Iron in the structure of 7-Fe Ferredoxin From Azotobacter Vinelandii At 100K, Na Dithionite Reduced At pH 8.5, Resolution 1.4 A (pdb 6fdr)

The binding sites of Iron atom in the structure of 7-Fe Ferredoxin From Azotobacter Vinelandii At 100K, Na Dithionite Reduced At pH 8.5, Resolution 1.4 A (pdb code 6fdr). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 6fdr structure was solved by C.G.SCHIPKE, D.B.GOODIN, D.E.MCREE, C.D.STOUT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 100.0-1.4 Space group P41212 a (A) 54.740 b (A) 54.740 c (A) 93.770 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.5 Rfree (%) n/a Iron Binding Sites: Iron binding site 1 out of 7 in 6fdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 6fdr. 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: Ile34, A: Cys39, A: Ile40, A: Cys42, A: Cys45, A: Sf4107, conact list: Atom Atom Distance (A) Fe HB2 A:Cys20 3.34 Fe CB A:Cys20 3.37 Fe HB3 A:Cys20 4.21 Fe HA A:Cys20 3.37 Fe SG A:Cys20 2.29 Fe C A:Cys20 4.65 Fe CA A:Cys20 3.90 Fe N A:Pro21 4.71 Fe CD A:Pro21 4.12 Fe HD2 A:Pro21 3.21 Fe HG2 A:Pro21 4.97 Fe HD3 A:Pro21 4.36 Fe CG2 A:Val22 4.44 Fe HG21 A:Val22 4.20 Fe HG22 A:Val22 4.81 Fe HG23 A:Val22 3.81 Fe H A:Val22 4.35 Fe SG A:Cys24 3.47 Fe H A:Cys24 4.34 Fe CD1 A:Phe25 4.71 Fe HD1 A:Phe25 4.55 Fe HE1 A:Phe25 3.40 Fe CZ A:Phe25 4.86 Fe HZ A:Phe25 4.84 Fe CE1 A:Phe25 4.08 Fe HG12 A:Ile34 4.96 Fe HA A:Cys39 4.43 Fe SG A:Cys39 4.94 Fe H A:Ile40 4.82 Fe SG A:Cys42 4.60 Fe HB3 A:Cys45 4.45 Fe SG A:Cys45 4.81 Fe S1 A:Sf4107 3.91 Fe FE1 A:Sf4107 0.00 Fe FE3 A:Sf4107 2.75 Fe S4 A:Sf4107 2.30 Fe FE2 A:Sf4107 2.76 Fe S2 A:Sf4107 2.29 Fe FE4 A:Sf4107 2.79 Fe S3 A:Sf4107 2.26 interactive model: Iron binding site 2 out of 7 in 6fdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 6fdr. 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: Val22, A: Cys24, A: Ile34, A: Cys39, A: Ile40, A: Asp41, A: Cys42, A: Ala43, A: Cys45, A: Sf4107, conact list: Atom Atom Distance (A) Fe HB2 A:Phe2 3.68 Fe N A:Phe2 4.89 Fe CB A:Phe2 4.60 Fe CD1 A:Phe2 4.81 Fe HD1 A:Phe2 4.35 Fe CG A:Phe2 4.97 Fe H A:Phe2 4.14 Fe SG A:Cys20 4.89 Fe HG23 A:Val22 4.84 Fe SG A:Cys24 3.91 Fe HG12 A:Ile34 4.85 Fe CG2 A:Ile34 4.59 Fe HD11 A:Ile34 4.51 Fe HG22 A:Ile34 4.24 Fe HG23 A:Ile34 4.01 Fe HB2 A:Cys39 3.49 Fe CB A:Cys39 3.39 Fe HB3 A:Cys39 4.24 Fe HA A:Cys39 3.23 Fe SG A:Cys39 2.30 Fe C A:Cys39 4.30 Fe CA A:Cys39 3.75 Fe N A:Ile40 4.04 Fe HG13 A:Ile40 4.96 Fe HG12 A:Ile40 4.98 Fe H A:Ile40 3.43 Fe N A:Asp41 4.09 Fe HA A:Asp41 4.08 Fe H A:Asp41 3.40 Fe CA A:Asp41 4.59 Fe N A:Cys42 4.68 Fe SG A:Cys42 4.92 Fe H A:Cys42 3.97 Fe H A:Ala43 4.61 Fe SG A:Cys45 4.80 Fe S1 A:Sf4107 2.32 Fe FE1 A:Sf4107 2.76 Fe FE3 A:Sf4107 2.77 Fe S4 A:Sf4107 2.23 Fe FE2 A:Sf4107 0.00 Fe S2 A:Sf4107 3.87 Fe FE4 A:Sf4107 2.78 Fe S3 A:Sf4107 2.28 interactive model: Iron binding site 3 out of 7 in 6fdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 6fdr. 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: Cys39, A: Ile40, A: Asp41, A: Cys42, A: Ala43, A: Leu44, A: Cys45, A: Sf4107, conact list: Atom Atom Distance (A) Fe HA A:Cys20 4.25 Fe SG A:Cys20 4.68 Fe HG3 A:Pro21 4.69 Fe CD A:Pro21 4.08 Fe CG A:Pro21 4.68 Fe HD2 A:Pro21 3.34 Fe HG2 A:Pro21 4.45 Fe HD3 A:Pro21 4.01 Fe HG23 A:Val22 4.81 Fe SG A:Cys39 4.77 Fe HG13 A:Ile40 4.18 Fe HG12 A:Ile40 4.56 Fe CG1 A:Ile40 4.86 Fe H A:Ile40 4.36 Fe N A:Asp41 4.68 Fe HA A:Asp41 4.67 Fe H A:Asp41 4.42 Fe C A:Asp41 4.59 Fe CA A:Asp41 4.92 Fe HB2 A:Cys42 4.33 Fe N A:Cys42 3.56 Fe CB A:Cys42 3.53 Fe HB3 A:Cys42 3.77 Fe HA A:Cys42 4.88 Fe SG A:Cys42 2.24 Fe H A:Cys42 2.95 Fe C A:Cys42 4.21 Fe CA A:Cys42 3.93 Fe N A:Ala43 3.85 Fe HA A:Ala43 4.65 Fe H A:Ala43 3.26 Fe C A:Ala43 4.92 Fe CA A:Ala43 4.73 Fe HB2 A:Leu44 4.11 Fe N A:Leu44 4.24 Fe CB A:Leu44 4.93 Fe HG A:Leu44 4.83 Fe H A:Leu44 3.54 Fe N A:Cys45 4.91 Fe HB3 A:Cys45 4.82 Fe SG A:Cys45 4.65 Fe H A:Cys45 4.10 Fe S1 A:Sf4107 2.26 Fe FE1 A:Sf4107 2.75 Fe FE3 A:Sf4107 0.00 Fe S4 A:Sf4107 2.25 Fe FE2 A:Sf4107 2.77 Fe S2 A:Sf4107 2.24 Fe FE4 A:Sf4107 2.72 Fe S3 A:Sf4107 3.84 interactive model: Iron binding site 4 out of 7 in 6fdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 6fdr. 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: Glu46, A: Ile54, A: Sf4107, conact list: Atom Atom Distance (A) Fe HB2 A:Phe2 3.76 Fe CB A:Phe2 4.52 Fe HB3 A:Phe2 4.61 Fe CG A:Phe2 4.78 Fe HB2 A:Cys20 4.78 Fe HA A:Cys20 4.86 Fe SG A:Cys20 4.85 Fe HE1 A:Phe25 3.86 Fe CZ A:Phe25 4.41 Fe HZ A:Phe25 3.88 Fe CE1 A:Phe25 4.41 Fe HG12 A:Ile34 4.69 Fe CD1 A:Ile34 4.79 Fe HD11 A:Ile34 4.31 Fe HD12 A:Ile34 4.41 Fe SG A:Cys39 4.76 Fe SG A:Cys42 4.62 Fe N A:Ala43 4.94 Fe HA A:Ala43 4.58 Fe H A:Ala43 4.36 Fe N A:Leu44 4.77 Fe H A:Leu44 4.49 Fe HB2 A:Cys45 3.89 Fe N A:Cys45 3.99 Fe CB A:Cys45 3.22 Fe HB3 A:Cys45 2.99 Fe HA A:Cys45 4.90 Fe SG A:Cys45 2.23 Fe H A:Cys45 3.27 Fe CA A:Cys45 4.25 Fe H A:Glu46 4.88 Fe HG23 A:Ile54 4.86 Fe HD12 A:Ile54 4.84 Fe S1 A:Sf4107 2.30 Fe FE1 A:Sf4107 2.79 Fe FE3 A:Sf4107 2.72 Fe S4 A:Sf4107 3.86 Fe FE2 A:Sf4107 2.78 Fe S2 A:Sf4107 2.23 Fe FE4 A:Sf4107 0.00 Fe S3 A:Sf4107 2.28 interactive model: Iron binding site 5 out of 7 in 6fdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 6fdr. 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: Asp15, A: Cys16, A: Cys49, A: Pro50, A: Ala51, A: Ala53, A: Ile54, A: F3s108, conact list: Atom Atom Distance (A) Fe HG12 A:Val4 4.96 Fe HB2 A:Cys8 4.38 Fe CB A:Cys8 4.90 Fe HA A:Cys8 4.46 Fe SG A:Cys8 4.71 Fe HA A:Lys12 4.97 Fe HB2 A:Tyr13 3.72 Fe N A:Tyr13 4.71 Fe CB A:Tyr13 4.66 Fe CD2 A:Tyr13 4.68 Fe HD2 A:Tyr13 3.79 Fe H A:Tyr13 4.03 Fe H A:Thr14 4.32 Fe H A:Asp15 4.85 Fe HB3 A:Cys16 4.33 Fe SG A:Cys16 4.71 Fe H A:Cys16 4.68 Fe HB2 A:Cys49 3.04 Fe CB A:Cys49 3.21 Fe HB3 A:Cys49 4.02 Fe HA A:Cys49 3.59 Fe SG A:Cys49 2.28 Fe C A:Cys49 4.55 Fe CA A:Cys49 3.96 Fe N A:Pro50 4.68 Fe CD A:Pro50 4.42 Fe HD2 A:Pro50 3.69 Fe HD3 A:Pro50 4.54 Fe HB2 A:Ala51 3.71 Fe N A:Ala51 4.73 Fe CB A:Ala51 4.53 Fe H A:Ala51 3.92 Fe HB1 A:Ala51 4.56 Fe HB2 A:Ala53 3.95 Fe CB A:Ala53 4.78 Fe H A:Ala53 4.47 Fe HB1 A:Ala53 4.75 Fe HG13 A:Ile54 4.42 Fe HD11 A:Ile54 4.79 Fe HD13 A:Ile54 4.68 Fe S1 A:F3s108 2.29 Fe FE1 A:F3s108 0.00 Fe FE3 A:F3s108 2.65 Fe S4 A:F3s108 3.78 Fe S2 A:F3s108 2.20 Fe FE4 A:F3s108 2.65 Fe S3 A:F3s108 2.33 interactive model: Iron binding site 6 out of 7 in 6fdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 6fdr. 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: Lys12, A: Tyr13, A: Thr14, A: Asp15, A: Cys16, A: Val17, A: Phe25, A: Leu32, A: Cys49, A: Ile54, A: F3s108, conact list: Atom Atom Distance (A) Fe SG A:Cys8 4.80 Fe HA A:Lys12 4.75 Fe HB2 A:Tyr13 4.46 Fe N A:Tyr13 4.84 Fe C A:Tyr13 4.99 Fe H A:Tyr13 4.52 Fe N A:Thr14 3.89 Fe C A:Thr14 4.50 Fe HG21 A:Thr14 4.98 Fe CA A:Thr14 3.99 Fe HA A:Thr14 3.27 Fe H A:Thr14 3.25 Fe N A:Asp15 4.35 Fe H A:Asp15 4.00 Fe HB2 A:Cys16 4.03 Fe N A:Cys16 4.00 Fe CB A:Cys16 3.34 Fe HB3 A:Cys16 3.12 Fe HA A:Cys16 4.96 Fe SG A:Cys16 2.30 Fe H A:Cys16 3.25 Fe CA A:Cys16 4.34 Fe HG12 A:Val17 4.82 Fe H A:Val17 4.72 Fe HE2 A:Phe25 4.76 Fe HB2 A:Leu32 4.18 Fe HD21 A:Leu32 4.46 Fe CB A:Leu32 4.90 Fe HB3 A:Leu32 4.81 Fe CD2 A:Leu32 4.43 Fe HD23 A:Leu32 3.58 Fe HB2 A:Cys49 4.14 Fe CB A:Cys49 4.83 Fe HA A:Cys49 4.85 Fe SG A:Cys49 4.65 Fe HG13 A:Ile54 4.97 Fe CD1 A:Ile54 4.81 Fe HD11 A:Ile54 4.77 Fe HD13 A:Ile54 4.02 Fe S1 A:F3s108 2.32 Fe FE1 A:F3s108 2.65 Fe FE3 A:F3s108 0.00 Fe S4 A:F3s108 2.21 Fe S2 A:F3s108 3.84 Fe FE4 A:F3s108 2.73 Fe S3 A:F3s108 2.32 interactive model: Iron binding site 7 out of 7 in 6fdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 6fdr. 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: Ala51, A: Ala53, A: F3s108, conact list: Atom Atom Distance (A) Fe HG13 A:Val4 3.89 Fe HG12 A:Val4 4.09 Fe CG1 A:Val4 4.44 Fe HG11 A:Val4 4.83 Fe O A:Cys8 4.59 Fe HB2 A:Cys8 3.08 Fe CB A:Cys8 3.21 Fe HB3 A:Cys8 4.04 Fe HA A:Cys8 3.52 Fe SG A:Cys8 2.26 Fe C A:Cys8 4.71 Fe CA A:Cys8 3.92 Fe N A:Lys12 4.33 Fe HG3 A:Lys12 4.56 Fe C A:Lys12 4.52 Fe CA A:Lys12 3.96 Fe HA A:Lys12 3.07 Fe H A:Lys12 3.96 Fe HB2 A:Tyr13 4.79 Fe N A:Tyr13 4.24 Fe HD2 A:Tyr13 4.98 Fe H A:Tyr13 3.66 Fe N A:Thr14 4.90 Fe HA A:Thr14 4.98 Fe H A:Thr14 4.05 Fe SG A:Cys16 4.83 Fe HB2 A:Leu32 3.67 Fe N A:Leu32 4.97 Fe CB A:Leu32 4.63 Fe HB3 A:Leu32 4.86 Fe H A:Leu32 4.38 Fe HD12 A:Leu32 4.87 Fe HD23 A:Leu32 4.60 Fe SG A:Cys49 4.64 Fe HB2 A:Ala51 4.94 Fe HB2 A:Ala53 4.45 Fe S1 A:F3s108 4.01 Fe FE1 A:F3s108 2.65 Fe FE3 A:F3s108 2.73 Fe S4 A:F3s108 2.24 Fe S2 A:F3s108 2.23 Fe FE4 A:F3s108 0.00 Fe S3 A:F3s108 2.23 interactive model: