was solved by W.YANG, S.G.BELL, H.WANG, M.BARTLAM, L.L.WONG, Z.RAO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.2-2.3 Space group C121 a (A) 137.554 b (A) 78.788 c (A) 89.200 alpha (°) 90.00 beta (°) 125.04 gamma (°) 90.00 Rfactor (%) 20 Rfree (%) 23.9 Iron Binding Sites: Iron binding site 1 out of 10 in 3lxf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3lxf. 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: Cys40, A: Gly42, A: Cys43, A: Cys44, A: Cys46, A: Cys49, A: Leu84, A: Cys86, A: Fes500, conact list: Atom Atom Distance (A) Fe SG A:Cys40 4.46 Fe N A:Gly42 4.66 Fe C A:Gly42 4.74 Fe CA A:Gly42 4.17 Fe N A:Cys43 5.00 Fe N A:Cys44 4.63 Fe CA A:Cys44 4.93 Fe O A:Cys46 4.79 Fe SG A:Cys46 4.53 Fe N A:Cys49 4.51 Fe CB A:Cys49 3.36 Fe SG A:Cys49 2.32 Fe CA A:Cys49 4.51 Fe CB A:Leu84 4.52 Fe CD1 A:Leu84 4.99 Fe CD2 A:Leu84 4.91 Fe N A:Cys86 4.21 Fe CB A:Cys86 3.26 Fe SG A:Cys86 2.35 Fe CA A:Cys86 4.29 Fe S1 A:Fes500 2.23 Fe S2 A:Fes500 2.20 Fe FE1 A:Fes500 0.00 Fe FE2 A:Fes500 2.83 interactive model: Iron binding site 2 out of 10 in 3lxf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3lxf. 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: Ala38, A: Leu39, A: Cys40, A: Gly41, A: Gly42, A: Cys43, A: Cys44, A: Ser45, A: Cys46, A: Ala47, A: Thr48, A: Cys49, A: Cys86, A: Fes500, conact list: Atom Atom Distance (A) Fe C A:Ala38 4.82 Fe CA A:Ala38 4.98 Fe N A:Leu39 4.80 Fe C A:Leu39 4.96 Fe N A:Cys40 3.75 Fe CB A:Cys40 3.35 Fe SG A:Cys40 2.30 Fe C A:Cys40 4.50 Fe CA A:Cys40 4.00 Fe N A:Gly41 4.58 Fe N A:Gly42 4.31 Fe CA A:Gly42 4.61 Fe N A:Cys43 4.60 Fe N A:Cys44 4.48 Fe C A:Cys44 4.98 Fe CA A:Cys44 4.82 Fe N A:Ser45 4.13 Fe C A:Ser45 4.48 Fe CA A:Ser45 4.89 Fe O A:Cys46 3.96 Fe N A:Cys46 3.47 Fe CB A:Cys46 3.50 Fe SG A:Cys46 2.19 Fe C A:Cys46 4.01 Fe CA A:Cys46 3.81 Fe N A:Ala47 4.85 Fe N A:Thr48 4.91 Fe OG1 A:Thr48 4.77 Fe SG A:Cys49 4.58 Fe SG A:Cys86 4.63 Fe S1 A:Fes500 2.21 Fe S2 A:Fes500 2.23 Fe FE1 A:Fes500 2.83 Fe FE2 A:Fes500 0.00 interactive model: Iron binding site 3 out of 10 in 3lxf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3lxf. 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: Cys40, B: Gly42, B: Cys44, B: Cys46, B: Cys49, B: Leu84, B: Cys86, B: Fes500, conact list: Atom Atom Distance (A) Fe SG B:Cys40 4.40 Fe N B:Gly42 4.66 Fe C B:Gly42 4.80 Fe CA B:Gly42 4.26 Fe N B:Cys44 4.55 Fe CA B:Cys44 4.81 Fe O B:Cys46 4.83 Fe SG B:Cys46 4.64 Fe N B:Cys49 4.52 Fe CB B:Cys49 3.39 Fe SG B:Cys49 2.30 Fe CA B:Cys49 4.54 Fe CB B:Leu84 4.46 Fe CD1 B:Leu84 4.88 Fe CD2 B:Leu84 4.82 Fe CG B:Leu84 4.95 Fe N B:Cys86 4.26 Fe CB B:Cys86 3.29 Fe SG B:Cys86 2.30 Fe CA B:Cys86 4.33 Fe S1 B:Fes500 2.21 Fe S2 B:Fes500 2.16 Fe FE1 B:Fes500 0.00 Fe FE2 B:Fes500 2.80 interactive model: Iron binding site 4 out of 10 in 3lxf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3lxf. 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: Ala38, B: Leu39, B: Cys40, B: Gly41, B: Gly42, B: Cys43, B: Cys44, B: Ser45, B: Cys46, B: Ala47, B: Thr48, B: Cys49, B: Cys86, B: Fes500, conact list: Atom Atom Distance (A) Fe O B:Ala38 4.97 Fe C B:Ala38 4.72 Fe N B:Leu39 4.78 Fe C B:Leu39 4.96 Fe N B:Cys40 3.75 Fe CB B:Cys40 3.39 Fe SG B:Cys40 2.31 Fe C B:Cys40 4.54 Fe CA B:Cys40 4.01 Fe N B:Gly41 4.47 Fe N B:Gly42 4.39 Fe CA B:Gly42 4.73 Fe N B:Cys43 4.66 Fe N B:Cys44 4.48 Fe C B:Cys44 4.97 Fe CA B:Cys44 4.83 Fe N B:Ser45 4.14 Fe C B:Ser45 4.56 Fe CA B:Ser45 4.93 Fe O B:Cys46 4.04 Fe N B:Cys46 3.57 Fe CB B:Cys46 3.63 Fe SG B:Cys46 2.32 Fe C B:Cys46 4.10 Fe CA B:Cys46 3.97 Fe N B:Ala47 4.89 Fe N B:Thr48 4.87 Fe OG1 B:Thr48 4.82 Fe SG B:Cys49 4.58 Fe SG B:Cys86 4.60 Fe S1 B:Fes500 2.18 Fe S2 B:Fes500 2.20 Fe FE1 B:Fes500 2.80 Fe FE2 B:Fes500 0.00 interactive model: Iron binding site 5 out of 10 in 3lxf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 3lxf. 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: Cys40, C: Gly42, C: Cys44, C: Cys46, C: Cys49, C: Leu84, C: Cys86, C: Fes500, conact list: Atom Atom Distance (A) Fe SG C:Cys40 4.64 Fe N C:Gly42 4.61 Fe C C:Gly42 4.83 Fe CA C:Gly42 4.22 Fe N C:Cys44 4.72 Fe CA C:Cys44 4.96 Fe O C:Cys46 4.81 Fe SG C:Cys46 4.60 Fe N C:Cys49 4.43 Fe CB C:Cys49 3.29 Fe SG C:Cys49 2.31 Fe CA C:Cys49 4.46 Fe CB C:Leu84 4.53 Fe CD2 C:Leu84 4.78 Fe N C:Cys86 4.22 Fe CB C:Cys86 3.30 Fe SG C:Cys86 2.36 Fe CA C:Cys86 4.32 Fe S1 C:Fes500 2.18 Fe S2 C:Fes500 2.17 Fe FE1 C:Fes500 0.00 Fe FE2 C:Fes500 2.90 interactive model: Iron binding site 6 out of 10 in 3lxf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 3lxf. 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: Ala38, C: Leu39, C: Cys40, C: Gly41, C: Gly42, C: Cys43, C: Cys44, C: Ser45, C: Cys46, C: Ala47, C: Thr48, C: Cys49, C: Cys86, C: Fes500, conact list: Atom Atom Distance (A) Fe C C:Ala38 4.84 Fe N C:Leu39 4.87 Fe N C:Cys40 3.83 Fe CB C:Cys40 3.53 Fe SG C:Cys40 2.32 Fe C C:Cys40 4.56 Fe CA C:Cys40 4.12 Fe N C:Gly41 4.54 Fe N C:Gly42 4.29 Fe CA C:Gly42 4.69 Fe N C:Cys43 4.76 Fe N C:Cys44 4.51 Fe C C:Cys44 4.91 Fe CA C:Cys44 4.81 Fe N C:Ser45 4.06 Fe C C:Ser45 4.45 Fe CA C:Ser45 4.84 Fe O C:Cys46 3.93 Fe N C:Cys46 3.46 Fe CB C:Cys46 3.53 Fe SG C:Cys46 2.23 Fe C C:Cys46 3.98 Fe CA C:Cys46 3.83 Fe N C:Ala47 4.78 Fe N C:Thr48 4.85 Fe OG1 C:Thr48 4.67 Fe SG C:Cys49 4.66 Fe SG C:Cys86 4.72 Fe S1 C:Fes500 2.18 Fe S2 C:Fes500 2.19 Fe FE1 C:Fes500 2.90 Fe FE2 C:Fes500 0.00 interactive model: Iron binding site 7 out of 10 in 3lxf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 3lxf. 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: Cys40, D: Gly42, D: Cys43, D: Cys44, D: Cys46, D: Cys49, D: Leu84, D: Cys86, D: Fes500, conact list: Atom Atom Distance (A) Fe SG D:Cys40 4.35 Fe N D:Gly42 4.53 Fe C D:Gly42 4.74 Fe CA D:Gly42 4.11 Fe N D:Cys43 4.97 Fe N D:Cys44 4.59 Fe CA D:Cys44 4.84 Fe SG D:Cys46 4.51 Fe N D:Cys49 4.56 Fe CB D:Cys49 3.39 Fe SG D:Cys49 2.39 Fe CA D:Cys49 4.57 Fe CB D:Leu84 4.63 Fe CD2 D:Leu84 4.91 Fe N D:Cys86 4.29 Fe CB D:Cys86 3.23 Fe SG D:Cys86 2.37 Fe CA D:Cys86 4.34 Fe S1 D:Fes500 2.18 Fe S2 D:Fes500 2.16 Fe FE1 D:Fes500 0.00 Fe FE2 D:Fes500 2.80 interactive model: Iron binding site 8 out of 10 in 3lxf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 3lxf. 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: Ala38, D: Leu39, D: Cys40, D: Gly41, D: Gly42, D: Cys43, D: Cys44, D: Ser45, D: Cys46, D: Ala47, D: Thr48, D: Cys49, D: Cys86, D: Fes500, conact list: Atom Atom Distance (A) Fe C D:Ala38 4.74 Fe CA D:Ala38 4.97 Fe N D:Leu39 4.69 Fe C D:Leu39 4.89 Fe N D:Cys40 3.69 Fe CB D:Cys40 3.28 Fe SG D:Cys40 2.24 Fe C D:Cys40 4.46 Fe CA D:Cys40 3.93 Fe N D:Gly41 4.59 Fe N D:Gly42 4.35 Fe CA D:Gly42 4.70 Fe N D:Cys43 4.65 Fe N D:Cys44 4.45 Fe C D:Cys44 4.95 Fe CA D:Cys44 4.80 Fe N D:Ser45 4.13 Fe C D:Ser45 4.55 Fe CA D:Ser45 4.91 Fe O D:Cys46 4.12 Fe N D:Cys46 3.59 Fe CB D:Cys46 3.47 Fe SG D:Cys46 2.25 Fe C D:Cys46 4.05 Fe CA D:Cys46 3.90 Fe N D:Ala47 4.74 Fe N D:Thr48 4.88 Fe OG1 D:Thr48 4.66 Fe SG D:Cys49 4.66 Fe SG D:Cys86 4.67 Fe S1 D:Fes500 2.17 Fe S2 D:Fes500 2.23 Fe FE1 D:Fes500 2.80 Fe FE2 D:Fes500 0.00 interactive model: Iron binding site 9 out of 10 in 3lxf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Iron in the PDB 3lxf. 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: Cys40, E: Gly42, E: Cys44, E: Cys46, E: Cys49, E: Leu84, E: Cys86, E: Fes500, conact list: Atom Atom Distance (A) Fe SG E:Cys40 4.48 Fe N E:Gly42 4.68 Fe C E:Gly42 4.81 Fe CA E:Gly42 4.16 Fe N E:Cys44 4.72 Fe CA E:Cys44 4.90 Fe O E:Cys46 4.99 Fe SG E:Cys46 4.60 Fe N E:Cys49 4.35 Fe CB E:Cys49 3.25 Fe SG E:Cys49 2.29 Fe CA E:Cys49 4.39 Fe CB E:Leu84 4.59 Fe CD1 E:Leu84 4.99 Fe CD2 E:Leu84 4.93 Fe N E:Cys86 4.25 Fe CB E:Cys86 3.12 Fe SG E:Cys86 2.28 Fe CA E:Cys86 4.23 Fe S1 E:Fes500 2.22 Fe S2 E:Fes500 2.15 Fe FE1 E:Fes500 0.00 Fe FE2 E:Fes500 2.89 interactive model: Iron binding site 10 out of 10 in 3lxf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Iron in the PDB 3lxf. 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: Ala38, E: Leu39, E: Cys40, E: Gly41, E: Gly42, E: Cys43, E: Cys44, E: Ser45, E: Cys46, E: Ala47, E: Thr48, E: Cys49, E: Cys86, E: Fes500, conact list: Atom Atom Distance (A) Fe C E:Ala38 4.80 Fe N E:Leu39 4.74 Fe C E:Leu39 4.98 Fe N E:Cys40 3.79 Fe CB E:Cys40 3.38 Fe SG E:Cys40 2.24 Fe C E:Cys40 4.54 Fe CA E:Cys40 4.05 Fe N E:Gly41 4.68 Fe N E:Gly42 4.37 Fe CA E:Gly42 4.60 Fe N E:Cys43 4.77 Fe N E:Cys44 4.43 Fe C E:Cys44 4.95 Fe CA E:Cys44 4.74 Fe N E:Ser45 4.10 Fe C E:Ser45 4.45 Fe CA E:Ser45 4.86 Fe O E:Cys46 4.04 Fe N E:Cys46 3.41 Fe CB E:Cys46 3.48 Fe SG E:Cys46 2.25 Fe C E:Cys46 4.02 Fe CA E:Cys46 3.80 Fe N E:Ala47 4.78 Fe N E:Thr48 4.80 Fe OG1 E:Thr48 4.68 Fe SG E:Cys49 4.72 Fe SG E:Cys86 4.63 Fe S1 E:Fes500 2.19 Fe S2 E:Fes500 2.22 Fe FE1 E:Fes500 2.89 Fe FE2 E:Fes500 0.00 interactive model: