Iron in the structure of Crystal Structures of Oxidized And Reduced Azotobacter Vinelandii Ferredoxin At pH 8 and pH 6 (pdb 1fdb)

The binding sites of Iron atom in the structure of Crystal Structures of Oxidized And Reduced Azotobacter Vinelandii Ferredoxin At pH 8 and pH 6 (pdb code 1fdb). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1fdb structure was solved by C.D.STOUT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-2.2 Space group P41212 a (A) 55.500 b (A) 55.500 c (A) 95.300 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 23.1 Rfree (%) n/a Iron Binding Sites: Iron binding site 1 out of 7 in 1fdb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1fdb. 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: Phe2, A: Cys20, A: Cys24, A: Ile34, A: Cys39, A: Ile40, A: Asp41, A: Cys42, A: Cys45, A: Sf4107, conact list: Atom Atom Distance (A) Fe N A:Phe2 4.98 Fe CB A:Phe2 4.37 Fe CD1 A:Phe2 4.74 Fe CG A:Phe2 4.78 Fe SG A:Cys20 4.81 Fe SG A:Cys24 4.12 Fe CG2 A:Ile34 4.55 Fe CB A:Cys39 3.47 Fe SG A:Cys39 2.32 Fe C A:Cys39 4.45 Fe CA A:Cys39 3.91 Fe N A:Ile40 4.10 Fe N A:Asp41 4.18 Fe CA A:Asp41 4.69 Fe N A:Cys42 4.78 Fe SG A:Cys42 4.85 Fe SG A:Cys45 4.65 Fe S1 A:Sf4107 3.82 Fe FE1 A:Sf4107 0.00 Fe FE3 A:Sf4107 2.54 Fe S4 A:Sf4107 2.31 Fe FE2 A:Sf4107 2.65 Fe S2 A:Sf4107 2.27 Fe FE4 A:Sf4107 2.70 Fe S3 A:Sf4107 2.32 interactive model: Iron binding site 2 out of 7 in 1fdb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1fdb. 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: Cys20, A: Pro21, A: Cys39, A: Ile40, A: Asp41, A: Cys42, A: Ala43, A: Leu44, A: Cys45, A: Sf4107, conact list: Atom Atom Distance (A) Fe SG A:Cys20 4.69 Fe CD A:Pro21 4.07 Fe CG A:Pro21 4.78 Fe SG A:Cys39 4.63 Fe CG1 A:Ile40 4.79 Fe N A:Asp41 4.74 Fe C A:Asp41 4.79 Fe CA A:Asp41 4.99 Fe N A:Cys42 3.75 Fe CB A:Cys42 3.53 Fe SG A:Cys42 2.28 Fe C A:Cys42 4.31 Fe CA A:Cys42 4.05 Fe N A:Ala43 3.91 Fe C A:Ala43 4.95 Fe CA A:Ala43 4.76 Fe N A:Leu44 4.28 Fe CB A:Leu44 4.78 Fe N A:Cys45 4.90 Fe SG A:Cys45 4.58 Fe S1 A:Sf4107 2.26 Fe FE1 A:Sf4107 2.65 Fe FE3 A:Sf4107 2.63 Fe S4 A:Sf4107 2.28 Fe FE2 A:Sf4107 0.00 Fe S2 A:Sf4107 3.85 Fe FE4 A:Sf4107 2.67 Fe S3 A:Sf4107 2.28 interactive model: Iron binding site 3 out of 7 in 1fdb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1fdb. 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: Phe2, A: Cys20, A: Phe25, A: Ile34, A: Cys39, A: Cys42, A: Ala43, A: Leu44, A: Cys45, A: Sf4107, conact list: Atom Atom Distance (A) Fe CB A:Phe2 4.33 Fe CD2 A:Phe2 4.99 Fe CG A:Phe2 4.55 Fe SG A:Cys20 4.81 Fe CZ A:Phe25 4.52 Fe CE1 A:Phe25 4.36 Fe CD1 A:Ile34 4.61 Fe SG A:Cys39 4.58 Fe SG A:Cys42 4.54 Fe N A:Ala43 4.92 Fe N A:Leu44 4.85 Fe N A:Cys45 4.09 Fe CB A:Cys45 3.37 Fe SG A:Cys45 2.29 Fe CA A:Cys45 4.35 Fe S1 A:Sf4107 2.30 Fe FE1 A:Sf4107 2.54 Fe FE3 A:Sf4107 0.00 Fe S4 A:Sf4107 2.29 Fe FE2 A:Sf4107 2.63 Fe S2 A:Sf4107 2.26 Fe FE4 A:Sf4107 2.70 Fe S3 A:Sf4107 3.82 interactive model: Iron binding site 4 out of 7 in 1fdb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1fdb. 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: Cys20, A: Pro21, A: Val22, A: Cys24, A: Phe25, A: Cys39, A: Cys42, A: Cys45, A: Sf4107, conact list: Atom Atom Distance (A) Fe N A:Cys20 4.93 Fe CB A:Cys20 3.40 Fe SG A:Cys20 2.30 Fe C A:Cys20 4.49 Fe CA A:Cys20 3.78 Fe N A:Pro21 4.58 Fe CD A:Pro21 4.19 Fe CG2 A:Val22 4.42 Fe SG A:Cys24 3.64 Fe CD1 A:Phe25 4.70 Fe CE1 A:Phe25 4.11 Fe SG A:Cys39 4.88 Fe SG A:Cys42 4.62 Fe SG A:Cys45 4.76 Fe S1 A:Sf4107 2.30 Fe FE1 A:Sf4107 2.70 Fe FE3 A:Sf4107 2.70 Fe S4 A:Sf4107 3.96 Fe FE2 A:Sf4107 2.67 Fe S2 A:Sf4107 2.28 Fe FE4 A:Sf4107 0.00 Fe S3 A:Sf4107 2.30 interactive model: Iron binding site 5 out of 7 in 1fdb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1fdb. 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: Cys8, A: Tyr13, A: Thr14, A: Asp15, A: Cys16, A: Phe25, A: Leu32, A: Cys49, A: Ile54, A: F3s108, conact list: Atom Atom Distance (A) Fe SG A:Cys8 4.74 Fe N A:Tyr13 4.99 Fe N A:Thr14 4.05 Fe C A:Thr14 4.54 Fe CA A:Thr14 4.08 Fe N A:Asp15 4.56 Fe N A:Cys16 4.03 Fe CB A:Cys16 3.30 Fe SG A:Cys16 2.28 Fe CA A:Cys16 4.32 Fe CE2 A:Phe25 4.82 Fe CB A:Leu32 4.87 Fe CD2 A:Leu32 4.36 Fe SG A:Cys49 4.64 Fe CD1 A:Ile54 4.60 Fe S1 A:F3s108 2.30 Fe FE1 A:F3s108 0.00 Fe FE3 A:F3s108 2.65 Fe S4 A:F3s108 3.90 Fe S2 A:F3s108 2.25 Fe FE4 A:F3s108 2.57 Fe S3 A:F3s108 2.29 interactive model: Iron binding site 6 out of 7 in 1fdb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1fdb. 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: Val4, A: Cys8, A: Lys12, A: Tyr13, A: Thr14, A: Cys16, A: Leu32, A: Cys49, A: F3s108, conact list: Atom Atom Distance (A) Fe CG1 A:Val4 4.44 Fe O A:Cys8 4.55 Fe CB A:Cys8 3.25 Fe SG A:Cys8 2.28 Fe C A:Cys8 4.69 Fe CA A:Cys8 3.94 Fe N A:Lys12 4.35 Fe C A:Lys12 4.63 Fe CA A:Lys12 4.00 Fe N A:Tyr13 4.34 Fe N A:Thr14 4.89 Fe SG A:Cys16 4.77 Fe CB A:Leu32 4.61 Fe SG A:Cys49 4.56 Fe S1 A:F3s108 2.29 Fe FE1 A:F3s108 2.65 Fe FE3 A:F3s108 0.00 Fe S4 A:F3s108 2.28 Fe S2 A:F3s108 3.86 Fe FE4 A:F3s108 2.60 Fe S3 A:F3s108 2.28 interactive model: Iron binding site 7 out of 7 in 1fdb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1fdb. 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: Cys8, A: Tyr13, A: Cys16, A: Cys49, A: Pro50, A: Ala51, A: Ala53, A: Ile54, A: F3s108, conact list: Atom Atom Distance (A) Fe CB A:Cys8 4.88 Fe SG A:Cys8 4.66 Fe N A:Tyr13 4.90 Fe CB A:Tyr13 4.87 Fe CD2 A:Tyr13 4.79 Fe CB A:Cys16 4.90 Fe SG A:Cys16 4.62 Fe N A:Cys49 4.96 Fe CB A:Cys49 3.35 Fe SG A:Cys49 2.27 Fe C A:Cys49 4.47 Fe CA A:Cys49 3.78 Fe N A:Pro50 4.66 Fe CD A:Pro50 4.31 Fe N A:Ala51 4.83 Fe CB A:Ala51 4.71 Fe CB A:Ala53 4.71 Fe CD1 A:Ile54 4.89 Fe S1 A:F3s108 3.84 Fe FE1 A:F3s108 2.57 Fe FE3 A:F3s108 2.60 Fe S4 A:F3s108 2.28 Fe S2 A:F3s108 2.28 Fe FE4 A:F3s108 0.00 Fe S3 A:F3s108 2.29 interactive model: