Iron in the structure of Protocatechuate 3,4-Dioxygenase Y408H Mutant (pdb 1yko)
The binding sites of Iron atom in the structure of Protocatechuate 3,4-Dioxygenase Y408H Mutant (pdb code 1yko). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1yko structure was solved by C.K.BROWN, D.H.OHLENDORF, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 37.3-2.5 | Space group | I121 | a (A) | 196.590 | b (A) | 127.630 | c (A) | 134.450 | alpha (°) | 90.00 | beta (°) | 97.60 | gamma (°) | 90.00 | Rfactor (%) | 18.3 | Rfree (%) | 21.7 |
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Iron Binding Sites:Iron binding site 1 out of 6 in 1yko
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1yko. 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: His408, B: Tyr447, B: Arg457, B: His460, B: His462, B: Gln477, A: Hoh606, B: Hoh643, B: Hoh801, B: Hoh901, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 B:His408 | 3.92 | Fe | CD2 B:His408 | 4.97 | Fe | CE1 B:His408 | 4.54 | Fe | CE2 B:Tyr447 | 3.73 | Fe | CZ B:Tyr447 | 3.27 | Fe | CE1 B:Tyr447 | 4.44 | Fe | OH B:Tyr447 | 2.07 | Fe | NH1 B:Arg457 | 4.17 | Fe | NE2 B:His460 | 2.38 | Fe | ND1 B:His460 | 4.40 | Fe | CD2 B:His460 | 3.46 | Fe | CE1 B:His460 | 3.21 | Fe | CG B:His460 | 4.55 | Fe | NE2 B:His462 | 2.26 | Fe | ND1 B:His462 | 4.16 | Fe | CD2 B:His462 | 3.45 | Fe | CE1 B:His462 | 2.94 | Fe | CG B:His462 | 4.43 | Fe | OE1 B:Gln477 | 4.94 | Fe | O A:Hoh606 | 3.95 | Fe | O B:Hoh643 | 4.70 | Fe | O B:Hoh801 | 3.06 | Fe | O B:Hoh901 | 2.02 |
| interactive model:
| Iron binding site 2 out of 6 in 1yko
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1yko. 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: Tyr16, D: His408, D: Tyr447, D: Arg457, D: His460, D: His462, C: Hoh1606, D: Hoh1643, D: Hoh1801, D: Hoh1901, | conact list:
Atom | Atom | Distance (A) | Fe | CD2 C:Tyr16 | 4.83 | Fe | NE2 D:His408 | 3.86 | Fe | CD2 D:His408 | 4.92 | Fe | CE1 D:His408 | 4.39 | Fe | CE2 D:Tyr447 | 3.90 | Fe | CZ D:Tyr447 | 3.29 | Fe | CE1 D:Tyr447 | 4.37 | Fe | OH D:Tyr447 | 2.02 | Fe | NH1 D:Arg457 | 4.18 | Fe | NE2 D:His460 | 2.60 | Fe | ND1 D:His460 | 4.62 | Fe | CD2 D:His460 | 3.68 | Fe | CE1 D:His460 | 3.42 | Fe | CG D:His460 | 4.78 | Fe | NE2 D:His462 | 2.31 | Fe | ND1 D:His462 | 4.15 | Fe | CD2 D:His462 | 3.53 | Fe | CE1 D:His462 | 2.90 | Fe | CG D:His462 | 4.48 | Fe | O C:Hoh1606 | 3.94 | Fe | O D:Hoh1643 | 4.64 | Fe | O D:Hoh1801 | 2.92 | Fe | O D:Hoh1901 | 1.86 |
| interactive model:
| Iron binding site 3 out of 6 in 1yko
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1yko. 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: F: His408, F: Tyr447, F: Arg457, F: His460, F: His462, F: Gln477, E: Hoh2606, F: Hoh2643, F: Hoh2801, F: Hoh2901, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 F:His408 | 3.97 | Fe | CE1 F:His408 | 4.51 | Fe | CE2 F:Tyr447 | 3.93 | Fe | CZ F:Tyr447 | 3.36 | Fe | CE1 F:Tyr447 | 4.46 | Fe | OH F:Tyr447 | 2.10 | Fe | NH1 F:Arg457 | 4.04 | Fe | NE2 F:His460 | 2.43 | Fe | ND1 F:His460 | 4.46 | Fe | CD2 F:His460 | 3.50 | Fe | CE1 F:His460 | 3.28 | Fe | CG F:His460 | 4.60 | Fe | NE2 F:His462 | 2.23 | Fe | ND1 F:His462 | 4.23 | Fe | CD2 F:His462 | 3.30 | Fe | CE1 F:His462 | 3.07 | Fe | CG F:His462 | 4.37 | Fe | OE1 F:Gln477 | 4.88 | Fe | O E:Hoh2606 | 4.06 | Fe | O F:Hoh2643 | 4.50 | Fe | O F:Hoh2801 | 2.95 | Fe | O F:Hoh2901 | 2.08 |
| interactive model:
| Iron binding site 4 out of 6 in 1yko
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1yko. 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: G: Tyr16, H: His408, H: Tyr447, H: Arg457, H: His460, H: His462, G: Hoh3606, H: Hoh3643, H: Hoh3801, H: Hoh3901, | conact list:
Atom | Atom | Distance (A) | Fe | CD2 G:Tyr16 | 4.98 | Fe | NE2 H:His408 | 3.84 | Fe | CD2 H:His408 | 4.92 | Fe | CE1 H:His408 | 4.36 | Fe | CE2 H:Tyr447 | 3.81 | Fe | CZ H:Tyr447 | 3.27 | Fe | CE1 H:Tyr447 | 4.38 | Fe | OH H:Tyr447 | 2.08 | Fe | NH1 H:Arg457 | 4.36 | Fe | NE2 H:His460 | 2.51 | Fe | ND1 H:His460 | 4.56 | Fe | CD2 H:His460 | 3.54 | Fe | CE1 H:His460 | 3.39 | Fe | CG H:His460 | 4.66 | Fe | NE2 H:His462 | 2.28 | Fe | ND1 H:His462 | 4.28 | Fe | CD2 H:His462 | 3.41 | Fe | CE1 H:His462 | 3.08 | Fe | CG H:His462 | 4.46 | Fe | O G:Hoh3606 | 4.05 | Fe | O H:Hoh3643 | 4.45 | Fe | O H:Hoh3801 | 2.97 | Fe | O H:Hoh3901 | 1.94 |
| interactive model:
| Iron binding site 5 out of 6 in 1yko
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1yko. 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: J: His408, J: Tyr447, J: Arg457, J: His460, J: His462, I: Hoh4606, J: Hoh4643, J: Hoh4801, J: Hoh4901, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 J:His408 | 3.72 | Fe | CD2 J:His408 | 4.67 | Fe | CE1 J:His408 | 4.48 | Fe | CE2 J:Tyr447 | 3.73 | Fe | CZ J:Tyr447 | 3.36 | Fe | CE1 J:Tyr447 | 4.56 | Fe | OH J:Tyr447 | 2.24 | Fe | NH1 J:Arg457 | 4.30 | Fe | NE2 J:His460 | 2.45 | Fe | ND1 J:His460 | 4.52 | Fe | CD2 J:His460 | 3.44 | Fe | CE1 J:His460 | 3.38 | Fe | CG J:His460 | 4.58 | Fe | NE2 J:His462 | 2.15 | Fe | ND1 J:His462 | 4.18 | Fe | CD2 J:His462 | 3.22 | Fe | CE1 J:His462 | 3.01 | Fe | CG J:His462 | 4.31 | Fe | O I:Hoh4606 | 3.83 | Fe | O J:Hoh4643 | 4.31 | Fe | O J:Hoh4801 | 3.22 | Fe | O J:Hoh4901 | 1.99 |
| interactive model:
| Iron binding site 6 out of 6 in 1yko
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1yko. 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: K: Tyr16, L: His408, L: Tyr447, L: Arg457, L: His460, L: His462, K: Hoh5606, L: Hoh5643, L: Hoh5801, L: Hoh5901, | conact list:
Atom | Atom | Distance (A) | Fe | CD2 K:Tyr16 | 4.93 | Fe | NE2 L:His408 | 3.81 | Fe | CD2 L:His408 | 4.86 | Fe | CE1 L:His408 | 4.46 | Fe | CE2 L:Tyr447 | 3.73 | Fe | CZ L:Tyr447 | 3.28 | Fe | CE1 L:Tyr447 | 4.45 | Fe | OH L:Tyr447 | 2.16 | Fe | NH1 L:Arg457 | 4.29 | Fe | NE2 L:His460 | 2.43 | Fe | ND1 L:His460 | 4.46 | Fe | CD2 L:His460 | 3.52 | Fe | CE1 L:His460 | 3.27 | Fe | CG L:His460 | 4.60 | Fe | NE2 L:His462 | 2.25 | Fe | ND1 L:His462 | 4.24 | Fe | CD2 L:His462 | 3.36 | Fe | CE1 L:His462 | 3.06 | Fe | CG L:His462 | 4.42 | Fe | O K:Hoh5606 | 4.03 | Fe | O L:Hoh5643 | 4.54 | Fe | O L:Hoh5801 | 2.93 | Fe | O L:Hoh5901 | 2.23 |
| interactive model:
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