Iron in the structure of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea (pdb 1iqc)

The binding sites of Iron atom in the structure of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea (pdb code 1iqc). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1iqc structure was solved by H.SHIMIZU, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.8 Space group P1211 a (A) 88.134 b (A) 55.111 c (A) 144.000 alpha (°) 90.00 beta (°) 103.60 gamma (°) 90.00 Rfactor (%) 22.2 Rfree (%) 25.7 Iron Binding Sites: Iron binding site 1 out of 8 in 1iqc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1iqc. 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: His43, A: Gln92, A: Pro96, A: Hem401, A: Hoh1479, A: Hoh1680, conact list: Atom Atom Distance (A) Fe NE2 A:His43 2.09 Fe ND1 A:His43 4.18 Fe CD2 A:His43 3.05 Fe CE1 A:His43 3.08 Fe CG A:His43 4.20 Fe NE2 A:Gln92 4.06 Fe CB A:Pro96 4.94 Fe CG A:Pro96 4.97 Fe C2D A:Hem401 4.29 Fe NC A:Hem401 1.95 Fe CHB A:Hem401 3.45 Fe CHC A:Hem401 3.38 Fe C3D A:Hem401 4.28 Fe NA A:Hem401 1.97 Fe CHA A:Hem401 3.40 Fe C2A A:Hem401 4.28 Fe C1D A:Hem401 3.05 Fe C4A A:Hem401 3.05 Fe C4B A:Hem401 3.03 Fe C3A A:Hem401 4.29 Fe C4C A:Hem401 3.04 Fe C2B A:Hem401 4.29 Fe C1C A:Hem401 3.02 Fe C2C A:Hem401 4.25 Fe ND A:Hem401 1.99 Fe CHD A:Hem401 3.43 Fe C1B A:Hem401 3.06 Fe NB A:Hem401 1.98 Fe FE A:Hem401 0.00 Fe C3C A:Hem401 4.26 Fe C3B A:Hem401 4.27 Fe C4D A:Hem401 3.03 Fe C1A A:Hem401 3.04 Fe O A:Hoh1479 4.71 Fe O A:Hoh1680 2.31 interactive model: Iron binding site 2 out of 8 in 1iqc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1iqc. 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: His187, A: Met258, A: Hem402, conact list: Atom Atom Distance (A) Fe NE2 A:His187 2.09 Fe ND1 A:His187 4.19 Fe CD2 A:His187 3.06 Fe CE1 A:His187 3.09 Fe CG A:His187 4.21 Fe CB A:Met258 4.37 Fe CE A:Met258 3.61 Fe CG A:Met258 3.44 Fe SD A:Met258 2.33 Fe C2D A:Hem402 4.25 Fe NC A:Hem402 1.98 Fe CHB A:Hem402 3.45 Fe CHC A:Hem402 3.41 Fe C3D A:Hem402 4.24 Fe NA A:Hem402 1.98 Fe CHA A:Hem402 3.42 Fe C2A A:Hem402 4.28 Fe C1D A:Hem402 3.02 Fe C4A A:Hem402 3.05 Fe C4B A:Hem402 3.03 Fe C3A A:Hem402 4.28 Fe C4C A:Hem402 3.03 Fe C2B A:Hem402 4.27 Fe C1C A:Hem402 3.03 Fe C2C A:Hem402 4.28 Fe ND A:Hem402 1.96 Fe CHD A:Hem402 3.41 Fe C1B A:Hem402 3.05 Fe NB A:Hem402 1.97 Fe FE A:Hem402 0.00 Fe C3C A:Hem402 4.28 Fe C3B A:Hem402 4.26 Fe C4D A:Hem402 3.03 Fe C1A A:Hem402 3.04 interactive model: Iron binding site 3 out of 8 in 1iqc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1iqc. 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: His43, B: Gln92, B: Pro96, B: Hem401, B: Hoh1413, B: Hoh1609, conact list: Atom Atom Distance (A) Fe NE2 B:His43 2.14 Fe ND1 B:His43 4.25 Fe CD2 B:His43 3.05 Fe CE1 B:His43 3.17 Fe CG B:His43 4.23 Fe NE2 B:Gln92 3.97 Fe CD B:Gln92 4.92 Fe CG B:Pro96 4.37 Fe C2D B:Hem401 4.24 Fe NC B:Hem401 1.98 Fe CHB B:Hem401 3.41 Fe CHC B:Hem401 3.45 Fe C3D B:Hem401 4.24 Fe NA B:Hem401 1.99 Fe CHA B:Hem401 3.42 Fe C2A B:Hem401 4.28 Fe C1D B:Hem401 3.02 Fe C4A B:Hem401 3.03 Fe C4B B:Hem401 3.05 Fe C3A B:Hem401 4.26 Fe C4C B:Hem401 3.02 Fe C2B B:Hem401 4.26 Fe C1C B:Hem401 3.05 Fe C2C B:Hem401 4.28 Fe ND B:Hem401 1.94 Fe CHD B:Hem401 3.39 Fe C1B B:Hem401 3.03 Fe NB B:Hem401 1.96 Fe FE B:Hem401 0.00 Fe C3C B:Hem401 4.29 Fe C3B B:Hem401 4.27 Fe C4D B:Hem401 3.02 Fe C1A B:Hem401 3.05 Fe O B:Hoh1413 4.30 Fe O B:Hoh1609 2.09 interactive model: Iron binding site 4 out of 8 in 1iqc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1iqc. 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: His187, B: Met258, B: Hem402, conact list: Atom Atom Distance (A) Fe NE2 B:His187 2.08 Fe ND1 B:His187 4.19 Fe CD2 B:His187 3.02 Fe CE1 B:His187 3.10 Fe CG B:His187 4.18 Fe CB B:Met258 4.42 Fe CE B:Met258 3.72 Fe CG B:Met258 3.47 Fe SD B:Met258 2.32 Fe C2D B:Hem402 4.32 Fe NC B:Hem402 2.02 Fe CHB B:Hem402 3.44 Fe CHC B:Hem402 3.43 Fe C3D B:Hem402 4.29 Fe NA B:Hem402 1.98 Fe CHA B:Hem402 3.42 Fe C2A B:Hem402 4.28 Fe C1D B:Hem402 3.08 Fe C4A B:Hem402 3.05 Fe C4B B:Hem402 3.05 Fe C3A B:Hem402 4.28 Fe C4C B:Hem402 3.09 Fe C2B B:Hem402 4.29 Fe C1C B:Hem402 3.07 Fe C2C B:Hem402 4.32 Fe ND B:Hem402 2.01 Fe CHD B:Hem402 3.48 Fe C1B B:Hem402 3.06 Fe NB B:Hem402 2.00 Fe FE B:Hem402 0.00 Fe C3C B:Hem402 4.34 Fe C3B B:Hem402 4.29 Fe C4D B:Hem402 3.05 Fe C1A B:Hem402 3.04 interactive model: Iron binding site 5 out of 8 in 1iqc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1iqc. 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: His43, C: Gln92, C: Pro96, C: Hem401, C: Hoh485, C: Hoh689, conact list: Atom Atom Distance (A) Fe NE2 C:His43 2.10 Fe ND1 C:His43 4.19 Fe CD2 C:His43 3.05 Fe CE1 C:His43 3.10 Fe CG C:His43 4.20 Fe NE2 C:Gln92 3.98 Fe CD C:Gln92 4.94 Fe CB C:Pro96 4.93 Fe CG C:Pro96 4.96 Fe C2D C:Hem401 4.24 Fe NC C:Hem401 2.01 Fe CHB C:Hem401 3.43 Fe CHC C:Hem401 3.42 Fe C3D C:Hem401 4.24 Fe NA C:Hem401 1.99 Fe CHA C:Hem401 3.42 Fe C2A C:Hem401 4.29 Fe C1D C:Hem401 3.03 Fe C4A C:Hem401 3.04 Fe C4B C:Hem401 3.01 Fe C3A C:Hem401 4.28 Fe C4C C:Hem401 3.04 Fe C2B C:Hem401 4.25 Fe C1C C:Hem401 3.07 Fe C2C C:Hem401 4.31 Fe ND C:Hem401 1.96 Fe CHD C:Hem401 3.41 Fe C1B C:Hem401 3.03 Fe NB C:Hem401 1.95 Fe FE C:Hem401 0.00 Fe C3C C:Hem401 4.28 Fe C3B C:Hem401 4.23 Fe C4D C:Hem401 3.02 Fe C1A C:Hem401 3.04 Fe O C:Hoh485 4.51 Fe O C:Hoh689 2.26 interactive model: Iron binding site 6 out of 8 in 1iqc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1iqc. 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: His187, C: Met258, C: Hem402, conact list: Atom Atom Distance (A) Fe NE2 C:His187 2.08 Fe ND1 C:His187 4.19 Fe CD2 C:His187 3.02 Fe CE1 C:His187 3.10 Fe CG C:His187 4.18 Fe CB C:Met258 4.42 Fe CE C:Met258 3.54 Fe CG C:Met258 3.52 Fe SD C:Met258 2.35 Fe C2D C:Hem402 4.27 Fe NC C:Hem402 1.99 Fe CHB C:Hem402 3.42 Fe CHC C:Hem402 3.43 Fe C3D C:Hem402 4.26 Fe NA C:Hem402 1.99 Fe CHA C:Hem402 3.43 Fe C2A C:Hem402 4.29 Fe C1D C:Hem402 3.04 Fe C4A C:Hem402 3.04 Fe C4B C:Hem402 3.03 Fe C3A C:Hem402 4.28 Fe C4C C:Hem402 3.04 Fe C2B C:Hem402 4.26 Fe C1C C:Hem402 3.05 Fe C2C C:Hem402 4.29 Fe ND C:Hem402 1.98 Fe CHD C:Hem402 3.43 Fe C1B C:Hem402 3.03 Fe NB C:Hem402 1.96 Fe FE C:Hem402 0.00 Fe C3C C:Hem402 4.29 Fe C3B C:Hem402 4.27 Fe C4D C:Hem402 3.04 Fe C1A C:Hem402 3.06 interactive model: Iron binding site 7 out of 8 in 1iqc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1iqc. 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: His43, D: Gln92, D: Pro96, D: Hem401, D: Hoh2540, conact list: Atom Atom Distance (A) Fe NE2 D:His43 2.10 Fe ND1 D:His43 4.17 Fe CD2 D:His43 2.99 Fe CE1 D:His43 3.11 Fe CG D:His43 4.14 Fe NE2 D:Gln92 4.20 Fe CG D:Pro96 4.35 Fe C2D D:Hem401 4.28 Fe NC D:Hem401 1.98 Fe CHB D:Hem401 3.44 Fe CHC D:Hem401 3.42 Fe C3D D:Hem401 4.28 Fe NA D:Hem401 1.99 Fe CHA D:Hem401 3.43 Fe C2A D:Hem401 4.29 Fe C1D D:Hem401 3.05 Fe C4A D:Hem401 3.05 Fe C4B D:Hem401 3.04 Fe C3A D:Hem401 4.29 Fe C4C D:Hem401 3.05 Fe C2B D:Hem401 4.28 Fe C1C D:Hem401 3.04 Fe C2C D:Hem401 4.27 Fe ND D:Hem401 1.98 Fe CHD D:Hem401 3.44 Fe C1B D:Hem401 3.05 Fe NB D:Hem401 1.99 Fe FE D:Hem401 0.00 Fe C3C D:Hem401 4.28 Fe C3B D:Hem401 4.29 Fe C4D D:Hem401 3.04 Fe C1A D:Hem401 3.05 Fe O D:Hoh2540 2.20 interactive model: Iron binding site 8 out of 8 in 1iqc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 1iqc. 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: His187, D: Met258, D: Hem402, conact list: Atom Atom Distance (A) Fe NE2 D:His187 2.08 Fe ND1 D:His187 4.19 Fe CD2 D:His187 3.03 Fe CE1 D:His187 3.10 Fe CG D:His187 4.19 Fe CB D:Met258 4.17 Fe CE D:Met258 3.90 Fe CG D:Met258 3.25 Fe SD D:Met258 2.40 Fe C2D D:Hem402 4.23 Fe NC D:Hem402 2.01 Fe CHB D:Hem402 3.43 Fe CHC D:Hem402 3.42 Fe C3D D:Hem402 4.21 Fe NA D:Hem402 1.99 Fe CHA D:Hem402 3.39 Fe C2A D:Hem402 4.27 Fe C1D D:Hem402 3.02 Fe C4A D:Hem402 3.05 Fe C4B D:Hem402 3.02 Fe C3A D:Hem402 4.28 Fe C4C D:Hem402 3.07 Fe C2B D:Hem402 4.26 Fe C1C D:Hem402 3.06 Fe C2C D:Hem402 4.31 Fe ND D:Hem402 1.93 Fe CHD D:Hem402 3.45 Fe C1B D:Hem402 3.04 Fe NB D:Hem402 1.97 Fe FE D:Hem402 0.00 Fe C3C D:Hem402 4.33 Fe C3B D:Hem402 4.25 Fe C4D D:Hem402 2.98 Fe C1A D:Hem402 3.03 interactive model: