Iron in the structure of Crystal Structure of Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii At 1.7 Angstrom Resolution. (pdb 1d3w)

The binding sites of Iron atom in the structure of Crystal Structure of Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii At 1.7 Angstrom Resolution. (pdb code 1d3w). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1d3w structure was solved by K.CHEN, J.HIRST, R.CAMBA, C.A.BONAGURA, C.D.STOUT, B.K.BURGES, F.A.ARMSTRONG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-1.7 Space group P41212 a (A) 55.370 b (A) 55.370 c (A) 92.535 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.9 Rfree (%) 24.7 Iron Binding Sites: Iron binding site 1 out of 7 in 1d3w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1d3w. 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: Ala1, A: Phe2, A: Cys20, 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 H1 A:Ala1 4.75 Fe N A:Ala1 4.81 Fe H2 A:Ala1 3.94 Fe N A:Phe2 4.81 Fe CB A:Phe2 4.49 Fe H A:Phe2 3.98 Fe CD1 A:Phe2 4.92 Fe CG A:Phe2 4.95 Fe SG A:Cys20 4.87 Fe SG A:Cys24 3.99 Fe CG2 A:Ile34 4.53 Fe CB A:Cys39 3.33 Fe SG A:Cys39 2.29 Fe C A:Cys39 4.28 Fe CA A:Cys39 3.76 Fe N A:Ile40 4.07 Fe H A:Ile40 3.53 Fe N A:Asp41 4.09 Fe H A:Asp41 3.33 Fe CA A:Asp41 4.58 Fe N A:Cys42 4.61 Fe SG A:Cys42 4.99 Fe H A:Cys42 3.76 Fe H A:Ala43 4.49 Fe SG A:Cys45 4.85 Fe S1 A:Sf4107 3.92 Fe FE1 A:Sf4107 0.00 Fe FE3 A:Sf4107 2.72 Fe S4 A:Sf4107 2.31 Fe FE2 A:Sf4107 2.77 Fe S2 A:Sf4107 2.32 Fe FE4 A:Sf4107 2.78 Fe S3 A:Sf4107 2.31 interactive model: Iron binding site 2 out of 7 in 1d3w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1d3w. 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 4.70 Fe CD A:Pro21 3.89 Fe CG A:Pro21 4.29 Fe SG A:Cys39 4.77 Fe H A:Ile40 4.37 Fe CG1 A:Ile40 4.87 Fe N A:Asp41 4.76 Fe H A:Asp41 4.50 Fe C A:Asp41 4.64 Fe CA A:Asp41 4.96 Fe N A:Cys42 3.55 Fe CB A:Cys42 3.48 Fe SG A:Cys42 2.30 Fe H A:Cys42 2.84 Fe C A:Cys42 4.14 Fe CA A:Cys42 3.90 Fe N A:Ala43 3.87 Fe H A:Ala43 3.46 Fe C A:Ala43 4.90 Fe CA A:Ala43 4.76 Fe N A:Leu44 4.26 Fe CB A:Leu44 4.83 Fe H A:Leu44 3.46 Fe N A:Cys45 4.79 Fe SG A:Cys45 4.73 Fe H A:Cys45 3.90 Fe S1 A:Sf4107 2.29 Fe FE1 A:Sf4107 2.77 Fe FE3 A:Sf4107 2.75 Fe S4 A:Sf4107 2.33 Fe FE2 A:Sf4107 0.00 Fe S2 A:Sf4107 3.93 Fe FE4 A:Sf4107 2.73 Fe S3 A:Sf4107 2.30 interactive model: Iron binding site 3 out of 7 in 1d3w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1d3w. 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: Sf4107, conact list: Atom Atom Distance (A) Fe CB A:Phe2 4.51 Fe CG A:Phe2 4.82 Fe SG A:Cys20 4.83 Fe CE2 A:Phe25 4.27 Fe CZ A:Phe25 4.27 Fe CD1 A:Ile34 4.54 Fe SG A:Cys39 4.71 Fe SG A:Cys42 4.69 Fe H A:Cys42 4.95 Fe N A:Ala43 4.95 Fe H A:Ala43 4.49 Fe N A:Leu44 4.87 Fe H A:Leu44 4.56 Fe N A:Cys45 3.96 Fe CB A:Cys45 3.27 Fe SG A:Cys45 2.29 Fe H A:Cys45 3.13 Fe CA A:Cys45 4.25 Fe H A:Glu46 4.64 Fe S1 A:Sf4107 2.30 Fe FE1 A:Sf4107 2.72 Fe FE3 A:Sf4107 0.00 Fe S4 A:Sf4107 2.30 Fe FE2 A:Sf4107 2.75 Fe S2 A:Sf4107 2.31 Fe FE4 A:Sf4107 2.76 Fe S3 A:Sf4107 3.90 interactive model: Iron binding site 4 out of 7 in 1d3w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1d3w. 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: Ile40, A: Cys42, A: Cys45, A: Sf4107, conact list: Atom Atom Distance (A) Fe N A:Cys20 4.91 Fe CB A:Cys20 3.29 Fe SG A:Cys20 2.28 Fe C A:Cys20 4.48 Fe CA A:Cys20 3.74 Fe N A:Pro21 4.55 Fe CD A:Pro21 4.09 Fe CG A:Pro21 4.79 Fe CG2 A:Val22 4.43 Fe H A:Val22 4.06 Fe SG A:Cys24 3.52 Fe H A:Cys24 4.10 Fe CE2 A:Phe25 4.04 Fe CD2 A:Phe25 4.63 Fe CZ A:Phe25 4.83 Fe SG A:Cys39 4.94 Fe H A:Ile40 4.72 Fe SG A:Cys42 4.67 Fe SG A:Cys45 4.80 Fe S1 A:Sf4107 2.30 Fe FE1 A:Sf4107 2.78 Fe FE3 A:Sf4107 2.76 Fe S4 A:Sf4107 3.93 Fe FE2 A:Sf4107 2.73 Fe S2 A:Sf4107 2.33 Fe FE4 A:Sf4107 0.00 Fe S3 A:Sf4107 2.30 interactive model: Iron binding site 5 out of 7 in 1d3w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1d3w. 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: Glu15, A: Cys16, A: Val17, A: Leu32, A: Cys49, A: Ile54, A: F3s108, conact list: Atom Atom Distance (A) Fe SG A:Cys8 4.79 Fe N A:Tyr13 4.95 Fe H A:Tyr13 4.58 Fe N A:Thr14 3.94 Fe H A:Thr14 3.29 Fe C A:Thr14 4.47 Fe CA A:Thr14 4.06 Fe N A:Glu15 4.34 Fe H A:Glu15 4.00 Fe N A:Cys16 3.95 Fe CB A:Cys16 3.31 Fe SG A:Cys16 2.28 Fe H A:Cys16 3.12 Fe CA A:Cys16 4.28 Fe H A:Val17 4.72 Fe CB A:Leu32 4.88 Fe CD1 A:Leu32 4.26 Fe CG A:Leu32 4.61 Fe CB A:Cys49 4.88 Fe SG A:Cys49 4.65 Fe CD1 A:Ile54 4.74 Fe S1 A:F3s108 2.31 Fe FE1 A:F3s108 0.00 Fe FE3 A:F3s108 2.71 Fe S4 A:F3s108 3.94 Fe S2 A:F3s108 2.29 Fe FE4 A:F3s108 2.64 Fe S3 A:F3s108 2.29 interactive model: Iron binding site 6 out of 7 in 1d3w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1d3w. 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 4.51 Fe O A:Cys8 4.52 Fe CB A:Cys8 3.25 Fe SG A:Cys8 2.28 Fe C A:Cys8 4.63 Fe CA A:Cys8 3.93 Fe N A:Lys12 4.36 Fe H A:Lys12 3.99 Fe C A:Lys12 4.54 Fe CA A:Lys12 3.94 Fe N A:Tyr13 4.27 Fe H A:Tyr13 3.62 Fe N A:Thr14 4.82 Fe H A:Thr14 3.86 Fe SG A:Cys16 4.82 Fe CB A:Leu32 4.62 Fe H A:Leu32 4.30 Fe CG A:Leu32 4.64 Fe SG A:Cys49 4.60 Fe S1 A:F3s108 2.31 Fe FE1 A:F3s108 2.71 Fe FE3 A:F3s108 0.00 Fe S4 A:F3s108 2.27 Fe S2 A:F3s108 3.92 Fe FE4 A:F3s108 2.61 Fe S3 A:F3s108 2.30 interactive model: Iron binding site 7 out of 7 in 1d3w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1d3w. 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: Glu15, A: Cys16, A: Cys49, A: Pro50, A: Ala51, A: Ala53, A: F3s108, conact list: Atom Atom Distance (A) Fe CB A:Cys8 4.84 Fe SG A:Cys8 4.64 Fe N A:Tyr13 4.85 Fe CB A:Tyr13 4.82 Fe CD2 A:Tyr13 4.59 Fe H A:Tyr13 4.07 Fe H A:Thr14 4.33 Fe H A:Glu15 4.81 Fe CB A:Cys16 4.95 Fe SG A:Cys16 4.67 Fe H A:Cys16 4.70 Fe CB A:Cys49 3.23 Fe SG A:Cys49 2.27 Fe C A:Cys49 4.51 Fe CA A:Cys49 3.85 Fe N A:Pro50 4.66 Fe CD A:Pro50 4.41 Fe N A:Ala51 4.70 Fe CB A:Ala51 4.54 Fe H A:Ala51 3.79 Fe CB A:Ala53 4.77 Fe H A:Ala53 4.32 Fe S1 A:F3s108 3.88 Fe FE1 A:F3s108 2.64 Fe FE3 A:F3s108 2.61 Fe S4 A:F3s108 2.29 Fe S2 A:F3s108 2.27 Fe FE4 A:F3s108 0.00 Fe S3 A:F3s108 2.29 interactive model: