Iron in the structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed With 6- Hydroxynicotinic Acid N-Oxide (pdb 3pck)

The binding sites of Iron atom in the structure of Structure of Protocatechuate 3,4-Dioxygenase Complexed With 6- Hydroxynicotinic Acid N-Oxide (pdb code 3pck). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3pck structure was solved by 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) 6.0-2.1 Space group I121 a (A) 196.900 b (A) 127.800 c (A) 134.400 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 3pck Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3pck. 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: Arg457, M: His460, M: His462, M: Nno550, A: Hoh606, M: Hoh628, M: Hoh744, conact list: Atom Atom Distance (A) Fe CE2 M:Tyr408 3.54 Fe CD2 M:Tyr408 4.86 Fe CZ M:Tyr408 2.96 Fe CE1 M:Tyr408 3.99 Fe OH M:Tyr408 1.93 Fe NH1 M:Arg457 4.41 Fe NE2 M:His460 2.36 Fe ND1 M:His460 4.35 Fe CD2 M:His460 3.47 Fe CE1 M:His460 3.15 Fe CG M:His460 4.54 Fe NE2 M:His462 2.14 Fe ND1 M:His462 4.19 Fe CD2 M:His462 3.21 Fe CE1 M:His462 3.04 Fe CG M:His462 4.29 Fe N1 M:Nno550 2.98 Fe C6 M:Nno550 2.87 Fe C5 M:Nno550 4.14 Fe O4 M:Nno550 2.19 Fe O3 M:Nno550 2.45 Fe C2 M:Nno550 4.22 Fe O A:Hoh606 4.31 Fe O M:Hoh628 4.23 Fe O M:Hoh744 2.32 interactive model: Iron binding site 2 out of 6 in 3pck Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3pck. 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: Arg457, N: His460, N: His462, N: Gln477, N: Nno550, B: Hoh606, N: Hoh729, N: Hoh853, conact list: Atom Atom Distance (A) Fe CE2 N:Tyr408 3.77 Fe CZ N:Tyr408 3.15 Fe CE1 N:Tyr408 4.09 Fe OH N:Tyr408 2.14 Fe NH1 N:Arg457 4.25 Fe NE2 N:His460 2.39 Fe ND1 N:His460 4.38 Fe CD2 N:His460 3.45 Fe CE1 N:His460 3.21 Fe CG N:His460 4.55 Fe NE2 N:His462 2.19 Fe ND1 N:His462 4.15 Fe CD2 N:His462 3.33 Fe CE1 N:His462 2.92 Fe CG N:His462 4.35 Fe OE1 N:Gln477 4.81 Fe N1 N:Nno550 2.86 Fe C6 N:Nno550 2.82 Fe C5 N:Nno550 4.10 Fe O4 N:Nno550 2.22 Fe O3 N:Nno550 2.31 Fe C2 N:Nno550 4.09 Fe O B:Hoh606 4.15 Fe O N:Hoh729 4.35 Fe O N:Hoh853 2.21 interactive model: Iron binding site 3 out of 6 in 3pck Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3pck. 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: Arg457, O: His460, O: His462, O: Nno550, C: Hoh606, O: Hoh765, O: Hoh891, conact list: Atom Atom Distance (A) Fe CE2 O:Tyr408 3.94 Fe CD1 O:Tyr408 4.99 Fe CZ O:Tyr408 3.02 Fe CE1 O:Tyr408 3.69 Fe OH O:Tyr408 1.95 Fe NH1 O:Arg457 4.24 Fe NE2 O:His460 2.35 Fe ND1 O:His460 4.27 Fe CD2 O:His460 3.55 Fe CE1 O:His460 3.00 Fe CG O:His460 4.54 Fe NE2 O:His462 2.30 Fe ND1 O:His462 4.36 Fe CD2 O:His462 3.32 Fe CE1 O:His462 3.17 Fe CG O:His462 4.44 Fe N1 O:Nno550 2.95 Fe C6 O:Nno550 2.76 Fe C5 O:Nno550 4.03 Fe O4 O:Nno550 1.99 Fe O3 O:Nno550 2.44 Fe C2 O:Nno550 4.21 Fe O C:Hoh606 4.32 Fe O O:Hoh765 4.09 Fe O O:Hoh891 2.32 interactive model: Iron binding site 4 out of 6 in 3pck Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3pck. 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: Arg457, P: His460, P: His462, P: Nno550, D: Hoh606, P: Hoh665, P: Hoh784, conact list: Atom Atom Distance (A) Fe CE2 P:Tyr408 3.62 Fe CD2 P:Tyr408 4.89 Fe CZ P:Tyr408 3.06 Fe CE1 P:Tyr408 4.05 Fe OH P:Tyr408 2.13 Fe NH1 P:Arg457 4.11 Fe NE2 P:His460 2.43 Fe ND1 P:His460 4.32 Fe CD2 P:His460 3.62 Fe CE1 P:His460 3.05 Fe CG P:His460 4.62 Fe NE2 P:His462 2.29 Fe ND1 P:His462 4.28 Fe CD2 P:His462 3.37 Fe CE1 P:His462 3.09 Fe CG P:His462 4.44 Fe N1 P:Nno550 2.80 Fe C6 P:Nno550 2.69 Fe C5 P:Nno550 3.98 Fe C4 P:Nno550 5.00 Fe O4 P:Nno550 2.04 Fe O3 P:Nno550 2.29 Fe C2 P:Nno550 4.06 Fe O D:Hoh606 4.09 Fe O P:Hoh665 4.27 Fe O P:Hoh784 2.06 interactive model: Iron binding site 5 out of 6 in 3pck Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 3pck. 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: E: Tyr16, Q: Tyr408, Q: Arg457, Q: His460, Q: His462, Q: Nno550, E: Hoh606, Q: Hoh650, Q: Hoh776, conact list: Atom Atom Distance (A) Fe CD2 E:Tyr16 4.91 Fe CE2 Q:Tyr408 3.49 Fe CD1 Q:Tyr408 4.99 Fe CD2 Q:Tyr408 4.77 Fe CZ Q:Tyr408 2.86 Fe CE1 Q:Tyr408 3.81 Fe OH Q:Tyr408 1.93 Fe NH1 Q:Arg457 4.48 Fe NE2 Q:His460 2.47 Fe ND1 Q:His460 4.52 Fe CD2 Q:His460 3.50 Fe CE1 Q:His460 3.37 Fe CG Q:His460 4.64 Fe NE2 Q:His462 2.26 Fe ND1 Q:His462 4.32 Fe CD2 Q:His462 3.24 Fe CE1 Q:His462 3.18 Fe CG Q:His462 4.39 Fe N1 Q:Nno550 3.13 Fe C6 Q:Nno550 2.90 Fe C5 Q:Nno550 4.10 Fe O4 Q:Nno550 2.16 Fe O3 Q:Nno550 2.69 Fe C2 Q:Nno550 4.37 Fe O E:Hoh606 4.08 Fe O Q:Hoh650 4.23 Fe O Q:Hoh776 2.23 interactive model: Iron binding site 6 out of 6 in 3pck Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 3pck. 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: Arg457, R: His460, R: His462, R: Gln477, R: Nno550, F: Hoh606, R: Hoh765, R: Hoh891, conact list: Atom Atom Distance (A) Fe CE2 R:Tyr408 3.97 Fe CZ R:Tyr408 3.06 Fe CE1 R:Tyr408 3.76 Fe OH R:Tyr408 2.03 Fe NH1 R:Arg457 4.37 Fe NE2 R:His460 2.46 Fe ND1 R:His460 4.45 Fe CD2 R:His460 3.56 Fe CE1 R:His460 3.27 Fe CG R:His460 4.64 Fe NE2 R:His462 2.08 Fe ND1 R:His462 4.14 Fe CD2 R:His462 3.15 Fe CE1 R:His462 2.99 Fe CG R:His462 4.25 Fe OE1 R:Gln477 4.93 Fe N1 R:Nno550 2.93 Fe C6 R:Nno550 2.82 Fe C5 R:Nno550 4.09 Fe O4 R:Nno550 2.16 Fe O3 R:Nno550 2.42 Fe C2 R:Nno550 4.18 Fe O F:Hoh606 3.96 Fe O R:Hoh765 4.43 Fe O R:Hoh891 2.13 interactive model: