Iron in the structure of Oxidized Form of Formate Dehydrogenase H From E. Coli (pdb 1fdo)

The binding sites of Iron atom in the structure of Oxidized Form of Formate Dehydrogenase H From E. Coli (pdb code 1fdo). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1fdo structure was solved by P.D.SUN, J.C.BOYINGTON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 6.0-2.8 Space group P41212 a (A) 146.600 b (A) 146.600 c (A) 81.100 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.2 Rfree (%) 28.1 Iron Binding Sites: Iron binding site 1 out of 4 in 1fdo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1fdo. 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: Cys11, A: Cys15, A: Cys42, A: Lys44, A: Gly45, A: Pro182, A: Sf4800, A: Hoh831, conact list: Atom Atom Distance (A) Fe SG A:Cys8 4.86 Fe SG A:Cys11 4.56 Fe SG A:Cys15 4.88 Fe O A:Cys42 4.72 Fe N A:Cys42 3.93 Fe CB A:Cys42 3.48 Fe SG A:Cys42 2.37 Fe C A:Cys42 4.74 Fe CA A:Cys42 4.25 Fe CE A:Lys44 4.60 Fe N A:Gly45 4.35 Fe CA A:Gly45 4.81 Fe CB A:Pro182 4.84 Fe CD A:Pro182 4.58 Fe CG A:Pro182 4.78 Fe S1 A:Sf4800 3.89 Fe FE1 A:Sf4800 0.00 Fe FE3 A:Sf4800 2.83 Fe S4 A:Sf4800 2.30 Fe FE2 A:Sf4800 2.72 Fe S2 A:Sf4800 2.28 Fe FE4 A:Sf4800 2.48 Fe S3 A:Sf4800 2.32 Fe O A:Hoh831 4.82 interactive model: Iron binding site 2 out of 4 in 1fdo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1fdo. 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: Tyr10, A: Cys11, A: Cys15, A: Cys42, A: Gly45, A: Sf4800, conact list: Atom Atom Distance (A) Fe CB A:Cys8 3.04 Fe SG A:Cys8 2.33 Fe C A:Cys8 4.81 Fe CA A:Cys8 4.46 Fe N A:Tyr10 4.73 Fe CB A:Tyr10 4.13 Fe CD2 A:Tyr10 4.78 Fe CG A:Tyr10 4.97 Fe CA A:Tyr10 4.83 Fe N A:Cys11 4.31 Fe SG A:Cys11 4.72 Fe CB A:Cys15 4.61 Fe SG A:Cys15 4.74 Fe SG A:Cys42 4.73 Fe N A:Gly45 4.39 Fe CA A:Gly45 4.22 Fe S1 A:Sf4800 2.27 Fe FE1 A:Sf4800 2.72 Fe FE3 A:Sf4800 2.69 Fe S4 A:Sf4800 2.28 Fe FE2 A:Sf4800 0.00 Fe S2 A:Sf4800 3.87 Fe FE4 A:Sf4800 2.57 Fe S3 A:Sf4800 2.25 interactive model: Iron binding site 3 out of 4 in 1fdo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1fdo. 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: Cys11, A: Ser13, A: Cys15, A: Leu41, A: Ile183, A: Sf4800, conact list: Atom Atom Distance (A) Fe CB A:Cys8 4.50 Fe SG A:Cys8 4.71 Fe SG A:Cys11 4.69 Fe CB A:Ser13 3.94 Fe OG A:Ser13 4.41 Fe N A:Cys15 4.17 Fe CB A:Cys15 2.94 Fe SG A:Cys15 2.24 Fe CA A:Cys15 4.16 Fe CD2 A:Leu41 4.59 Fe CB A:Ile183 4.63 Fe CD1 A:Ile183 4.23 Fe CG1 A:Ile183 4.47 Fe S1 A:Sf4800 2.24 Fe FE1 A:Sf4800 2.83 Fe FE3 A:Sf4800 0.00 Fe S4 A:Sf4800 2.30 Fe FE2 A:Sf4800 2.69 Fe S2 A:Sf4800 2.37 Fe FE4 A:Sf4800 2.69 Fe S3 A:Sf4800 4.02 interactive model: Iron binding site 4 out of 4 in 1fdo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1fdo. 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: Tyr10, A: Cys11, A: Ser13, A: Cys15, A: Cys42, A: Pro182, A: Sf4800, A: Hoh831, conact list: Atom Atom Distance (A) Fe SG A:Cys8 4.69 Fe CB A:Tyr10 4.93 Fe C A:Tyr10 5.00 Fe O A:Cys11 4.47 Fe N A:Cys11 3.79 Fe CB A:Cys11 3.52 Fe SG A:Cys11 2.35 Fe C A:Cys11 4.36 Fe CA A:Cys11 3.98 Fe N A:Ser13 4.64 Fe CB A:Ser13 3.93 Fe OG A:Ser13 3.66 Fe CA A:Ser13 4.92 Fe SG A:Cys15 4.69 Fe SG A:Cys42 4.64 Fe CD A:Pro182 4.58 Fe S1 A:Sf4800 2.32 Fe FE1 A:Sf4800 2.48 Fe FE3 A:Sf4800 2.69 Fe S4 A:Sf4800 3.69 Fe FE2 A:Sf4800 2.57 Fe S2 A:Sf4800 2.23 Fe FE4 A:Sf4800 0.00 Fe S3 A:Sf4800 2.32 Fe O A:Hoh831 4.33 interactive model: