Iron in the structure of 7-Fe Ferredoxin From Bacillus Schlegelii, uc(Nmr), Minimized Average Structure (pdb 1bd6)

The binding sites of Iron atom in the structure of 7-Fe Ferredoxin From Bacillus Schlegelii, uc(Nmr), Minimized Average Structure (pdb code 1bd6). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1bd6 structure was solved by S.AONO, D.BENTROP, I.BERTINI, A.DONAIRE, C.LUCHINAT, Y.NIIKURA, A.ROSATO, with NMR in Solution technique. Iron Binding Sites: Iron binding site 1 out of 7 in 1bd6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1bd6. 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: Ile4, A: Cys8, A: Thr11, A: Lys12, A: Asp13, A: Ala14, A: Cys16, A: Gln31, A: Tyr32, A: Cys49, A: Pro50, A: Ala53, A: Ile54, A: F3s78, conact list: Atom Atom Distance (A) Fe CD1 A:Ile4 4.63 Fe HD13 A:Ile4 3.81 Fe HD12 A:Ile4 4.43 Fe O A:Cys8 4.80 Fe HB2 A:Cys8 2.78 Fe CB A:Cys8 3.05 Fe HB3 A:Cys8 3.81 Fe HA A:Cys8 3.79 Fe SG A:Cys8 2.11 Fe C A:Cys8 4.89 Fe CA A:Cys8 4.06 Fe HB A:Thr11 4.63 Fe H A:Lys12 4.92 Fe HA A:Asp13 4.79 Fe HB1 A:Ala14 4.11 Fe SG A:Cys16 4.52 Fe HB2 A:Gln31 4.89 Fe HE21 A:Gln31 4.98 Fe HD1 A:Tyr32 4.15 Fe H A:Tyr32 4.89 Fe SG A:Cys49 4.63 Fe HD2 A:Pro50 4.88 Fe HB2 A:Ala53 4.30 Fe HG13 A:Ile54 4.86 Fe S1 A:F3s78 2.23 Fe FE1 A:F3s78 0.00 Fe FE3 A:F3s78 2.61 Fe S4 A:F3s78 3.82 Fe S2 A:F3s78 2.33 Fe FE4 A:F3s78 2.62 Fe S3 A:F3s78 2.25 interactive model: Iron binding site 2 out of 7 in 1bd6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1bd6. 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: Ile4, A: Cys8, A: Ala14, A: Cys16, A: Cys49, A: Pro50, A: Ala53, A: Ile54, A: F3s78, conact list: Atom Atom Distance (A) Fe HD13 A:Ile4 4.60 Fe HB2 A:Cys8 3.76 Fe CB A:Cys8 4.62 Fe SG A:Cys8 4.51 Fe HB2 A:Ala14 4.82 Fe CB A:Ala14 4.87 Fe HB1 A:Ala14 4.04 Fe CB A:Cys16 4.91 Fe HB3 A:Cys16 4.24 Fe SG A:Cys16 4.44 Fe H A:Cys16 4.98 Fe HB2 A:Cys49 3.41 Fe CB A:Cys49 3.36 Fe HB3 A:Cys49 4.28 Fe HA A:Cys49 3.44 Fe SG A:Cys49 2.19 Fe C A:Cys49 4.58 Fe CA A:Cys49 3.93 Fe N A:Pro50 4.52 Fe CD A:Pro50 3.98 Fe HD2 A:Pro50 2.96 Fe HG2 A:Pro50 4.89 Fe HD3 A:Pro50 4.28 Fe HB2 A:Ala53 3.52 Fe CB A:Ala53 4.17 Fe HB3 A:Ala53 4.95 Fe H A:Ala53 4.48 Fe HB1 A:Ala53 3.81 Fe N A:Ile54 4.85 Fe HG13 A:Ile54 3.38 Fe HG12 A:Ile54 4.74 Fe CD1 A:Ile54 4.54 Fe CG1 A:Ile54 4.35 Fe HD11 A:Ile54 4.86 Fe H A:Ile54 4.21 Fe HD13 A:Ile54 3.82 Fe S1 A:F3s78 2.12 Fe FE1 A:F3s78 2.61 Fe FE3 A:F3s78 0.00 Fe S4 A:F3s78 2.35 Fe S2 A:F3s78 3.74 Fe FE4 A:F3s78 2.52 Fe S3 A:F3s78 2.16 interactive model: Iron binding site 3 out of 7 in 1bd6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1bd6. 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: Ile4, A: Cys8, A: Ala14, A: Ser15, A: Cys16, A: Val17, A: Tyr32, A: Cys49, A: Pro50, A: Ile54, A: F3s78, conact list: Atom Atom Distance (A) Fe HD13 A:Ile4 4.52 Fe HD12 A:Ile4 4.94 Fe HB2 A:Cys8 4.93 Fe SG A:Cys8 4.50 Fe HB1 A:Ala14 4.05 Fe HB3 A:Ser15 4.83 Fe HA A:Ser15 3.84 Fe C A:Ser15 4.41 Fe CA A:Ser15 4.64 Fe HB2 A:Cys16 4.05 Fe N A:Cys16 3.51 Fe CB A:Cys16 3.15 Fe HB3 A:Cys16 3.02 Fe HA A:Cys16 4.54 Fe SG A:Cys16 2.15 Fe H A:Cys16 2.88 Fe CA A:Cys16 3.94 Fe H A:Val17 4.34 Fe HB2 A:Tyr32 4.94 Fe HD1 A:Tyr32 4.45 Fe HB2 A:Cys49 4.40 Fe CB A:Cys49 4.91 Fe HA A:Cys49 4.69 Fe SG A:Cys49 4.37 Fe HD2 A:Pro50 4.87 Fe HG13 A:Ile54 4.16 Fe HG12 A:Ile54 4.80 Fe CD1 A:Ile54 4.29 Fe CG1 A:Ile54 4.69 Fe HD11 A:Ile54 4.87 Fe HD13 A:Ile54 3.24 Fe HD12 A:Ile54 4.84 Fe S1 A:F3s78 3.66 Fe FE1 A:F3s78 2.62 Fe FE3 A:F3s78 2.52 Fe S4 A:F3s78 2.23 Fe S2 A:F3s78 2.22 Fe FE4 A:F3s78 0.00 Fe S3 A:F3s78 2.10 interactive model: Iron binding site 4 out of 7 in 1bd6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1bd6. 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: Ile25, A: Cys39, A: Ile40, A: Cys42, A: Cys45, A: Sf479, conact list: Atom Atom Distance (A) Fe HB2 A:Cys20 2.90 Fe N A:Cys20 4.94 Fe CB A:Cys20 3.00 Fe HB3 A:Cys20 3.92 Fe HA A:Cys20 3.34 Fe SG A:Cys20 2.05 Fe C A:Cys20 4.43 Fe CA A:Cys20 3.73 Fe N A:Pro21 4.55 Fe CD A:Pro21 4.19 Fe HD2 A:Pro21 3.23 Fe HD3 A:Pro21 4.50 Fe CG2 A:Val22 4.44 Fe HG21 A:Val22 4.09 Fe HG22 A:Val22 4.94 Fe HG23 A:Val22 3.77 Fe H A:Val22 4.02 Fe SG A:Cys24 4.42 Fe H A:Cys24 4.55 Fe CD1 A:Ile25 4.22 Fe HD11 A:Ile25 4.56 Fe HD13 A:Ile25 3.61 Fe HD12 A:Ile25 3.92 Fe HB2 A:Cys39 4.54 Fe CB A:Cys39 4.84 Fe HA A:Cys39 4.34 Fe SG A:Cys39 4.41 Fe H A:Ile40 4.84 Fe SG A:Cys42 4.51 Fe HB3 A:Cys45 4.36 Fe SG A:Cys45 4.53 Fe H A:Cys45 4.99 Fe S1 A:Sf479 3.74 Fe FE1 A:Sf479 0.00 Fe FE3 A:Sf479 2.55 Fe S4 A:Sf479 2.26 Fe FE2 A:Sf479 2.52 Fe S2 A:Sf479 2.20 Fe FE4 A:Sf479 2.60 Fe S3 A:Sf479 2.27 interactive model: Iron binding site 5 out of 7 in 1bd6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1bd6. 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: Tyr2, A: Cys20, A: Pro21, A: Val22, A: Cys24, A: Ile25, A: Ile34, A: Cys39, A: Ile40, A: Asp41, A: Cys42, A: Cys45, A: Sf479, conact list: Atom Atom Distance (A) Fe HB2 A:Ala1 4.78 Fe HB3 A:Ala1 4.78 Fe HB2 A:Tyr2 3.51 Fe CB A:Tyr2 4.58 Fe HB3 A:Tyr2 4.82 Fe HD1 A:Tyr2 4.77 Fe H A:Tyr2 4.30 Fe SG A:Cys20 4.36 Fe HD2 A:Pro21 4.94 Fe HG23 A:Val22 4.74 Fe SG A:Cys24 4.78 Fe HD13 A:Ile25 5.00 Fe HG21 A:Ile34 4.91 Fe HG22 A:Ile34 4.30 Fe HB2 A:Cys39 3.25 Fe CB A:Cys39 3.15 Fe HB3 A:Cys39 4.05 Fe HA A:Cys39 3.51 Fe SG A:Cys39 2.05 Fe C A:Cys39 4.39 Fe CA A:Cys39 3.84 Fe N A:Ile40 4.25 Fe HG13 A:Ile40 4.39 Fe H A:Ile40 3.69 Fe N A:Asp41 4.91 Fe HA A:Asp41 4.90 Fe H A:Asp41 4.42 Fe N A:Cys42 4.60 Fe CB A:Cys42 4.93 Fe HB3 A:Cys42 4.64 Fe SG A:Cys42 4.37 Fe H A:Cys42 3.78 Fe SG A:Cys45 4.36 Fe S1 A:Sf479 2.17 Fe FE1 A:Sf479 2.52 Fe FE3 A:Sf479 2.48 Fe S4 A:Sf479 2.12 Fe FE2 A:Sf479 0.00 Fe S2 A:Sf479 3.58 Fe FE4 A:Sf479 2.52 Fe S3 A:Sf479 2.18 interactive model: Iron binding site 6 out of 7 in 1bd6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1bd6. 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: Tyr2, A: Cys20, A: Pro21, A: Val22, A: Cys39, A: Ile40, A: Cys42, A: Gly43, A: Ala44, A: Cys45, A: Sf479, conact list: Atom Atom Distance (A) Fe HB2 A:Tyr2 4.99 Fe HB2 A:Cys20 4.74 Fe CB A:Cys20 4.98 Fe HA A:Cys20 4.20 Fe SG A:Cys20 4.39 Fe CD A:Pro21 4.27 Fe HD2 A:Pro21 3.33 Fe HG2 A:Pro21 4.54 Fe HD3 A:Pro21 4.35 Fe HG23 A:Val22 4.95 Fe SG A:Cys39 4.27 Fe HG13 A:Ile40 4.17 Fe H A:Ile40 4.60 Fe O A:Cys42 4.18 Fe HB2 A:Cys42 4.22 Fe N A:Cys42 4.20 Fe CB A:Cys42 3.35 Fe HB3 A:Cys42 3.44 Fe SG A:Cys42 2.13 Fe H A:Cys42 3.71 Fe C A:Cys42 4.16 Fe CA A:Cys42 4.06 Fe N A:Gly43 4.86 Fe HB2 A:Ala44 3.83 Fe N A:Ala44 4.75 Fe CB A:Ala44 4.82 Fe H A:Ala44 3.96 Fe N A:Cys45 4.74 Fe CB A:Cys45 4.87 Fe HB3 A:Cys45 4.48 Fe SG A:Cys45 4.11 Fe H A:Cys45 3.75 Fe S1 A:Sf479 2.27 Fe FE1 A:Sf479 2.55 Fe FE3 A:Sf479 0.00 Fe S4 A:Sf479 2.18 Fe FE2 A:Sf479 2.48 Fe S2 A:Sf479 2.06 Fe FE4 A:Sf479 2.50 Fe S3 A:Sf479 3.69 interactive model: Iron binding site 7 out of 7 in 1bd6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1bd6. 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: Tyr2, A: Cys20, A: Pro21, A: Ile25, A: Ile34, A: Cys39, A: Cys42, A: Ala44, A: Cys45, A: Glu46, A: Ile54, A: Sf479, conact list: Atom Atom Distance (A) Fe HB2 A:Tyr2 4.00 Fe CB A:Tyr2 4.74 Fe HB3 A:Tyr2 4.45 Fe HB2 A:Cys20 4.05 Fe CB A:Cys20 4.74 Fe HA A:Cys20 4.68 Fe SG A:Cys20 4.47 Fe HD2 A:Pro21 4.99 Fe CD1 A:Ile25 4.97 Fe HD13 A:Ile25 4.43 Fe HD12 A:Ile25 4.43 Fe HG22 A:Ile34 4.69 Fe HD12 A:Ile34 4.29 Fe SG A:Cys39 4.30 Fe O A:Cys42 4.88 Fe SG A:Cys42 4.34 Fe H A:Cys42 4.90 Fe HB2 A:Ala44 4.71 Fe HB2 A:Cys45 3.83 Fe N A:Cys45 4.21 Fe CB A:Cys45 3.14 Fe HB3 A:Cys45 2.99 Fe SG A:Cys45 2.04 Fe H A:Cys45 3.45 Fe CA A:Cys45 4.26 Fe H A:Glu46 4.30 Fe HG22 A:Ile54 4.60 Fe HG23 A:Ile54 4.74 Fe HD12 A:Ile54 4.54 Fe S1 A:Sf479 2.09 Fe FE1 A:Sf479 2.60 Fe FE3 A:Sf479 2.50 Fe S4 A:Sf479 3.71 Fe FE2 A:Sf479 2.52 Fe S2 A:Sf479 2.16 Fe FE4 A:Sf479 0.00 Fe S3 A:Sf479 2.20 interactive model: