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

The binding sites of Iron atom in the structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed With 4- Hydroxybenzoate (pdb code 3pcc). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3pcc structure was solved by N.ELANGO, A.M.ORVILLE, J.D.LIPSCOMB, D.H.OHLENDORF, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 6.0-2.0 Space group I121 a (A) 197.410 b (A) 127.970 c (A) 134.880 alpha (°) 90.00 beta (°) 97.80 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Iron Binding Sites: Iron binding site 1 out of 6 in 3pcc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3pcc. 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: Tyr16, M: Tyr408, M: Tyr447, M: Arg457, M: His460, M: His462, M: Phb550, A: Hoh606, M: Hoh626, M: Hoh743, conact list: Atom Atom Distance (A) Fe CD2 A:Tyr16 4.99 Fe CE2 M:Tyr408 3.59 Fe CD2 M:Tyr408 4.93 Fe CZ M:Tyr408 3.01 Fe CE1 M:Tyr408 4.05 Fe OH M:Tyr408 1.95 Fe CE2 M:Tyr447 3.78 Fe CZ M:Tyr447 3.29 Fe CE1 M:Tyr447 4.42 Fe OH M:Tyr447 2.10 Fe NH1 M:Arg457 4.35 Fe NE2 M:His460 2.27 Fe ND1 M:His460 4.19 Fe CD2 M:His460 3.47 Fe CE1 M:His460 2.95 Fe CG M:His460 4.48 Fe NE2 M:His462 2.31 Fe ND1 M:His462 4.32 Fe CD2 M:His462 3.41 Fe CE1 M:His462 3.17 Fe CG M:His462 4.48 Fe C5 M:Phb550 3.90 Fe C4 M:Phb550 3.26 Fe C3 M:Phb550 4.22 Fe O4 M:Phb550 2.14 Fe O A:Hoh606 4.37 Fe O M:Hoh626 4.21 Fe O M:Hoh743 2.13 interactive model: Iron binding site 2 out of 6 in 3pcc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3pcc. 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: Gln477, N: Phb550, B: Hoh606, N: Hoh728, N: Hoh854, conact list: Atom Atom Distance (A) Fe CE2 N:Tyr408 3.61 Fe CD2 N:Tyr408 4.91 Fe CZ N:Tyr408 2.96 Fe CE1 N:Tyr408 3.94 Fe OH N:Tyr408 1.88 Fe CE2 N:Tyr447 4.61 Fe CZ N:Tyr447 3.45 Fe CE1 N:Tyr447 3.89 Fe OH N:Tyr447 2.29 Fe NH1 N:Arg457 4.30 Fe NE2 N:His460 2.38 Fe ND1 N:His460 4.43 Fe CD2 N:His460 3.41 Fe CE1 N:His460 3.28 Fe CG N:His460 4.54 Fe NE2 N:His462 2.24 Fe ND1 N:His462 4.23 Fe CD2 N:His462 3.36 Fe CE1 N:His462 3.00 Fe CG N:His462 4.43 Fe OE1 N:Gln477 4.97 Fe C5 N:Phb550 3.71 Fe C4 N:Phb550 3.15 Fe C3 N:Phb550 4.18 Fe O4 N:Phb550 2.08 Fe O B:Hoh606 4.28 Fe O N:Hoh728 4.19 Fe O N:Hoh854 2.11 interactive model: Iron binding site 3 out of 6 in 3pcc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3pcc. 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: Gln477, O: Phb550, C: Hoh606, O: Hoh643, O: Hoh840, conact list: Atom Atom Distance (A) Fe CE2 O:Tyr408 3.90 Fe CZ O:Tyr408 3.04 Fe CE1 O:Tyr408 3.79 Fe OH O:Tyr408 1.95 Fe CE2 O:Tyr447 3.96 Fe CZ O:Tyr447 3.43 Fe CE1 O:Tyr447 4.54 Fe OH O:Tyr447 2.14 Fe NH1 O:Arg457 4.41 Fe NE2 O:His460 2.21 Fe ND1 O:His460 4.20 Fe CD2 O:His460 3.31 Fe CE1 O:His460 2.98 Fe CG O:His460 4.37 Fe NE2 O:His462 2.16 Fe ND1 O:His462 4.23 Fe CD2 O:His462 3.22 Fe CE1 O:His462 3.05 Fe CG O:His462 4.31 Fe OE1 O:Gln477 4.96 Fe C5 O:Phb550 3.92 Fe C4 O:Phb550 3.27 Fe C3 O:Phb550 4.22 Fe O4 O:Phb550 2.17 Fe O C:Hoh606 4.39 Fe O O:Hoh643 4.18 Fe O O:Hoh840 2.07 interactive model: Iron binding site 4 out of 6 in 3pcc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3pcc. 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: Phb550, D: Hoh606, P: Hoh663, P: Hoh777, conact list: Atom Atom Distance (A) Fe CE2 P:Tyr408 3.62 Fe CD2 P:Tyr408 4.92 Fe CZ P:Tyr408 2.97 Fe CE1 P:Tyr408 3.90 Fe OH P:Tyr408 1.85 Fe CE2 P:Tyr447 3.79 Fe CZ P:Tyr447 3.31 Fe CE1 P:Tyr447 4.45 Fe OH P:Tyr447 2.05 Fe NH1 P:Arg457 4.43 Fe NE2 P:His460 2.26 Fe ND1 P:His460 4.29 Fe CD2 P:His460 3.30 Fe CE1 P:His460 3.04 Fe CG P:His460 4.42 Fe NE2 P:His462 2.20 Fe ND1 P:His462 4.21 Fe CD2 P:His462 3.29 Fe CE1 P:His462 3.05 Fe CG P:His462 4.36 Fe C5 P:Phb550 3.99 Fe C4 P:Phb550 3.45 Fe C3 P:Phb550 4.46 Fe O4 P:Phb550 2.30 Fe O D:Hoh606 4.35 Fe O P:Hoh663 4.21 Fe O P:Hoh777 2.09 interactive model: Iron binding site 5 out of 6 in 3pcc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 3pcc. 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: Phb550, E: Hoh606, Q: Hoh646, Q: Hoh769, conact list: Atom Atom Distance (A) Fe CE2 Q:Tyr408 3.87 Fe CZ Q:Tyr408 2.99 Fe CE1 Q:Tyr408 3.73 Fe OH Q:Tyr408 1.88 Fe CE2 Q:Tyr447 3.82 Fe CZ Q:Tyr447 3.27 Fe CE1 Q:Tyr447 4.37 Fe OH Q:Tyr447 1.98 Fe NH1 Q:Arg457 4.33 Fe NE2 Q:His460 2.25 Fe ND1 Q:His460 4.30 Fe CD2 Q:His460 3.29 Fe CE1 Q:His460 3.13 Fe CG Q:His460 4.41 Fe NE2 Q:His462 2.22 Fe ND1 Q:His462 4.22 Fe CD2 Q:His462 3.27 Fe CE1 Q:His462 3.06 Fe CG Q:His462 4.38 Fe OE1 Q:Gln477 4.82 Fe C5 Q:Phb550 3.87 Fe C4 Q:Phb550 3.25 Fe C3 Q:Phb550 4.19 Fe O4 Q:Phb550 2.08 Fe O E:Hoh606 4.39 Fe O Q:Hoh646 4.19 Fe O Q:Hoh769 2.17 interactive model: Iron binding site 6 out of 6 in 3pcc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 3pcc. 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: Phb550, F: Hoh606, R: Hoh770, R: Hoh899, conact list: Atom Atom Distance (A) Fe CE2 R:Tyr408 3.80 Fe CD1 R:Tyr408 4.84 Fe CZ R:Tyr408 2.84 Fe CE1 R:Tyr408 3.51 Fe OH R:Tyr408 1.74 Fe CE2 R:Tyr447 3.83 Fe CZ R:Tyr447 3.42 Fe CE1 R:Tyr447 4.59 Fe OH R:Tyr447 2.24 Fe NH1 R:Arg457 4.29 Fe NE2 R:His460 2.31 Fe ND1 R:His460 4.36 Fe CD2 R:His460 3.33 Fe CE1 R:His460 3.19 Fe CG R:His460 4.47 Fe NE2 R:His462 2.30 Fe ND1 R:His462 4.40 Fe CD2 R:His462 3.32 Fe CE1 R:His462 3.25 Fe CG R:His462 4.45 Fe C5 R:Phb550 3.83 Fe C4 R:Phb550 3.24 Fe C3 R:Phb550 4.24 Fe O4 R:Phb550 2.11 Fe O F:Hoh606 4.23 Fe O R:Hoh770 4.16 Fe O R:Hoh899 2.19 interactive model: