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 |
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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:
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