Iron in the structure of 4-Hydroxyphenylpyruvate Dioxygenase (pdb 1sp8)
The binding sites of Iron atom in the structure of 4-Hydroxyphenylpyruvate Dioxygenase (pdb code 1sp8). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1sp8 structure was solved by I.M.FRITZE, L.LINDEN, J.FREIGANG, G.AUERBACH, R.HUBER, S.STEINBACHER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 19.8-2.0 | Space group | P212121 | a (A) | 89.000 | b (A) | 110.900 | c (A) | 174.800 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 90.00 | Rfactor (%) | 27.5 | Rfree (%) | 32.4 |
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Iron Binding Sites:Iron binding site 1 out of 4 in 1sp8
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1sp8. 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: His219, A: Val221, A: His301, A: Ala303, A: Phe374, A: Glu387, A: Phe412, A: Hoh501, A: Hoh502, A: Hoh718, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 A:His219 | 2.12 | Fe | ND1 A:His219 | 4.17 | Fe | CD2 A:His219 | 3.20 | Fe | CE1 A:His219 | 3.01 | Fe | CG A:His219 | 4.29 | Fe | CG2 A:Val221 | 4.55 | Fe | NE2 A:His301 | 2.18 | Fe | ND1 A:His301 | 4.18 | Fe | CD2 A:His301 | 3.31 | Fe | CE1 A:His301 | 2.98 | Fe | CG A:His301 | 4.37 | Fe | CB A:Ala303 | 4.55 | Fe | CZ A:Phe374 | 4.83 | Fe | CE1 A:Phe374 | 4.58 | Fe | OE1 A:Glu387 | 2.09 | Fe | CB A:Glu387 | 4.69 | Fe | OE2 A:Glu387 | 3.61 | Fe | CD A:Glu387 | 3.18 | Fe | CG A:Glu387 | 4.47 | Fe | O A:Phe412 | 4.86 | Fe | CD1 A:Phe412 | 4.70 | Fe | O A:Hoh501 | 2.11 | Fe | O A:Hoh502 | 2.12 | Fe | O A:Hoh718 | 4.82 |
| interactive model:
| Iron binding site 2 out of 4 in 1sp8
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1sp8. 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: His219, B: Val221, B: His301, B: Ala303, B: Phe374, B: Glu387, B: Hoh501, B: Hoh502, B: Hoh503, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 B:His219 | 2.14 | Fe | ND1 B:His219 | 4.18 | Fe | CD2 B:His219 | 3.20 | Fe | CE1 B:His219 | 3.03 | Fe | CG B:His219 | 4.30 | Fe | CG2 B:Val221 | 4.39 | Fe | NE2 B:His301 | 2.15 | Fe | ND1 B:His301 | 4.14 | Fe | CD2 B:His301 | 3.28 | Fe | CE1 B:His301 | 2.95 | Fe | CG B:His301 | 4.33 | Fe | CB B:Ala303 | 4.39 | Fe | CZ B:Phe374 | 4.65 | Fe | CE1 B:Phe374 | 4.43 | Fe | OE1 B:Glu387 | 2.11 | Fe | CB B:Glu387 | 4.60 | Fe | OE2 B:Glu387 | 3.67 | Fe | CD B:Glu387 | 3.21 | Fe | CG B:Glu387 | 4.47 | Fe | O B:Hoh501 | 2.09 | Fe | O B:Hoh502 | 2.10 | Fe | O B:Hoh503 | 2.13 |
| interactive model:
| Iron binding site 3 out of 4 in 1sp8
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1sp8. 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: C: His219, C: Val221, C: His301, C: Ala303, C: Phe374, C: Glu387, C: Phe412, C: Hoh501, C: Hoh502, C: Hoh503, C: Hoh660, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 C:His219 | 2.14 | Fe | ND1 C:His219 | 4.20 | Fe | CD2 C:His219 | 3.21 | Fe | CE1 C:His219 | 3.04 | Fe | CG C:His219 | 4.31 | Fe | CG2 C:Val221 | 4.66 | Fe | NE2 C:His301 | 2.15 | Fe | ND1 C:His301 | 4.17 | Fe | CD2 C:His301 | 3.26 | Fe | CE1 C:His301 | 2.99 | Fe | CG C:His301 | 4.34 | Fe | CB C:Ala303 | 4.56 | Fe | CZ C:Phe374 | 4.73 | Fe | CE1 C:Phe374 | 4.50 | Fe | OE1 C:Glu387 | 2.11 | Fe | CB C:Glu387 | 4.75 | Fe | OE2 C:Glu387 | 3.58 | Fe | CD C:Glu387 | 3.19 | Fe | CG C:Glu387 | 4.51 | Fe | O C:Phe412 | 4.81 | Fe | O C:Hoh501 | 2.11 | Fe | O C:Hoh502 | 2.10 | Fe | O C:Hoh503 | 2.11 | Fe | O C:Hoh660 | 4.61 |
| interactive model:
| Iron binding site 4 out of 4 in 1sp8
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1sp8. 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: D: His219, D: Val221, D: His301, D: Ala303, D: Phe374, D: Glu387, D: Phe412, D: Hoh501, D: Hoh502, D: Hoh503, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 D:His219 | 2.13 | Fe | ND1 D:His219 | 4.21 | Fe | CD2 D:His219 | 3.13 | Fe | CE1 D:His219 | 3.09 | Fe | CG D:His219 | 4.26 | Fe | CG2 D:Val221 | 4.44 | Fe | NE2 D:His301 | 2.16 | Fe | ND1 D:His301 | 4.19 | Fe | CD2 D:His301 | 3.23 | Fe | CE1 D:His301 | 3.03 | Fe | CG D:His301 | 4.32 | Fe | CB D:Ala303 | 4.50 | Fe | CZ D:Phe374 | 4.77 | Fe | CE1 D:Phe374 | 4.42 | Fe | OE1 D:Glu387 | 2.10 | Fe | CB D:Glu387 | 4.65 | Fe | OE2 D:Glu387 | 3.60 | Fe | CD D:Glu387 | 3.18 | Fe | CG D:Glu387 | 4.47 | Fe | O D:Phe412 | 5.00 | Fe | CD1 D:Phe412 | 4.95 | Fe | O D:Hoh501 | 2.12 | Fe | O D:Hoh502 | 2.12 | Fe | O D:Hoh503 | 2.13 |
| interactive model:
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