Iron in the structure of Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa At 2.15 Angstroms Resolution (pdb 2pcd)

The binding sites of Iron atom in the structure of Structure of Protocatechuate 3,4-Dioxygenase From Pseudomonas Aeruginosa At 2.15 Angstroms Resolution (pdb code 2pcd). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2pcd structure was solved by D.H.OHLENDORF, A.M.ORVILLE, J.D.LIPSCOMB, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 5.0-2.1 Space group I121 a (A) 197.170 b (A) 127.030 c (A) 134.180 alpha (°) 90.00 beta (°) 97.64 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Iron Binding Sites: Iron binding site 1 out of 6 in 2pcd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2pcd. 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: Gln477, A: Hoh205, M: Hoh620, M: Hoh718, M: Hoh719, M: Hoh733, conact list: Atom Atom Distance (A) Fe CD2 A:Tyr16 4.94 Fe CE2 M:Tyr408 3.45 Fe CD2 M:Tyr408 4.77 Fe CZ M:Tyr408 2.88 Fe CE1 M:Tyr408 3.92 Fe OH M:Tyr408 1.81 Fe CE2 M:Tyr447 3.64 Fe CZ M:Tyr447 3.14 Fe CE1 M:Tyr447 4.29 Fe OH M:Tyr447 1.90 Fe NH1 M:Arg457 4.51 Fe NE2 M:His460 2.26 Fe ND1 M:His460 4.20 Fe CD2 M:His460 3.46 Fe CE1 M:His460 2.97 Fe CG M:His460 4.46 Fe NE2 M:His462 2.33 Fe ND1 M:His462 4.25 Fe CD2 M:His462 3.49 Fe CE1 M:His462 3.05 Fe CG M:His462 4.48 Fe OE1 M:Gln477 4.98 Fe O A:Hoh205 4.29 Fe O M:Hoh620 4.22 Fe O M:Hoh718 4.16 Fe O M:Hoh719 3.17 Fe O M:Hoh733 1.91 interactive model: Iron binding site 2 out of 6 in 2pcd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2pcd. 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: Tyr16, N: Tyr408, N: Tyr447, N: Arg457, N: His460, N: His462, B: Hoh245, N: Hoh629, N: Hoh731, N: Hoh733, N: Hoh749, conact list: Atom Atom Distance (A) Fe CD2 B:Tyr16 4.87 Fe CE2 N:Tyr408 3.42 Fe CD2 N:Tyr408 4.75 Fe CZ N:Tyr408 2.82 Fe CE1 N:Tyr408 3.86 Fe OH N:Tyr408 1.73 Fe CE2 N:Tyr447 3.75 Fe CZ N:Tyr447 3.25 Fe CE1 N:Tyr447 4.39 Fe OH N:Tyr447 2.00 Fe NH1 N:Arg457 4.59 Fe NE2 N:His460 2.28 Fe ND1 N:His460 4.30 Fe CD2 N:His460 3.37 Fe CE1 N:His460 3.13 Fe CG N:His460 4.45 Fe NE2 N:His462 2.30 Fe ND1 N:His462 4.33 Fe CD2 N:His462 3.35 Fe CE1 N:His462 3.15 Fe CG N:His462 4.44 Fe O B:Hoh245 4.14 Fe O N:Hoh629 4.11 Fe O N:Hoh731 4.22 Fe O N:Hoh733 3.27 Fe O N:Hoh749 2.16 interactive model: Iron binding site 3 out of 6 in 2pcd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2pcd. 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, O: Tyr408, O: Tyr447, O: Arg457, O: His460, O: His462, O: Gln477, C: Hoh205, O: Hoh629, O: Hoh731, O: Hoh733, O: Hoh748, conact list: Atom Atom Distance (A) Fe CD2 C:Tyr16 4.89 Fe CE2 O:Tyr408 3.89 Fe CD1 O:Tyr408 4.95 Fe CZ O:Tyr408 2.97 Fe CE1 O:Tyr408 3.65 Fe OH O:Tyr408 1.94 Fe CE2 O:Tyr447 3.90 Fe CZ O:Tyr447 3.41 Fe CE1 O:Tyr447 4.54 Fe OH O:Tyr447 2.14 Fe NH1 O:Arg457 4.64 Fe NE2 O:His460 2.17 Fe ND1 O:His460 4.15 Fe CD2 O:His460 3.31 Fe CE1 O:His460 2.92 Fe CG O:His460 4.37 Fe NE2 O:His462 2.10 Fe ND1 O:His462 4.17 Fe CD2 O:His462 3.17 Fe CE1 O:His462 3.00 Fe CG O:His462 4.27 Fe OE1 O:Gln477 4.94 Fe O C:Hoh205 4.16 Fe O O:Hoh629 4.23 Fe O O:Hoh731 4.33 Fe O O:Hoh733 3.42 Fe O O:Hoh748 2.15 interactive model: Iron binding site 4 out of 6 in 2pcd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2pcd. 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, D: Hoh723, P: Hoh630, P: Hoh730, P: Hoh731, P: Hoh746, conact list: Atom Atom Distance (A) Fe CE2 P:Tyr408 3.52 Fe CD2 P:Tyr408 4.85 Fe CZ P:Tyr408 2.90 Fe CE1 P:Tyr408 3.88 Fe OH P:Tyr408 1.82 Fe CE2 P:Tyr447 3.78 Fe CZ P:Tyr447 3.31 Fe CE1 P:Tyr447 4.46 Fe OH P:Tyr447 2.07 Fe NH1 P:Arg457 4.61 Fe NE2 P:His460 2.25 Fe ND1 P:His460 4.23 Fe CD2 P:His460 3.39 Fe CE1 P:His460 2.98 Fe CG P:His460 4.43 Fe NE2 P:His462 2.23 Fe ND1 P:His462 4.27 Fe CD2 P:His462 3.30 Fe CE1 P:His462 3.09 Fe CG P:His462 4.39 Fe O D:Hoh723 4.19 Fe O P:Hoh630 4.17 Fe O P:Hoh730 4.26 Fe O P:Hoh731 3.19 Fe O P:Hoh746 2.20 interactive model: Iron binding site 5 out of 6 in 2pcd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 2pcd. 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: Tyr447, Q: Arg457, Q: His460, Q: His462, Q: Gln477, E: Hoh208, Q: Hoh999, Q: Hoh1155, Q: Hoh1157, Q: Hoh1183, conact list: Atom Atom Distance (A) Fe CD2 E:Tyr16 4.91 Fe CE2 Q:Tyr408 3.81 Fe CZ Q:Tyr408 2.96 Fe CE1 Q:Tyr408 3.75 Fe OH Q:Tyr408 1.84 Fe CE2 Q:Tyr447 3.83 Fe CZ Q:Tyr447 3.27 Fe CE1 Q:Tyr447 4.38 Fe OH Q:Tyr447 1.97 Fe NH1 Q:Arg457 4.45 Fe NE2 Q:His460 2.17 Fe ND1 Q:His460 4.20 Fe CD2 Q:His460 3.29 Fe CE1 Q:His460 2.99 Fe CG Q:His460 4.35 Fe NE2 Q:His462 2.18 Fe ND1 Q:His462 4.19 Fe CD2 Q:His462 3.27 Fe CE1 Q:His462 2.99 Fe CG Q:His462 4.35 Fe OE1 Q:Gln477 4.91 Fe O E:Hoh208 4.15 Fe O Q:Hoh999 4.17 Fe O Q:Hoh1155 4.02 Fe O Q:Hoh1157 3.17 Fe O Q:Hoh1183 2.18 interactive model: Iron binding site 6 out of 6 in 2pcd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 2pcd. 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, F: Hoh1201, R: Hoh1238, R: Hoh1394, R: Hoh1396, R: Hoh1422, conact list: Atom Atom Distance (A) Fe CE2 R:Tyr408 3.56 Fe CD2 R:Tyr408 4.90 Fe CZ R:Tyr408 2.94 Fe CE1 R:Tyr408 3.97 Fe OH R:Tyr408 1.82 Fe CE2 R:Tyr447 3.71 Fe CZ R:Tyr447 3.24 Fe CE1 R:Tyr447 4.38 Fe OH R:Tyr447 1.98 Fe NH1 R:Arg457 4.44 Fe NE2 R:His460 2.28 Fe ND1 R:His460 4.26 Fe CD2 R:His460 3.37 Fe CE1 R:His460 3.06 Fe CG R:His460 4.44 Fe NE2 R:His462 2.34 Fe ND1 R:His462 4.40 Fe CD2 R:His462 3.41 Fe CE1 R:His462 3.21 Fe CG R:His462 4.51 Fe OE1 R:Gln477 4.90 Fe O F:Hoh1201 4.20 Fe O R:Hoh1238 4.15 Fe O R:Hoh1394 4.10 Fe O R:Hoh1396 2.96 Fe O R:Hoh1422 1.98 interactive model: