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

The binding sites of Iron atom in the structure of Structure of Porcine Electron Transfer Flavoprotein- Ubiquinone Oxidoreductase in Complexed With Ubiquinone (pdb code 2gmh). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2gmh 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) 29.7-2.5 Space group P4212 a (A) 154.322 b (A) 154.322 c (A) 128.536 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.1 Rfree (%) 25.4 Iron Binding Sites: Iron binding site 1 out of 8 in 2gmh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2gmh. 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: 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 4.21 Fe CD2 A:Leu504 4.94 Fe CG A:Leu504 4.87 Fe SG A:Cys528 4.80 Fe CG2 A:Val532 4.44 Fe N A:Cys553 4.91 Fe CB A:Cys553 3.39 Fe SG A:Cys553 2.33 Fe C A:Cys553 4.22 Fe CA A:Cys553 3.66 Fe N A:Val554 3.91 Fe C A:Val554 4.90 Fe CA A:Val554 5.00 Fe N A:His555 3.96 Fe CA A:His555 4.48 Fe N A:Cys556 4.64 Fe SG A:Cys556 4.85 Fe SG A:Cys559 4.85 Fe CD1 A:Trp570 4.68 Fe NE1 A:Trp570 4.37 Fe S1 A:Sf4610 3.86 Fe FE1 A:Sf4610 0.00 Fe FE3 A:Sf4610 2.76 Fe S4 A:Sf4610 2.29 Fe FE2 A:Sf4610 2.74 Fe S2 A:Sf4610 2.27 Fe FE4 A:Sf4610 2.72 Fe S3 A:Sf4610 2.31 interactive model: Iron binding site 2 out of 8 in 2gmh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2gmh. 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: Cys553, A: Cys556, A: Cys559, A: Sf4610, conact list: Atom Atom Distance (A) Fe CB A:Cys528 3.38 Fe SG A:Cys528 2.23 Fe C A:Cys528 4.52 Fe CA A:Cys528 3.96 Fe N A:Pro529 4.52 Fe CD A:Pro529 3.91 Fe CG A:Pro529 4.72 Fe N A:Ala530 4.64 Fe CB A:Ala530 4.57 Fe CB A:Val532 4.21 Fe CG2 A:Val532 3.97 Fe CE1 A:Tyr533 4.59 Fe SG A:Cys553 4.97 Fe SG A:Cys556 4.65 Fe SG A:Cys559 4.73 Fe S1 A:Sf4610 2.27 Fe FE1 A:Sf4610 2.74 Fe FE3 A:Sf4610 2.75 Fe S4 A:Sf4610 2.29 Fe FE2 A:Sf4610 0.00 Fe S2 A:Sf4610 3.85 Fe FE4 A:Sf4610 2.73 Fe S3 A:Sf4610 2.30 interactive model: Iron binding site 3 out of 8 in 2gmh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2gmh. 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 4.68 Fe CD A:Pro529 3.89 Fe CG A:Pro529 4.24 Fe SG A:Cys553 4.80 Fe CG2 A:Val554 4.68 Fe N A:His555 4.69 Fe C A:His555 4.62 Fe CA A:His555 4.92 Fe N A:Cys556 3.60 Fe CB A:Cys556 3.61 Fe SG A:Cys556 2.21 Fe C A:Cys556 4.35 Fe CA A:Cys556 4.04 Fe N A:Lys557 3.82 Fe C A:Lys557 4.81 Fe CA A:Lys557 4.67 Fe N A:Thr558 4.05 Fe CB A:Thr558 4.54 Fe OG1 A:Thr558 4.78 Fe CA A:Thr558 4.82 Fe N A:Cys559 4.71 Fe SG A:Cys559 4.69 Fe S1 A:Sf4610 2.31 Fe FE1 A:Sf4610 2.76 Fe FE3 A:Sf4610 0.00 Fe S4 A:Sf4610 2.19 Fe FE2 A:Sf4610 2.75 Fe S2 A:Sf4610 2.30 Fe FE4 A:Sf4610 2.69 Fe S3 A:Sf4610 3.86 interactive model: Iron binding site 4 out of 8 in 2gmh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2gmh. 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: Cys553, A: Cys556, A: Lys557, A: Thr558, A: Cys559, A: Trp570, A: Sf4610, conact list: Atom Atom Distance (A) Fe CD1 A:Leu504 3.87 Fe CG A:Leu504 4.76 Fe SG A:Cys528 4.74 Fe CZ A:Tyr533 4.80 Fe CE1 A:Tyr533 4.38 Fe OH A:Tyr533 4.25 Fe SG A:Cys553 4.66 Fe SG A:Cys556 4.62 Fe N A:Lys557 4.99 Fe N A:Thr558 4.65 Fe C A:Thr558 4.95 Fe N A:Cys559 3.82 Fe CB A:Cys559 3.33 Fe SG A:Cys559 2.29 Fe CA A:Cys559 4.21 Fe CD1 A:Trp570 4.55 Fe S1 A:Sf4610 2.18 Fe FE1 A:Sf4610 2.72 Fe FE3 A:Sf4610 2.69 Fe S4 A:Sf4610 3.80 Fe FE2 A:Sf4610 2.73 Fe S2 A:Sf4610 2.18 Fe FE4 A:Sf4610 0.00 Fe S3 A:Sf4610 2.19 interactive model: Iron binding site 5 out of 8 in 2gmh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 2gmh. 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: Val532, B: Cys553, B: Val554, B: His555, B: Cys556, B: Cys559, B: Trp570, B: Sf4613, conact list: Atom Atom Distance (A) Fe CD1 B:Leu504 4.76 Fe SG B:Cys528 4.84 Fe CG2 B:Val532 4.38 Fe O B:Cys553 4.95 Fe N B:Cys553 4.47 Fe CB B:Cys553 3.06 Fe SG B:Cys553 2.54 Fe C B:Cys553 3.88 Fe CA B:Cys553 3.25 Fe N B:Val554 3.70 Fe C B:Val554 4.91 Fe CA B:Val554 4.87 Fe N B:His555 4.12 Fe CA B:His555 4.70 Fe N B:Cys556 4.63 Fe SG B:Cys556 4.86 Fe SG B:Cys559 4.88 Fe CD1 B:Trp570 4.83 Fe NE1 B:Trp570 4.67 Fe S1 B:Sf4613 3.86 Fe FE1 B:Sf4613 0.00 Fe FE3 B:Sf4613 2.75 Fe S4 B:Sf4613 2.30 Fe FE2 B:Sf4613 2.76 Fe S2 B:Sf4613 2.27 Fe FE4 B:Sf4613 2.74 Fe S3 B:Sf4613 2.33 interactive model: Iron binding site 6 out of 8 in 2gmh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 2gmh. 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: Sf4613, conact list: Atom Atom Distance (A) Fe CB B:Cys528 3.62 Fe SG B:Cys528 2.26 Fe C B:Cys528 4.64 Fe CA B:Cys528 4.09 Fe N B:Pro529 4.47 Fe CD B:Pro529 3.73 Fe CG B:Pro529 4.46 Fe N B:Ala530 4.61 Fe CB B:Ala530 4.59 Fe CB B:Val532 4.37 Fe CG2 B:Val532 4.04 Fe CD1 B:Tyr533 4.93 Fe CE1 B:Tyr533 4.26 Fe CA B:Cys553 4.91 Fe SG B:Cys556 4.70 Fe SG B:Cys559 4.67 Fe S1 B:Sf4613 2.28 Fe FE1 B:Sf4613 2.76 Fe FE3 B:Sf4613 2.76 Fe S4 B:Sf4613 2.31 Fe FE2 B:Sf4613 0.00 Fe S2 B:Sf4613 3.87 Fe FE4 B:Sf4613 2.74 Fe S3 B:Sf4613 2.30 interactive model: Iron binding site 7 out of 8 in 2gmh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 2gmh. 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: Cys553, B: Val554, B: His555, B: Cys556, B: Lys557, B: Thr558, B: Cys559, B: Sf4613, conact list: Atom Atom Distance (A) Fe SG B:Cys528 4.74 Fe CD B:Pro529 3.90 Fe CG B:Pro529 3.91 Fe SG B:Cys553 4.87 Fe N B:Val554 4.87 Fe CG2 B:Val554 4.83 Fe N B:His555 4.84 Fe C B:His555 4.80 Fe N B:Cys556 3.67 Fe CB B:Cys556 3.60 Fe SG B:Cys556 2.26 Fe C B:Cys556 4.32 Fe CA B:Cys556 4.01 Fe N B:Lys557 3.93 Fe C B:Lys557 4.97 Fe CA B:Lys557 4.86 Fe N B:Thr558 4.18 Fe CB B:Thr558 4.44 Fe OG1 B:Thr558 4.61 Fe CA B:Thr558 4.86 Fe N B:Cys559 4.80 Fe SG B:Cys559 4.68 Fe S1 B:Sf4613 2.32 Fe FE1 B:Sf4613 2.75 Fe FE3 B:Sf4613 0.00 Fe S4 B:Sf4613 2.18 Fe FE2 B:Sf4613 2.76 Fe S2 B:Sf4613 2.31 Fe FE4 B:Sf4613 2.70 Fe S3 B:Sf4613 3.86 interactive model: Iron binding site 8 out of 8 in 2gmh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 2gmh. 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: Lys557, B: Thr558, B: Cys559, B: Trp570, B: Sf4613, conact list: Atom Atom Distance (A) Fe CD1 B:Leu504 4.16 Fe SG B:Cys528 4.76 Fe CZ B:Tyr533 4.83 Fe CE1 B:Tyr533 4.51 Fe OH B:Tyr533 4.11 Fe SG B:Cys553 4.81 Fe SG B:Cys556 4.71 Fe N B:Lys557 4.87 Fe N B:Thr558 4.68 Fe N B:Cys559 3.91 Fe CB B:Cys559 3.41 Fe SG B:Cys559 2.27 Fe CA B:Cys559 4.30 Fe CD1 B:Trp570 4.61 Fe S1 B:Sf4613 2.18 Fe FE1 B:Sf4613 2.74 Fe FE3 B:Sf4613 2.70 Fe S4 B:Sf4613 3.82 Fe FE2 B:Sf4613 2.74 Fe S2 B:Sf4613 2.18 Fe FE4 B:Sf4613 0.00 Fe S3 B:Sf4613 2.19 interactive model: