Iron in the structure of Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb (pdb 1ykn)

The binding sites of Iron atom in the structure of Protocatechuate 3,4-Dioxygenase Y408E Mutant Bound to Dhb (pdb code 1ykn). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1ykn 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) 8.5-2.1 Space group I121 a (A) 195.821 b (A) 128.569 c (A) 134.356 alpha (°) 90.00 beta (°) 97.98 gamma (°) 90.00 Rfactor (%) 14.9 Rfree (%) 19.2 Iron Binding Sites: Iron binding site 1 out of 6 in 1ykn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1ykn. 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: Glu408, B: Tyr447, B: Arg457, B: His460, B: His462, B: Gln477, B: Dhb550, B: Hoh606, B: Hoh643, B: Hoh901, conact list: Atom Atom Distance (A) Fe OE1 B:Glu408 3.81 Fe OE2 B:Glu408 4.63 Fe CD B:Glu408 4.54 Fe CE2 B:Tyr447 4.19 Fe CZ B:Tyr447 3.75 Fe CE1 B:Tyr447 4.85 Fe OH B:Tyr447 2.49 Fe NH1 B:Arg457 4.26 Fe NE2 B:His460 2.43 Fe ND1 B:His460 4.53 Fe CD2 B:His460 3.34 Fe CE1 B:His460 3.42 Fe CG B:His460 4.53 Fe NE2 B:His462 2.21 Fe ND1 B:His462 4.12 Fe CD2 B:His462 3.36 Fe CE1 B:His462 2.94 Fe CG B:His462 4.35 Fe OE1 B:Gln477 4.79 Fe C5 B:Dhb550 4.11 Fe C4 B:Dhb550 3.47 Fe C3 B:Dhb550 4.33 Fe O4 B:Dhb550 2.39 Fe O3 B:Dhb550 4.39 Fe O B:Hoh606 4.19 Fe O B:Hoh643 4.53 Fe O B:Hoh901 2.67 interactive model: Iron binding site 2 out of 6 in 1ykn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1ykn. 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: Glu408, D: Tyr447, D: Arg457, D: His460, D: His462, D: Gln477, D: Dhb1550, C: Hoh1606, D: Hoh1643, D: Hoh1901, conact list: Atom Atom Distance (A) Fe OE1 D:Glu408 3.81 Fe OE2 D:Glu408 4.38 Fe CD D:Glu408 4.35 Fe CE2 D:Tyr447 4.25 Fe CZ D:Tyr447 3.73 Fe CE1 D:Tyr447 4.83 Fe OH D:Tyr447 2.57 Fe NH1 D:Arg457 4.17 Fe NE2 D:His460 2.34 Fe ND1 D:His460 4.32 Fe CD2 D:His460 3.40 Fe CE1 D:His460 3.18 Fe CG D:His460 4.49 Fe NE2 D:His462 2.37 Fe ND1 D:His462 4.28 Fe CD2 D:His462 3.48 Fe CE1 D:His462 3.11 Fe CG D:His462 4.50 Fe OE1 D:Gln477 4.96 Fe C5 D:Dhb1550 4.39 Fe C4 D:Dhb1550 3.41 Fe C3 D:Dhb1550 3.98 Fe O4 D:Dhb1550 2.37 Fe O3 D:Dhb1550 3.73 Fe O C:Hoh1606 4.28 Fe O D:Hoh1643 4.32 Fe O D:Hoh1901 2.74 interactive model: Iron binding site 3 out of 6 in 1ykn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1ykn. 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: Glu408, F: Tyr447, F: Arg457, F: His460, F: His462, F: Gln477, F: Dhb2550, E: Hoh2606, F: Hoh2643, F: Hoh2901, conact list: Atom Atom Distance (A) Fe OE1 F:Glu408 3.81 Fe OE2 F:Glu408 4.54 Fe CD F:Glu408 4.45 Fe CE2 F:Tyr447 4.07 Fe CZ F:Tyr447 3.55 Fe CE1 F:Tyr447 4.68 Fe OH F:Tyr447 2.28 Fe NH1 F:Arg457 4.14 Fe NE2 F:His460 2.28 Fe ND1 F:His460 4.30 Fe CD2 F:His460 3.36 Fe CE1 F:His460 3.11 Fe CG F:His460 4.46 Fe NE2 F:His462 2.52 Fe ND1 F:His462 4.59 Fe CD2 F:His462 3.41 Fe CE1 F:His462 3.51 Fe CG F:His462 4.57 Fe OE1 F:Gln477 4.70 Fe C5 F:Dhb2550 4.44 Fe C4 F:Dhb2550 3.45 Fe C3 F:Dhb2550 4.07 Fe O4 F:Dhb2550 2.24 Fe O3 F:Dhb2550 3.78 Fe O E:Hoh2606 4.48 Fe O F:Hoh2643 4.24 Fe O F:Hoh2901 2.47 interactive model: Iron binding site 4 out of 6 in 1ykn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1ykn. 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: H: Glu408, H: Tyr447, H: Arg457, H: His460, H: His462, H: Gln477, H: Dhb3550, G: Hoh3606, H: Hoh3643, H: Hoh3901, conact list: Atom Atom Distance (A) Fe OE1 H:Glu408 4.39 Fe OE2 H:Glu408 4.46 Fe CD H:Glu408 4.67 Fe CE2 H:Tyr447 4.34 Fe CZ H:Tyr447 3.74 Fe CE1 H:Tyr447 4.81 Fe OH H:Tyr447 2.51 Fe NH1 H:Arg457 4.22 Fe NE2 H:His460 2.40 Fe ND1 H:His460 4.44 Fe CD2 H:His460 3.40 Fe CE1 H:His460 3.28 Fe CG H:His460 4.55 Fe NE2 H:His462 2.25 Fe ND1 H:His462 4.24 Fe CD2 H:His462 3.30 Fe CE1 H:His462 3.10 Fe CG H:His462 4.37 Fe OE1 H:Gln477 4.60 Fe CD H:Gln477 4.97 Fe C5 H:Dhb3550 4.33 Fe C4 H:Dhb3550 3.42 Fe C3 H:Dhb3550 4.04 Fe O4 H:Dhb3550 2.28 Fe O3 H:Dhb3550 3.82 Fe O G:Hoh3606 4.37 Fe O H:Hoh3643 4.50 Fe O H:Hoh3901 2.39 interactive model: Iron binding site 5 out of 6 in 1ykn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1ykn. 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: Glu408, J: Tyr447, J: Arg457, J: His460, J: His462, J: Gln477, J: Dhb4550, I: Hoh4606, J: Hoh4643, J: Hoh4901, conact list: Atom Atom Distance (A) Fe OE1 J:Glu408 3.48 Fe OE2 J:Glu408 4.19 Fe CD J:Glu408 4.11 Fe CE2 J:Tyr447 4.13 Fe CZ J:Tyr447 3.73 Fe CE1 J:Tyr447 4.88 Fe OH J:Tyr447 2.54 Fe NH1 J:Arg457 4.48 Fe NE2 J:His460 2.58 Fe ND1 J:His460 4.62 Fe CD2 J:His460 3.54 Fe CE1 J:His460 3.48 Fe CG J:His460 4.67 Fe NE2 J:His462 2.32 Fe ND1 J:His462 4.38 Fe CD2 J:His462 3.29 Fe CE1 J:His462 3.27 Fe CG J:His462 4.42 Fe OE1 J:Gln477 4.99 Fe C5 J:Dhb4550 4.35 Fe C4 J:Dhb4550 3.51 Fe C3 J:Dhb4550 4.28 Fe O4 J:Dhb4550 2.38 Fe O3 J:Dhb4550 4.17 Fe O I:Hoh4606 4.25 Fe O J:Hoh4643 4.27 Fe O J:Hoh4901 2.26 interactive model: Iron binding site 6 out of 6 in 1ykn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1ykn. 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: L: Glu408, L: Tyr447, L: Arg457, L: His460, L: His462, L: Gln477, L: Dhb5550, K: Hoh5606, L: Hoh5643, L: Hoh5901, conact list: Atom Atom Distance (A) Fe OE1 L:Glu408 3.86 Fe OE2 L:Glu408 4.75 Fe CD L:Glu408 4.62 Fe CE2 L:Tyr447 4.47 Fe CZ L:Tyr447 3.92 Fe CE1 L:Tyr447 4.97 Fe OH L:Tyr447 2.63 Fe NH1 L:Arg457 4.23 Fe NE2 L:His460 2.23 Fe ND1 L:His460 4.29 Fe CD2 L:His460 3.22 Fe CE1 L:His460 3.16 Fe CG L:His460 4.35 Fe NE2 L:His462 2.26 Fe ND1 L:His462 4.26 Fe CD2 L:His462 3.21 Fe CE1 L:His462 3.18 Fe CG L:His462 4.31 Fe OE1 L:Gln477 4.54 Fe C5 L:Dhb5550 4.48 Fe C4 L:Dhb5550 3.54 Fe C3 L:Dhb5550 4.18 Fe O4 L:Dhb5550 2.42 Fe O3 L:Dhb5550 3.95 Fe O K:Hoh5606 4.42 Fe O L:Hoh5643 4.33 Fe O L:Hoh5901 2.44 interactive model: