Iron in the structure of Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase (pdb 2gmj)

The binding sites of Iron atom in the structure of Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase (pdb code 2gmj). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2gmj structure was solved by J.ZHANG, F.E.FRERMAN, J.-J.P.KIM, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.8-2.6 Space group P4212 a (A) 154.839 b (A) 154.839 c (A) 130.199 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.8 Rfree (%) 25.5 Iron Binding Sites: Iron binding site 1 out of 8 in 2gmj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2gmj. 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: Leu504, A: Cys528, A: Tyr533, A: Cys556, A: Lys557, A: Thr558, A: Cys559, A: Asp560, A: Trp570, A: Sf4610, conact list: Atom Atom Distance (A) Fe CD1 A:Leu504 4.00 Fe CG A:Leu504 4.95 Fe SG A:Cys528 4.98 Fe CZ A:Tyr533 4.87 Fe CE1 A:Tyr533 4.35 Fe OH A:Tyr533 4.40 Fe SG A:Cys556 5.00 Fe N A:Lys557 4.95 Fe C A:Lys557 4.84 Fe N A:Thr558 4.64 Fe C A:Thr558 4.75 Fe N A:Cys559 3.57 Fe CB A:Cys559 2.95 Fe SG A:Cys559 2.68 Fe C A:Cys559 4.92 Fe CA A:Cys559 3.87 Fe N A:Asp560 4.99 Fe CD1 A:Trp570 4.83 Fe S1 A:Sf4610 3.82 Fe FE1 A:Sf4610 0.00 Fe FE3 A:Sf4610 2.75 Fe S4 A:Sf4610 2.27 Fe FE2 A:Sf4610 2.73 Fe S2 A:Sf4610 2.30 Fe FE4 A:Sf4610 2.81 Fe S3 A:Sf4610 2.28 interactive model: Iron binding site 2 out of 8 in 2gmj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2gmj. 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: Cys528, A: Pro529, A: Ala530, A: Val532, A: Tyr533, A: Cys556, A: Sf4610, conact list: Atom Atom Distance (A) Fe CB A:Cys528 3.42 Fe SG A:Cys528 2.54 Fe C A:Cys528 4.65 Fe CA A:Cys528 4.06 Fe N A:Pro529 4.52 Fe CD A:Pro529 4.18 Fe N A:Ala530 4.69 Fe CB A:Ala530 4.77 Fe CB A:Val532 4.36 Fe CG2 A:Val532 4.31 Fe CE1 A:Tyr533 4.77 Fe SG A:Cys556 4.96 Fe S1 A:Sf4610 2.33 Fe FE1 A:Sf4610 2.73 Fe FE3 A:Sf4610 2.80 Fe S4 A:Sf4610 2.30 Fe FE2 A:Sf4610 0.00 Fe S2 A:Sf4610 3.86 Fe FE4 A:Sf4610 2.85 Fe S3 A:Sf4610 2.25 interactive model: Iron binding site 3 out of 8 in 2gmj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2gmj. 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: Leu504, A: Val532, A: Cys553, A: Val554, A: His555, A: Cys556, A: Cys559, A: Trp570, A: Sf4610, conact list: Atom Atom Distance (A) Fe CD1 A:Leu504 4.07 Fe CD2 A:Leu504 4.84 Fe CG A:Leu504 4.75 Fe CG2 A:Val532 4.88 Fe CB A:Cys553 3.49 Fe SG A:Cys553 2.45 Fe C A:Cys553 4.41 Fe CA A:Cys553 3.87 Fe N A:Val554 4.19 Fe N A:His555 4.17 Fe CA A:His555 4.56 Fe N A:Cys556 4.58 Fe SG A:Cys559 4.96 Fe CD1 A:Trp570 4.37 Fe NE1 A:Trp570 4.23 Fe S1 A:Sf4610 2.26 Fe FE1 A:Sf4610 2.75 Fe FE3 A:Sf4610 0.00 Fe S4 A:Sf4610 2.20 Fe FE2 A:Sf4610 2.80 Fe S2 A:Sf4610 2.26 Fe FE4 A:Sf4610 2.78 Fe S3 A:Sf4610 3.82 interactive model: Iron binding site 4 out of 8 in 2gmj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2gmj. 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: Cys528, A: Pro529, A: Cys553, A: Val554, A: His555, A: Cys556, A: Lys557, A: Thr558, A: Cys559, A: Sf4610, conact list: Atom Atom Distance (A) Fe SG A:Cys528 4.93 Fe CD A:Pro529 4.19 Fe CG A:Pro529 4.63 Fe SG A:Cys553 4.89 Fe CG2 A:Val554 4.91 Fe N A:His555 4.85 Fe C A:His555 4.61 Fe CA A:His555 4.99 Fe N A:Cys556 3.53 Fe CB A:Cys556 3.67 Fe SG A:Cys556 2.49 Fe C A:Cys556 4.13 Fe CA A:Cys556 3.95 Fe N A:Lys557 3.58 Fe C A:Lys557 4.53 Fe CA A:Lys557 4.42 Fe N A:Thr558 3.92 Fe CB A:Thr558 4.52 Fe OG1 A:Thr558 4.64 Fe CA A:Thr558 4.71 Fe N A:Cys559 4.59 Fe S1 A:Sf4610 2.21 Fe FE1 A:Sf4610 2.81 Fe FE3 A:Sf4610 2.78 Fe S4 A:Sf4610 3.91 Fe FE2 A:Sf4610 2.85 Fe S2 A:Sf4610 2.19 Fe FE4 A:Sf4610 0.00 Fe S3 A:Sf4610 2.21 interactive model: Iron binding site 5 out of 8 in 2gmj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 2gmj. 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: B: Leu504, B: Cys528, B: Tyr533, B: Cys553, B: Cys556, B: Thr558, B: Cys559, B: Trp570, B: Sf4612, conact list: Atom Atom Distance (A) Fe CD1 B:Leu504 4.82 Fe CD2 B:Leu504 4.51 Fe CG B:Leu504 4.78 Fe SG B:Cys528 4.62 Fe CZ B:Tyr533 4.83 Fe CE1 B:Tyr533 4.25 Fe OH B:Tyr533 4.36 Fe SG B:Cys553 4.74 Fe SG B:Cys556 4.95 Fe N B:Thr558 4.79 Fe N B:Cys559 3.99 Fe CB B:Cys559 3.31 Fe SG B:Cys559 2.35 Fe CA B:Cys559 4.29 Fe CD1 B:Trp570 4.88 Fe S1 B:Sf4612 3.88 Fe FE1 B:Sf4612 0.00 Fe FE3 B:Sf4612 2.77 Fe S4 B:Sf4612 2.27 Fe FE2 B:Sf4612 2.77 Fe S2 B:Sf4612 2.32 Fe FE4 B:Sf4612 2.73 Fe S3 B:Sf4612 2.32 interactive model: Iron binding site 6 out of 8 in 2gmj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 2gmj. 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: B: Cys528, B: Pro529, B: Ala530, B: Val532, B: Tyr533, B: Cys553, B: Cys556, B: Cys559, B: Sf4612, conact list: Atom Atom Distance (A) Fe CB B:Cys528 3.71 Fe SG B:Cys528 2.39 Fe C B:Cys528 4.37 Fe CA B:Cys528 3.94 Fe N B:Pro529 4.29 Fe CD B:Pro529 3.99 Fe CG B:Pro529 4.59 Fe N B:Ala530 4.38 Fe CB B:Ala530 4.55 Fe CA B:Ala530 4.95 Fe CB B:Val532 4.22 Fe CG2 B:Val532 4.06 Fe CG1 B:Val532 4.99 Fe CE1 B:Tyr533 4.60 Fe CA B:Cys553 4.72 Fe SG B:Cys556 4.87 Fe SG B:Cys559 5.00 Fe S1 B:Sf4612 2.36 Fe FE1 B:Sf4612 2.77 Fe FE3 B:Sf4612 2.85 Fe S4 B:Sf4612 2.34 Fe FE2 B:Sf4612 0.00 Fe S2 B:Sf4612 3.94 Fe FE4 B:Sf4612 2.75 Fe S3 B:Sf4612 2.27 interactive model: Iron binding site 7 out of 8 in 2gmj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 2gmj. 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: B: Leu504, B: Val532, B: Cys553, B: Val554, B: His555, B: Cys556, B: Cys559, B: Trp570, B: Sf4612, conact list: Atom Atom Distance (A) Fe CD1 B:Leu504 4.90 Fe CD2 B:Leu504 4.96 Fe CG2 B:Val532 4.77 Fe O B:Cys553 4.95 Fe N B:Cys553 4.64 Fe CB B:Cys553 3.19 Fe SG B:Cys553 2.52 Fe C B:Cys553 3.85 Fe CA B:Cys553 3.33 Fe N B:Val554 3.58 Fe C B:Val554 4.71 Fe CA B:Val554 4.72 Fe N B:His555 3.88 Fe C B:His555 4.96 Fe CA B:His555 4.46 Fe N B:Cys556 4.43 Fe SG B:Cys556 4.80 Fe SG B:Cys559 4.87 Fe CD1 B:Trp570 4.77 Fe NE1 B:Trp570 4.58 Fe S1 B:Sf4612 2.31 Fe FE1 B:Sf4612 2.77 Fe FE3 B:Sf4612 0.00 Fe S4 B:Sf4612 2.22 Fe FE2 B:Sf4612 2.85 Fe S2 B:Sf4612 2.29 Fe FE4 B:Sf4612 2.68 Fe S3 B:Sf4612 3.89 interactive model: Iron binding site 8 out of 8 in 2gmj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 2gmj. 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: B: Cys528, B: Pro529, B: Val554, B: His555, B: Cys556, B: Lys557, B: Thr558, B: Cys559, B: Sf4612, conact list: Atom Atom Distance (A) Fe SG B:Cys528 4.92 Fe CD B:Pro529 3.97 Fe CG B:Pro529 4.11 Fe N B:Val554 4.98 Fe CG2 B:Val554 4.81 Fe N B:His555 4.93 Fe C B:His555 4.90 Fe N B:Cys556 3.80 Fe CB B:Cys556 3.81 Fe SG B:Cys556 2.41 Fe C B:Cys556 4.36 Fe CA B:Cys556 4.14 Fe N B:Lys557 3.95 Fe C B:Lys557 4.93 Fe CA B:Lys557 4.84 Fe N B:Thr558 4.09 Fe CB B:Thr558 4.54 Fe OG1 B:Thr558 4.89 Fe CA B:Thr558 4.83 Fe N B:Cys559 4.73 Fe SG B:Cys559 4.60 Fe S1 B:Sf4612 2.17 Fe FE1 B:Sf4612 2.73 Fe FE3 B:Sf4612 2.68 Fe S4 B:Sf4612 3.79 Fe FE2 B:Sf4612 2.75 Fe S2 B:Sf4612 2.19 Fe FE4 B:Sf4612 0.00 Fe S3 B:Sf4612 2.22 interactive model: