Iron in the structure of Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum (pdb 1ma1)

The binding sites of Iron atom in the structure of Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum (pdb code 1ma1). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1ma1 structure was solved by J.J.ADAMS, B.F.ANDERSON, J.P.RENAULT, C.VERCHERE-BEAUR, I.MORGENSTERN-BADARAU, G.B.JAMESON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.6 Space group C121 a (A) 187.619 b (A) 114.082 c (A) 58.087 alpha (°) 90.00 beta (°) 94.95 gamma (°) 90.00 Rfactor (%) 21.5 Rfree (%) 24.7 Iron Binding Sites: Iron binding site 1 out of 6 in 1ma1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1ma1. 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: His32, A: His36, A: His80, A: Trp131, A: Asp166, A: Trp168, A: His170, A: Ala171, A: Hoh272, conact list: Atom Atom Distance (A) Fe NE2 A:His32 2.12 Fe ND1 A:His32 4.12 Fe CD2 A:His32 3.00 Fe CE1 A:His32 3.09 Fe CG A:His32 4.12 Fe CB A:His36 4.92 Fe NE2 A:His80 2.14 Fe ND1 A:His80 4.03 Fe CD2 A:His80 3.21 Fe CE1 A:His80 2.89 Fe CG A:His80 4.22 Fe CZ2 A:Trp131 4.44 Fe CH2 A:Trp131 4.51 Fe CB A:Asp166 4.33 Fe OD2 A:Asp166 1.92 Fe OD1 A:Asp166 3.68 Fe CG A:Asp166 3.11 Fe CB A:Trp168 4.31 Fe CD1 A:Trp168 4.79 Fe CG A:Trp168 4.47 Fe NE2 A:His170 2.12 Fe ND1 A:His170 4.26 Fe CD2 A:His170 2.88 Fe CE1 A:His170 3.27 Fe CG A:His170 4.12 Fe CB A:Ala171 4.73 Fe O A:Hoh272 1.92 interactive model: Iron binding site 2 out of 6 in 1ma1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1ma1. 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: His32, B: His36, B: Tyr40, B: His80, B: Trp131, B: Asp166, B: Trp168, B: His170, B: Ala171, B: Hoh246, conact list: Atom Atom Distance (A) Fe NE2 B:His32 2.11 Fe ND1 B:His32 4.13 Fe CD2 B:His32 2.98 Fe CE1 B:His32 3.10 Fe CG B:His32 4.12 Fe CB B:His36 4.94 Fe CE2 B:Tyr40 4.98 Fe NE2 B:His80 2.13 Fe ND1 B:His80 4.04 Fe CD2 B:His80 3.20 Fe CE1 B:His80 2.90 Fe CG B:His80 4.22 Fe CZ2 B:Trp131 4.39 Fe CH2 B:Trp131 4.46 Fe CB B:Asp166 4.32 Fe OD2 B:Asp166 1.93 Fe OD1 B:Asp166 3.72 Fe CG B:Asp166 3.12 Fe CB B:Trp168 4.31 Fe CD1 B:Trp168 4.81 Fe CD2 B:Trp168 5.00 Fe CG B:Trp168 4.49 Fe NE2 B:His170 2.12 Fe ND1 B:His170 4.25 Fe CD2 B:His170 2.87 Fe CE1 B:His170 3.26 Fe CG B:His170 4.11 Fe CB B:Ala171 4.75 Fe O B:Hoh246 1.91 interactive model: Iron binding site 3 out of 6 in 1ma1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1ma1. 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: His32, C: His36, C: Tyr40, C: His80, C: Trp131, C: Asp166, C: Trp168, C: His170, C: Ala171, C: Hoh290, conact list: Atom Atom Distance (A) Fe NE2 C:His32 2.11 Fe ND1 C:His32 4.10 Fe CD2 C:His32 2.98 Fe CE1 C:His32 3.08 Fe CG C:His32 4.10 Fe CB C:His36 4.94 Fe CE2 C:Tyr40 4.99 Fe NE2 C:His80 2.13 Fe ND1 C:His80 4.03 Fe CD2 C:His80 3.22 Fe CE1 C:His80 2.88 Fe CG C:His80 4.23 Fe CZ2 C:Trp131 4.42 Fe CH2 C:Trp131 4.55 Fe CB C:Asp166 4.33 Fe OD2 C:Asp166 1.93 Fe OD1 C:Asp166 3.70 Fe CG C:Asp166 3.12 Fe CB C:Trp168 4.35 Fe CD1 C:Trp168 4.77 Fe CG C:Trp168 4.51 Fe NE2 C:His170 2.12 Fe ND1 C:His170 4.26 Fe CD2 C:His170 2.85 Fe CE1 C:His170 3.28 Fe CG C:His170 4.10 Fe CB C:Ala171 4.79 Fe O C:Hoh290 1.92 interactive model: Iron binding site 4 out of 6 in 1ma1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1ma1. 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: His32, D: His36, D: Tyr40, D: His80, D: Trp131, D: Asp166, D: Trp168, D: His170, D: Ala171, D: Hoh286, conact list: Atom Atom Distance (A) Fe NE2 D:His32 2.11 Fe ND1 D:His32 4.12 Fe CD2 D:His32 2.97 Fe CE1 D:His32 3.10 Fe CG D:His32 4.10 Fe CB D:His36 4.94 Fe CE2 D:Tyr40 4.95 Fe NE2 D:His80 2.13 Fe ND1 D:His80 4.03 Fe CD2 D:His80 3.22 Fe CE1 D:His80 2.88 Fe CG D:His80 4.22 Fe CZ2 D:Trp131 4.39 Fe CH2 D:Trp131 4.49 Fe CB D:Asp166 4.32 Fe OD2 D:Asp166 1.92 Fe OD1 D:Asp166 3.73 Fe CG D:Asp166 3.12 Fe CB D:Trp168 4.31 Fe CD1 D:Trp168 4.78 Fe CG D:Trp168 4.50 Fe NE2 D:His170 2.12 Fe ND1 D:His170 4.26 Fe CD2 D:His170 2.87 Fe CE1 D:His170 3.28 Fe CG D:His170 4.11 Fe CB D:Ala171 4.72 Fe O D:Hoh286 1.92 interactive model: Iron binding site 5 out of 6 in 1ma1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1ma1. 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: His32, E: His36, E: Tyr40, E: His80, E: Trp131, E: Asp166, E: Trp168, E: His170, E: Ala171, E: Hoh299, conact list: Atom Atom Distance (A) Fe NE2 E:His32 2.11 Fe ND1 E:His32 4.10 Fe CD2 E:His32 2.98 Fe CE1 E:His32 3.08 Fe CG E:His32 4.09 Fe CB E:His36 4.97 Fe CE2 E:Tyr40 4.96 Fe NE2 E:His80 2.13 Fe ND1 E:His80 4.03 Fe CD2 E:His80 3.21 Fe CE1 E:His80 2.89 Fe CG E:His80 4.22 Fe CZ2 E:Trp131 4.42 Fe CH2 E:Trp131 4.54 Fe CB E:Asp166 4.32 Fe OD2 E:Asp166 1.92 Fe OD1 E:Asp166 3.65 Fe CG E:Asp166 3.10 Fe CB E:Trp168 4.29 Fe CD1 E:Trp168 4.79 Fe CD2 E:Trp168 4.99 Fe CG E:Trp168 4.46 Fe NE2 E:His170 2.12 Fe ND1 E:His170 4.27 Fe CD2 E:His170 2.88 Fe CE1 E:His170 3.27 Fe CG E:His170 4.12 Fe CB E:Ala171 4.76 Fe O E:Hoh299 1.92 interactive model: Iron binding site 6 out of 6 in 1ma1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1ma1. 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: His32, F: His36, F: Tyr40, F: His80, F: Trp131, F: Asp166, F: Trp168, F: His170, F: Ala171, F: Hoh265, conact list: Atom Atom Distance (A) Fe NE2 F:His32 2.15 Fe ND1 F:His32 4.29 Fe CD2 F:His32 2.87 Fe CE1 F:His32 3.31 Fe CG F:His32 4.15 Fe CB F:His36 4.94 Fe CE2 F:Tyr40 4.99 Fe NE2 F:His80 2.13 Fe ND1 F:His80 4.03 Fe CD2 F:His80 3.20 Fe CE1 F:His80 2.89 Fe CG F:His80 4.21 Fe CZ2 F:Trp131 4.43 Fe CH2 F:Trp131 4.51 Fe CB F:Asp166 4.31 Fe OD2 F:Asp166 1.93 Fe OD1 F:Asp166 3.66 Fe CG F:Asp166 3.10 Fe CB F:Trp168 4.27 Fe CD1 F:Trp168 4.75 Fe CG F:Trp168 4.43 Fe NE2 F:His170 2.12 Fe ND1 F:His170 4.26 Fe CD2 F:His170 2.87 Fe CE1 F:His170 3.27 Fe CG F:His170 4.11 Fe CB F:Ala171 4.78 Fe O F:Hoh265 1.92 interactive model: