Iron in the structure of X-Ray Structure Of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii (pdb 2ji3)

The binding sites of Iron atom in the structure of X-Ray Structure Of the Iron-Peroxide Intermediate of Superoxide Reductase (E114A Mutant) From Desulfoarculus Baarsii (pdb code 2ji3). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2ji3 structure was solved by G.KATONA, P.CARPENTIER, V.NIVIERE, P.AMARA, V.ADAM, J.OHANA, N.TSANOV, D.BOURGEOIS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 47.1-1.9 Space group I222 a (A) 69.450 b (A) 82.900 c (A) 202.660 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.7 Rfree (%) 24.9 Iron Binding Sites: Iron binding site 1 out of 8 in 2ji3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2ji3. 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: Cys10, A: Val12, A: Cys13, A: Gly14, A: Asn15, A: Cys29, A: Cys30, B: Gly25, conact list: Atom Atom Distance (A) Fe CB A:Cys10 3.13 Fe SG A:Cys10 2.25 Fe CA A:Cys10 4.57 Fe CB A:Val12 4.59 Fe C A:Val12 4.82 Fe N A:Cys13 3.68 Fe CB A:Cys13 3.31 Fe SG A:Cys13 2.20 Fe C A:Cys13 4.75 Fe CA A:Cys13 4.05 Fe N A:Gly14 4.82 Fe CB A:Asn15 4.83 Fe ND2 A:Asn15 4.18 Fe CG A:Asn15 4.82 Fe O A:Cys29 4.19 Fe CB A:Cys29 3.33 Fe SG A:Cys29 2.23 Fe C A:Cys29 3.73 Fe CA A:Cys29 4.09 Fe N A:Cys30 3.60 Fe CB A:Cys30 3.30 Fe SG A:Cys30 2.36 Fe CA A:Cys30 4.06 Fe N B:Gly25 4.52 Fe C B:Gly25 4.76 Fe CA B:Gly25 4.02 interactive model: Iron binding site 2 out of 8 in 2ji3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2ji3. 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: His49, A: His69, A: His75, A: Cys116, A: Ile118, A: His119, A: No31131, conact list: Atom Atom Distance (A) Fe NE2 A:His49 2.22 Fe ND1 A:His49 4.24 Fe CD2 A:His49 3.27 Fe CE1 A:His49 3.10 Fe CG A:His49 4.36 Fe NE2 A:His69 2.26 Fe ND1 A:His69 4.34 Fe CD2 A:His69 3.27 Fe CE1 A:His69 3.20 Fe CG A:His69 4.40 Fe NE2 A:His75 2.20 Fe ND1 A:His75 4.24 Fe CD2 A:His75 3.25 Fe CE1 A:His75 3.08 Fe CG A:His75 4.35 Fe CB A:Cys116 3.68 Fe SG A:Cys116 2.53 Fe CB A:Ile118 4.92 Fe NE2 A:His119 4.06 Fe N A:His119 4.25 Fe CB A:His119 3.60 Fe ND1 A:His119 2.04 Fe CD2 A:His119 4.21 Fe CE1 A:His119 2.89 Fe CG A:His119 3.15 Fe CA A:His119 4.59 Fe O1 A:No31131 4.68 Fe O2 A:No31131 4.67 Fe N A:No31131 3.95 Fe O3 A:No31131 2.77 interactive model: Iron binding site 3 out of 8 in 2ji3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2ji3. 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: Gly25, B: Cys10, B: Val12, B: Cys13, B: Gly14, B: Asn15, B: Cys29, B: Cys30, conact list: Atom Atom Distance (A) Fe O A:Gly25 4.92 Fe N A:Gly25 4.34 Fe C A:Gly25 4.65 Fe CA A:Gly25 3.95 Fe CB B:Cys10 3.23 Fe SG B:Cys10 2.29 Fe CA B:Cys10 4.65 Fe CB B:Val12 4.70 Fe C B:Val12 4.78 Fe N B:Cys13 3.65 Fe CB B:Cys13 3.16 Fe SG B:Cys13 2.20 Fe C B:Cys13 4.69 Fe CA B:Cys13 3.96 Fe N B:Gly14 4.79 Fe CB B:Asn15 4.97 Fe ND2 B:Asn15 4.23 Fe CG B:Asn15 4.91 Fe O B:Cys29 4.16 Fe CB B:Cys29 3.33 Fe SG B:Cys29 2.36 Fe C B:Cys29 3.73 Fe CA B:Cys29 4.09 Fe N B:Cys30 3.63 Fe CB B:Cys30 3.36 Fe SG B:Cys30 2.37 Fe CA B:Cys30 4.09 interactive model: Iron binding site 4 out of 8 in 2ji3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2ji3. 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: His49, B: His69, B: His75, B: Cys116, B: Ile118, B: His119, B: Per1130, conact list: Atom Atom Distance (A) Fe NE2 B:His49 2.34 Fe ND1 B:His49 4.42 Fe CD2 B:His49 3.28 Fe CE1 B:His49 3.32 Fe CG B:His49 4.43 Fe NE2 B:His69 2.21 Fe ND1 B:His69 4.25 Fe CD2 B:His69 3.29 Fe CE1 B:His69 3.08 Fe CG B:His69 4.38 Fe NE2 B:His75 2.25 Fe ND1 B:His75 4.29 Fe CD2 B:His75 3.26 Fe CE1 B:His75 3.16 Fe CG B:His75 4.37 Fe CB B:Cys116 3.69 Fe SG B:Cys116 2.53 Fe CB B:Ile118 4.77 Fe NE2 B:His119 4.04 Fe N B:His119 4.27 Fe CB B:His119 3.71 Fe ND1 B:His119 2.07 Fe CD2 B:His119 4.23 Fe CE1 B:His119 2.86 Fe CG B:His119 3.21 Fe CA B:His119 4.66 Fe O1 B:Per1130 2.00 Fe O2 B:Per1130 3.10 interactive model: Iron binding site 5 out of 8 in 2ji3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 2ji3. 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: Cys10, C: Val12, C: Cys13, C: Gly14, C: Asn15, C: Cys29, C: Cys30, D: Gly25, C: Hoh2021, conact list: Atom Atom Distance (A) Fe CB C:Cys10 3.16 Fe SG C:Cys10 2.24 Fe CA C:Cys10 4.59 Fe CB C:Val12 4.58 Fe C C:Val12 4.79 Fe N C:Cys13 3.70 Fe CB C:Cys13 3.24 Fe SG C:Cys13 2.24 Fe C C:Cys13 4.81 Fe CA C:Cys13 4.05 Fe N C:Gly14 4.86 Fe CB C:Asn15 4.96 Fe ND2 C:Asn15 4.25 Fe CG C:Asn15 4.98 Fe O C:Cys29 4.15 Fe CB C:Cys29 3.38 Fe SG C:Cys29 2.26 Fe C C:Cys29 3.74 Fe CA C:Cys29 4.12 Fe N C:Cys30 3.65 Fe CB C:Cys30 3.33 Fe SG C:Cys30 2.35 Fe CA C:Cys30 4.10 Fe N D:Gly25 4.48 Fe C D:Gly25 4.78 Fe CA D:Gly25 4.08 Fe O C:Hoh2021 4.80 interactive model: Iron binding site 6 out of 8 in 2ji3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 2ji3. 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: His49, C: His69, C: His75, C: Cys116, C: Ile118, C: His119, C: Per1130, conact list: Atom Atom Distance (A) Fe NE2 C:His49 2.39 Fe ND1 C:His49 4.38 Fe CD2 C:His49 3.44 Fe CE1 C:His49 3.23 Fe CG C:His49 4.51 Fe NE2 C:His69 2.30 Fe ND1 C:His69 4.34 Fe CD2 C:His69 3.36 Fe CE1 C:His69 3.18 Fe CG C:His69 4.46 Fe NE2 C:His75 2.38 Fe ND1 C:His75 4.48 Fe CD2 C:His75 3.28 Fe CE1 C:His75 3.39 Fe CG C:His75 4.47 Fe CB C:Cys116 3.64 Fe SG C:Cys116 2.48 Fe CB C:Ile118 4.86 Fe NE2 C:His119 4.34 Fe N C:His119 4.22 Fe CB C:His119 3.61 Fe ND1 C:His119 2.28 Fe CD2 C:His119 4.41 Fe CE1 C:His119 3.20 Fe CG C:His119 3.29 Fe CA C:His119 4.57 Fe O1 C:Per1130 1.97 Fe O2 C:Per1130 3.08 interactive model: Iron binding site 7 out of 8 in 2ji3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 2ji3. 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: Gly25, D: Cys10, D: Val12, D: Cys13, D: Gly14, D: Asn15, D: Cys29, D: Cys30, conact list: Atom Atom Distance (A) Fe N C:Gly25 4.48 Fe C C:Gly25 4.66 Fe CA C:Gly25 3.94 Fe CB D:Cys10 3.21 Fe SG D:Cys10 2.20 Fe CA D:Cys10 4.63 Fe CB D:Val12 4.54 Fe C D:Val12 4.76 Fe N D:Cys13 3.69 Fe CB D:Cys13 3.26 Fe SG D:Cys13 2.18 Fe C D:Cys13 4.79 Fe CA D:Cys13 4.04 Fe N D:Gly14 4.88 Fe CB D:Asn15 4.96 Fe ND2 D:Asn15 4.31 Fe CG D:Asn15 4.94 Fe O D:Cys29 4.18 Fe CB D:Cys29 3.27 Fe SG D:Cys29 2.35 Fe C D:Cys29 3.69 Fe CA D:Cys29 4.03 Fe N D:Cys30 3.55 Fe CB D:Cys30 3.34 Fe SG D:Cys30 2.25 Fe CA D:Cys30 4.05 interactive model: Iron binding site 8 out of 8 in 2ji3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 2ji3. 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: His49, D: His69, D: His75, D: Cys116, D: Ile118, D: His119, D: Per1129, D: Hoh2058, conact list: Atom Atom Distance (A) Fe NE2 D:His49 2.17 Fe ND1 D:His49 4.17 Fe CD2 D:His49 3.21 Fe CE1 D:His49 3.04 Fe CG D:His49 4.28 Fe NE2 D:His69 2.24 Fe ND1 D:His69 4.35 Fe CD2 D:His69 3.16 Fe CE1 D:His69 3.26 Fe CG D:His69 4.34 Fe NE2 D:His75 2.29 Fe ND1 D:His75 4.27 Fe CD2 D:His75 3.40 Fe CE1 D:His75 3.08 Fe CG D:His75 4.45 Fe CB D:Cys116 3.77 Fe SG D:Cys116 2.60 Fe CB D:Ile118 4.75 Fe NE2 D:His119 4.11 Fe N D:His119 4.27 Fe CB D:His119 3.71 Fe ND1 D:His119 2.27 Fe CD2 D:His119 4.23 Fe CE1 D:His119 3.04 Fe CG D:His119 3.25 Fe CA D:His119 4.65 Fe O1 D:Per1129 2.04 Fe O2 D:Per1129 3.07 Fe O D:Hoh2058 4.71 interactive model: