Iron in the structure of H55A Mutant of Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris (pdb 3bk9)

The binding sites of Iron atom in the structure of H55A Mutant of Tryptophan 2,3-Dioxygenase From Xanthomonas Campestris (pdb code 3bk9). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3bk9 structure was solved by C.BRUCKMANN, C.G.MOWAT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 54.1-2.1 Space group P1211 a (A) 78.222 b (A) 117.606 c (A) 139.283 alpha (°) 90.00 beta (°) 95.73 gamma (°) 90.00 Rfactor (%) 20 Rfree (%) 28.5 Iron Binding Sites: Iron binding site 1 out of 8 in 3bk9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3bk9. 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: Gly125, A: His240, A: Val244, A: Trp402, A: Hem401, A: Hoh552, conact list: Atom Atom Distance (A) Fe N A:Gly125 4.88 Fe NE2 A:His240 2.30 Fe ND1 A:His240 4.30 Fe CD2 A:His240 3.30 Fe CE1 A:His240 3.18 Fe CG A:His240 4.39 Fe CG2 A:Val244 4.94 Fe N A:Trp402 4.61 Fe CD1 A:Trp402 4.56 Fe CA A:Trp402 4.77 Fe C2D A:Hem401 4.28 Fe NC A:Hem401 2.08 Fe CHB A:Hem401 3.42 Fe CHC A:Hem401 3.34 Fe C3D A:Hem401 4.23 Fe NA A:Hem401 2.15 Fe CHA A:Hem401 3.43 Fe C2A A:Hem401 4.34 Fe C1D A:Hem401 3.08 Fe C4A A:Hem401 3.14 Fe C4B A:Hem401 2.95 Fe C3A A:Hem401 4.38 Fe C4C A:Hem401 3.15 Fe C2B A:Hem401 4.20 Fe C1C A:Hem401 3.07 Fe C2C A:Hem401 4.33 Fe ND A:Hem401 1.98 Fe CHD A:Hem401 3.52 Fe C1B A:Hem401 3.00 Fe NB A:Hem401 1.90 Fe FE A:Hem401 0.00 Fe C3C A:Hem401 4.36 Fe C3B A:Hem401 4.16 Fe C4D A:Hem401 2.99 Fe C1A A:Hem401 3.13 Fe O A:Hoh552 2.78 interactive model: Iron binding site 2 out of 8 in 3bk9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3bk9. 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: Gly125, B: His240, B: Val244, B: Trp402, B: Hem401, B: Hoh1541, conact list: Atom Atom Distance (A) Fe N B:Gly125 4.79 Fe NE2 B:His240 2.21 Fe ND1 B:His240 4.26 Fe CD2 B:His240 3.20 Fe CE1 B:His240 3.14 Fe CG B:His240 4.32 Fe CG2 B:Val244 4.81 Fe N B:Trp402 4.79 Fe CD1 B:Trp402 4.58 Fe NE1 B:Trp402 4.88 Fe C2D B:Hem401 4.23 Fe NC B:Hem401 2.08 Fe CHB B:Hem401 3.34 Fe CHC B:Hem401 3.44 Fe C3D B:Hem401 4.20 Fe NA B:Hem401 2.08 Fe CHA B:Hem401 3.41 Fe C2A B:Hem401 4.28 Fe C1D B:Hem401 3.07 Fe C4A B:Hem401 3.06 Fe C4B B:Hem401 2.94 Fe C3A B:Hem401 4.28 Fe C4C B:Hem401 3.12 Fe C2B B:Hem401 4.11 Fe C1C B:Hem401 3.05 Fe C2C B:Hem401 4.24 Fe ND B:Hem401 1.99 Fe CHD B:Hem401 3.49 Fe C1B B:Hem401 2.95 Fe NB B:Hem401 1.88 Fe FE B:Hem401 0.00 Fe C3C B:Hem401 4.28 Fe C3B B:Hem401 4.08 Fe C4D B:Hem401 3.00 Fe C1A B:Hem401 3.09 Fe O B:Hoh1541 2.59 interactive model: Iron binding site 3 out of 8 in 3bk9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3bk9. 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: Gly125, C: His240, C: Val244, C: Trp402, C: Hem401, C: Hoh632, conact list: Atom Atom Distance (A) Fe N C:Gly125 4.86 Fe NE2 C:His240 2.29 Fe ND1 C:His240 4.28 Fe CD2 C:His240 3.27 Fe CE1 C:His240 3.17 Fe CG C:His240 4.36 Fe CG2 C:Val244 4.83 Fe N C:Trp402 4.74 Fe CD1 C:Trp402 4.49 Fe CA C:Trp402 5.00 Fe NE1 C:Trp402 4.87 Fe C2D C:Hem401 4.18 Fe NC C:Hem401 2.12 Fe CHB C:Hem401 3.30 Fe CHC C:Hem401 3.48 Fe C3D C:Hem401 4.18 Fe NA C:Hem401 2.07 Fe CHA C:Hem401 3.45 Fe C2A C:Hem401 4.40 Fe C1D C:Hem401 2.97 Fe C4A C:Hem401 3.01 Fe C4B C:Hem401 2.95 Fe C3A C:Hem401 4.31 Fe C4C C:Hem401 3.10 Fe C2B C:Hem401 4.17 Fe C1C C:Hem401 3.15 Fe C2C C:Hem401 4.35 Fe ND C:Hem401 1.89 Fe CHD C:Hem401 3.38 Fe C1B C:Hem401 2.91 Fe NB C:Hem401 1.86 Fe FE C:Hem401 0.00 Fe C3C C:Hem401 4.34 Fe C3B C:Hem401 4.12 Fe C4D C:Hem401 2.95 Fe C1A C:Hem401 3.16 Fe O C:Hoh632 2.88 interactive model: Iron binding site 4 out of 8 in 3bk9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3bk9. 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: Gly125, D: His240, D: Val244, D: Trp402, D: Hem401, D: Hoh621, conact list: Atom Atom Distance (A) Fe N D:Gly125 4.74 Fe CA D:Gly125 4.83 Fe NE2 D:His240 2.38 Fe ND1 D:His240 4.40 Fe CD2 D:His240 3.35 Fe CE1 D:His240 3.28 Fe CG D:His240 4.46 Fe CG2 D:Val244 4.72 Fe N D:Trp402 4.42 Fe CD1 D:Trp402 4.42 Fe CA D:Trp402 4.99 Fe NE1 D:Trp402 4.68 Fe C2D D:Hem401 4.17 Fe NC D:Hem401 2.09 Fe CHB D:Hem401 3.49 Fe CHC D:Hem401 3.22 Fe C3D D:Hem401 4.13 Fe NA D:Hem401 2.03 Fe CHA D:Hem401 3.27 Fe C2A D:Hem401 4.24 Fe C1D D:Hem401 2.99 Fe C4A D:Hem401 3.12 Fe C4B D:Hem401 2.85 Fe C3A D:Hem401 4.29 Fe C4C D:Hem401 3.18 Fe C2B D:Hem401 4.26 Fe C1C D:Hem401 3.02 Fe C2C D:Hem401 4.30 Fe ND D:Hem401 1.85 Fe CHD D:Hem401 3.50 Fe C1B D:Hem401 3.05 Fe NB D:Hem401 1.86 Fe FE D:Hem401 0.00 Fe C3C D:Hem401 4.36 Fe C3B D:Hem401 4.13 Fe C4D D:Hem401 2.87 Fe C1A D:Hem401 2.97 Fe O D:Hoh621 2.68 interactive model: Iron binding site 5 out of 8 in 3bk9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 3bk9. 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: Gly125, E: His240, E: Val244, E: Trp402, E: Hem401, E: Hoh642, conact list: Atom Atom Distance (A) Fe N E:Gly125 4.84 Fe CA E:Gly125 4.80 Fe NE2 E:His240 2.31 Fe ND1 E:His240 4.37 Fe CD2 E:His240 3.34 Fe CE1 E:His240 3.24 Fe CG E:His240 4.45 Fe CG2 E:Val244 4.84 Fe N E:Trp402 4.69 Fe CD1 E:Trp402 4.59 Fe CA E:Trp402 4.99 Fe C2D E:Hem401 4.46 Fe NC E:Hem401 2.08 Fe CHB E:Hem401 3.42 Fe CHC E:Hem401 3.51 Fe C3D E:Hem401 4.48 Fe NA E:Hem401 2.11 Fe CHA E:Hem401 3.54 Fe C2A E:Hem401 4.38 Fe C1D E:Hem401 3.21 Fe C4A E:Hem401 3.11 Fe C4B E:Hem401 3.14 Fe C3A E:Hem401 4.36 Fe C4C E:Hem401 3.07 Fe C2B E:Hem401 4.32 Fe C1C E:Hem401 3.13 Fe C2C E:Hem401 4.32 Fe ND E:Hem401 2.26 Fe CHD E:Hem401 3.44 Fe C1B E:Hem401 3.09 Fe NB E:Hem401 2.13 Fe FE E:Hem401 0.00 Fe C3C E:Hem401 4.29 Fe C3B E:Hem401 4.35 Fe C4D E:Hem401 3.24 Fe C1A E:Hem401 3.16 Fe O E:Hoh642 2.59 interactive model: Iron binding site 6 out of 8 in 3bk9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 3bk9. 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: Gly125, F: His240, F: Val244, F: Trp402, F: Hem401, F: Hoh662, conact list: Atom Atom Distance (A) Fe N F:Gly125 4.82 Fe CA F:Gly125 4.94 Fe NE2 F:His240 2.24 Fe ND1 F:His240 4.28 Fe CD2 F:His240 3.26 Fe CE1 F:His240 3.14 Fe CG F:His240 4.37 Fe CG2 F:Val244 4.82 Fe N F:Trp402 4.69 Fe CD1 F:Trp402 4.47 Fe CA F:Trp402 4.95 Fe NE1 F:Trp402 4.72 Fe C2D F:Hem401 4.49 Fe NC F:Hem401 2.08 Fe CHB F:Hem401 3.49 Fe CHC F:Hem401 3.45 Fe C3D F:Hem401 4.46 Fe NA F:Hem401 1.95 Fe CHA F:Hem401 3.43 Fe C2A F:Hem401 4.21 Fe C1D F:Hem401 3.26 Fe C4A F:Hem401 3.03 Fe C4B F:Hem401 3.16 Fe C3A F:Hem401 4.24 Fe C4C F:Hem401 3.12 Fe C2B F:Hem401 4.43 Fe C1C F:Hem401 3.10 Fe C2C F:Hem401 4.35 Fe ND F:Hem401 2.27 Fe CHD F:Hem401 3.55 Fe C1B F:Hem401 3.20 Fe NB F:Hem401 2.20 Fe FE F:Hem401 0.00 Fe C3C F:Hem401 4.35 Fe C3B F:Hem401 4.42 Fe C4D F:Hem401 3.21 Fe C1A F:Hem401 2.99 Fe O F:Hoh662 2.91 interactive model: Iron binding site 7 out of 8 in 3bk9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 3bk9. 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: G: Gly125, G: His240, G: Val244, G: Trp402, G: Hem401, G: Hoh663, conact list: Atom Atom Distance (A) Fe N G:Gly125 4.71 Fe CA G:Gly125 4.77 Fe NE2 G:His240 2.36 Fe ND1 G:His240 4.39 Fe CD2 G:His240 3.39 Fe CE1 G:His240 3.24 Fe CG G:His240 4.49 Fe CG2 G:Val244 4.71 Fe N G:Trp402 4.66 Fe CD1 G:Trp402 4.51 Fe CA G:Trp402 4.94 Fe NE1 G:Trp402 4.94 Fe C2D G:Hem401 4.26 Fe NC G:Hem401 2.18 Fe CHB G:Hem401 3.35 Fe CHC G:Hem401 3.59 Fe C3D G:Hem401 4.36 Fe NA G:Hem401 2.10 Fe CHA G:Hem401 3.59 Fe C2A G:Hem401 4.37 Fe C1D G:Hem401 3.01 Fe C4A G:Hem401 3.07 Fe C4B G:Hem401 3.18 Fe C3A G:Hem401 4.31 Fe C4C G:Hem401 3.12 Fe C2B G:Hem401 4.28 Fe C1C G:Hem401 3.24 Fe C2C G:Hem401 4.43 Fe ND G:Hem401 2.12 Fe CHD G:Hem401 3.35 Fe C1B G:Hem401 3.02 Fe NB G:Hem401 2.10 Fe FE G:Hem401 0.00 Fe C3C G:Hem401 4.38 Fe C3B G:Hem401 4.36 Fe C4D G:Hem401 3.18 Fe C1A G:Hem401 3.18 Fe O G:Hoh663 2.94 interactive model: Iron binding site 8 out of 8 in 3bk9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 3bk9. 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: Gly125, H: His240, H: Val244, H: Trp402, H: Hem401, H: Hoh1542, conact list: Atom Atom Distance (A) Fe N H:Gly125 4.90 Fe CA H:Gly125 4.86 Fe NE2 H:His240 2.21 Fe ND1 H:His240 4.26 Fe CD2 H:His240 3.15 Fe CE1 H:His240 3.16 Fe CG H:His240 4.28 Fe CG2 H:Val244 4.86 Fe N H:Trp402 4.54 Fe CD1 H:Trp402 4.54 Fe NE1 H:Trp402 4.79 Fe C2D H:Hem401 4.38 Fe NC H:Hem401 2.11 Fe CHB H:Hem401 3.48 Fe CHC H:Hem401 3.42 Fe C3D H:Hem401 4.37 Fe NA H:Hem401 2.12 Fe CHA H:Hem401 3.48 Fe C2A H:Hem401 4.35 Fe C1D H:Hem401 3.18 Fe C4A H:Hem401 3.13 Fe C4B H:Hem401 3.08 Fe C3A H:Hem401 4.36 Fe C4C H:Hem401 3.14 Fe C2B H:Hem401 4.37 Fe C1C H:Hem401 3.11 Fe C2C H:Hem401 4.36 Fe ND H:Hem401 2.18 Fe CHD H:Hem401 3.54 Fe C1B H:Hem401 3.15 Fe NB H:Hem401 2.10 Fe FE H:Hem401 0.00 Fe C3C H:Hem401 4.35 Fe C3B H:Hem401 4.33 Fe C4D H:Hem401 3.15 Fe C1A H:Hem401 3.13 Fe O H:Hoh1542 2.95 interactive model: