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 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: