Iron in the structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed With 3-Iodo-4- Hydroxybenzoate (pdb 3pci)

The binding sites of Iron atom in the structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed With 3-Iodo-4- Hydroxybenzoate (pdb code 3pci). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3pci structure was solved by A.M.ORVILLE, N.ELANGO, J.D.LIPSCOMB, D.H.OHLENDORF, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 6.0-2.2 Space group I121 a (A) 197.000 b (A) 127.070 c (A) 134.080 alpha (°) 90.00 beta (°) 97.53 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Iron Binding Sites: Iron binding site 1 out of 6 in 3pci Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3pci. 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: M: Tyr408, M: Tyr447, M: Arg457, M: His460, M: His462, M: Gln477, M: Ihb550, A: Hoh205, M: Hoh625, conact list: Atom Atom Distance (A) Fe CE2 M:Tyr408 3.38 Fe CD2 M:Tyr408 4.72 Fe CZ M:Tyr408 2.89 Fe CE1 M:Tyr408 4.00 Fe OH M:Tyr408 1.80 Fe CE2 M:Tyr447 3.81 Fe CZ M:Tyr447 3.38 Fe CE1 M:Tyr447 4.55 Fe OH M:Tyr447 2.22 Fe NH1 M:Arg457 4.55 Fe NE2 M:His460 2.30 Fe ND1 M:His460 4.25 Fe CD2 M:His460 3.48 Fe CE1 M:His460 3.03 Fe CG M:His460 4.49 Fe NE2 M:His462 2.34 Fe ND1 M:His462 4.33 Fe CD2 M:His462 3.37 Fe CE1 M:His462 3.20 Fe CG M:His462 4.45 Fe OE1 M:Gln477 4.99 Fe C6 M:Ihb550 4.78 Fe C5 M:Ihb550 3.41 Fe I3 M:Ihb550 4.41 Fe C4 M:Ihb550 2.80 Fe C3 M:Ihb550 3.89 Fe O4 M:Ihb550 1.59 Fe O A:Hoh205 4.48 Fe O M:Hoh625 4.03 interactive model: Iron binding site 2 out of 6 in 3pci Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3pci. 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: N: Tyr408, N: Tyr447, N: Arg457, N: His460, N: His462, N: Ihb550, B: Hoh252, N: Hoh631, conact list: Atom Atom Distance (A) Fe CE2 N:Tyr408 3.88 Fe CD1 N:Tyr408 4.89 Fe CZ N:Tyr408 2.90 Fe CE1 N:Tyr408 3.58 Fe OH N:Tyr408 1.76 Fe CE2 N:Tyr447 3.79 Fe CZ N:Tyr447 3.32 Fe CE1 N:Tyr447 4.48 Fe OH N:Tyr447 2.12 Fe NH1 N:Arg457 4.60 Fe NE2 N:His460 2.26 Fe ND1 N:His460 4.24 Fe CD2 N:His460 3.35 Fe CE1 N:His460 3.05 Fe CG N:His460 4.41 Fe NE2 N:His462 2.35 Fe ND1 N:His462 4.37 Fe CD2 N:His462 3.39 Fe CE1 N:His462 3.20 Fe CG N:His462 4.49 Fe C6 N:Ihb550 4.69 Fe C5 N:Ihb550 3.34 Fe I3 N:Ihb550 4.30 Fe C4 N:Ihb550 2.74 Fe C3 N:Ihb550 3.83 Fe O4 N:Ihb550 1.58 Fe O B:Hoh252 4.37 Fe O N:Hoh631 4.08 interactive model: Iron binding site 3 out of 6 in 3pci Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3pci. 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: O: Tyr408, O: Tyr447, O: Arg457, O: His460, O: His462, O: Ihb550, C: Hoh205, O: Hoh632, conact list: Atom Atom Distance (A) Fe CE2 O:Tyr408 3.94 Fe CZ O:Tyr408 3.02 Fe CE1 O:Tyr408 3.71 Fe OH O:Tyr408 1.89 Fe CE2 O:Tyr447 3.80 Fe CZ O:Tyr447 3.36 Fe CE1 O:Tyr447 4.52 Fe OH O:Tyr447 2.15 Fe NH1 O:Arg457 4.42 Fe NE2 O:His460 2.20 Fe ND1 O:His460 4.26 Fe CD2 O:His460 3.23 Fe CE1 O:His460 3.08 Fe CG O:His460 4.35 Fe NE2 O:His462 2.20 Fe ND1 O:His462 4.28 Fe CD2 O:His462 3.21 Fe CE1 O:His462 3.14 Fe CG O:His462 4.34 Fe C6 O:Ihb550 4.85 Fe C5 O:Ihb550 3.48 Fe I3 O:Ihb550 4.43 Fe C4 O:Ihb550 2.86 Fe C3 O:Ihb550 3.94 Fe O4 O:Ihb550 1.62 Fe O C:Hoh205 4.51 Fe O O:Hoh632 3.97 interactive model: Iron binding site 4 out of 6 in 3pci Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3pci. 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: P: Tyr408, P: Tyr447, P: Arg457, P: His460, P: His462, P: Ihb550, D: Hoh744, P: Hoh631, conact list: Atom Atom Distance (A) Fe CE2 P:Tyr408 3.45 Fe CD2 P:Tyr408 4.79 Fe CZ P:Tyr408 2.90 Fe CE1 P:Tyr408 3.97 Fe OH P:Tyr408 1.79 Fe CE2 P:Tyr447 3.72 Fe CZ P:Tyr447 3.26 Fe CE1 P:Tyr447 4.44 Fe OH P:Tyr447 2.10 Fe NH1 P:Arg457 4.40 Fe NE2 P:His460 2.20 Fe ND1 P:His460 4.16 Fe CD2 P:His460 3.37 Fe CE1 P:His460 2.92 Fe CG P:His460 4.40 Fe NE2 P:His462 2.27 Fe ND1 P:His462 4.24 Fe CD2 P:His462 3.32 Fe CE1 P:His462 3.10 Fe CG P:His462 4.40 Fe C6 P:Ihb550 4.81 Fe C5 P:Ihb550 3.45 Fe I3 P:Ihb550 4.33 Fe C4 P:Ihb550 2.81 Fe C3 P:Ihb550 3.87 Fe O4 P:Ihb550 1.59 Fe O D:Hoh744 4.18 Fe O P:Hoh631 4.00 interactive model: Iron binding site 5 out of 6 in 3pci Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 3pci. 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: Q: Tyr408, Q: Tyr447, Q: Arg457, Q: His460, Q: His462, Q: Gln477, Q: Ihb550, E: Hoh205, Q: Hoh1027, conact list: Atom Atom Distance (A) Fe CE2 Q:Tyr408 3.87 Fe CD1 Q:Tyr408 4.82 Fe CZ Q:Tyr408 2.88 Fe CE1 Q:Tyr408 3.52 Fe OH Q:Tyr408 1.84 Fe CE2 Q:Tyr447 3.91 Fe CZ Q:Tyr447 3.33 Fe CE1 Q:Tyr447 4.41 Fe OH Q:Tyr447 2.02 Fe NH1 Q:Arg457 4.51 Fe NE2 Q:His460 2.14 Fe ND1 Q:His460 4.21 Fe CD2 Q:His460 3.17 Fe CE1 Q:His460 3.06 Fe CG Q:His460 4.27 Fe NE2 Q:His462 2.25 Fe ND1 Q:His462 4.33 Fe CD2 Q:His462 3.26 Fe CE1 Q:His462 3.17 Fe CG Q:His462 4.40 Fe OE1 Q:Gln477 4.86 Fe C6 Q:Ihb550 4.86 Fe C5 Q:Ihb550 3.48 Fe I3 Q:Ihb550 4.36 Fe C4 Q:Ihb550 2.83 Fe C3 Q:Ihb550 3.93 Fe O4 Q:Ihb550 1.55 Fe O E:Hoh205 4.23 Fe O Q:Hoh1027 4.05 interactive model: Iron binding site 6 out of 6 in 3pci Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 3pci. 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: R: Tyr408, R: Tyr447, R: Arg457, R: His460, R: His462, R: Gln477, R: Ihb550, F: Hoh1236, R: Hoh1273, conact list: Atom Atom Distance (A) Fe CE2 R:Tyr408 3.60 Fe CD2 R:Tyr408 4.93 Fe CZ R:Tyr408 3.02 Fe CE1 R:Tyr408 4.05 Fe OH R:Tyr408 1.96 Fe CE2 R:Tyr447 3.96 Fe CZ R:Tyr447 3.42 Fe CE1 R:Tyr447 4.50 Fe OH R:Tyr447 2.17 Fe NH1 R:Arg457 4.44 Fe NE2 R:His460 2.22 Fe ND1 R:His460 4.26 Fe CD2 R:His460 3.28 Fe CE1 R:His460 3.09 Fe CG R:His460 4.38 Fe NE2 R:His462 2.32 Fe ND1 R:His462 4.40 Fe CD2 R:His462 3.28 Fe CE1 R:His462 3.28 Fe CG R:His462 4.43 Fe OE1 R:Gln477 4.96 Fe C6 R:Ihb550 4.95 Fe C5 R:Ihb550 3.59 Fe I3 R:Ihb550 4.21 Fe C4 R:Ihb550 2.84 Fe C3 R:Ihb550 3.86 Fe O4 R:Ihb550 1.53 Fe O F:Hoh1236 4.26 Fe O R:Hoh1273 4.06 interactive model: