Iron in the structure of Superoxide Dismutase From Aeropyrum Pernix K1, Fe-Bound Form (pdb 3ak3)

The binding sites of Iron atom in the structure of Superoxide Dismutase From Aeropyrum Pernix K1, Fe-Bound Form (pdb code 3ak3). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3ak3 structure was solved by T.NAKAMURA, K.UEGAKI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 49.8-1.5 Space group P1211 a (A) 69.057 b (A) 71.755 c (A) 76.404 alpha (°) 90.00 beta (°) 91.72 gamma (°) 90.00 Rfactor (%) 22.5 Rfree (%) 25.6 Iron Binding Sites: Iron binding site 1 out of 4 in 3ak3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3ak3. 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: His31, A: Tyr39, A: His79, A: Trp130, A: His150, A: Asp165, A: Trp167, A: His169, A: Hoh217, A: Hoh288, conact list: Atom Atom Distance (A) Fe NE2 A:His31 2.18 Fe ND1 A:His31 4.27 Fe CD2 A:His31 3.13 Fe CE1 A:His31 3.17 Fe CG A:His31 4.28 Fe CE2 A:Tyr39 4.92 Fe OH A:Tyr39 4.44 Fe NE2 A:His79 2.14 Fe ND1 A:His79 4.19 Fe CD2 A:His79 3.23 Fe CE1 A:His79 3.02 Fe CG A:His79 4.32 Fe CZ2 A:Trp130 4.55 Fe CH2 A:Trp130 4.64 Fe NE2 A:His150 4.81 Fe CB A:Asp165 4.31 Fe OD2 A:Asp165 1.93 Fe OD1 A:Asp165 3.50 Fe CG A:Asp165 3.04 Fe CB A:Trp167 4.47 Fe CD1 A:Trp167 4.86 Fe CG A:Trp167 4.60 Fe NE2 A:His169 2.17 Fe ND1 A:His169 4.25 Fe CD2 A:His169 3.20 Fe CE1 A:His169 3.11 Fe CG A:His169 4.32 Fe O A:Hoh217 2.10 Fe O A:Hoh288 2.22 interactive model: Iron binding site 2 out of 4 in 3ak3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3ak3. 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: His31, B: Tyr39, B: His79, B: Trp130, B: His150, B: Asp165, B: Trp167, B: His169, B: Hoh221, B: Hoh250, conact list: Atom Atom Distance (A) Fe NE2 B:His31 2.13 Fe ND1 B:His31 4.22 Fe CD2 B:His31 3.10 Fe CE1 B:His31 3.12 Fe CG B:His31 4.25 Fe OH B:Tyr39 4.27 Fe NE2 B:His79 2.19 Fe ND1 B:His79 4.24 Fe CD2 B:His79 3.24 Fe CE1 B:His79 3.08 Fe CG B:His79 4.34 Fe CZ2 B:Trp130 4.59 Fe CH2 B:Trp130 4.62 Fe NE2 B:His150 4.84 Fe CB B:Asp165 4.30 Fe OD2 B:Asp165 2.01 Fe OD1 B:Asp165 3.47 Fe CG B:Asp165 3.05 Fe CB B:Trp167 4.57 Fe CD1 B:Trp167 4.86 Fe CG B:Trp167 4.65 Fe NE2 B:His169 2.20 Fe ND1 B:His169 4.27 Fe CD2 B:His169 3.24 Fe CE1 B:His169 3.12 Fe CG B:His169 4.36 Fe O B:Hoh221 2.07 Fe O B:Hoh250 2.26 interactive model: Iron binding site 3 out of 4 in 3ak3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3ak3. 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: His31, C: Tyr39, C: His79, C: Trp130, C: His150, C: Asp165, C: Trp167, C: His169, C: Hoh219, C: Hoh253, conact list: Atom Atom Distance (A) Fe NE2 C:His31 2.16 Fe ND1 C:His31 4.23 Fe CD2 C:His31 3.13 Fe CE1 C:His31 3.13 Fe CG C:His31 4.26 Fe CE2 C:Tyr39 4.98 Fe OH C:Tyr39 4.23 Fe NE2 C:His79 2.22 Fe ND1 C:His79 4.27 Fe CD2 C:His79 3.28 Fe CE1 C:His79 3.10 Fe CG C:His79 4.38 Fe CZ2 C:Trp130 4.65 Fe CH2 C:Trp130 4.75 Fe NE2 C:His150 4.80 Fe CB C:Asp165 4.24 Fe OD2 C:Asp165 1.88 Fe OD1 C:Asp165 3.46 Fe CG C:Asp165 2.98 Fe CB C:Trp167 4.58 Fe CD1 C:Trp167 4.85 Fe CG C:Trp167 4.65 Fe NE2 C:His169 2.31 Fe ND1 C:His169 4.41 Fe CD2 C:His169 3.27 Fe CE1 C:His169 3.29 Fe CG C:His169 4.43 Fe O C:Hoh219 2.00 Fe O C:Hoh253 1.95 interactive model: Iron binding site 4 out of 4 in 3ak3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3ak3. 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: His31, D: Tyr39, D: His79, D: Trp130, D: His150, D: Asp165, D: Trp167, D: His169, D: Hoh219, D: Hoh267, conact list: Atom Atom Distance (A) Fe NE2 D:His31 2.15 Fe ND1 D:His31 4.22 Fe CD2 D:His31 3.14 Fe CE1 D:His31 3.10 Fe CG D:His31 4.27 Fe CE2 D:Tyr39 4.90 Fe OH D:Tyr39 4.19 Fe NE2 D:His79 2.22 Fe ND1 D:His79 4.27 Fe CD2 D:His79 3.30 Fe CE1 D:His79 3.10 Fe CG D:His79 4.39 Fe CZ2 D:Trp130 4.68 Fe CH2 D:Trp130 4.71 Fe NE2 D:His150 4.88 Fe CB D:Asp165 4.37 Fe OD2 D:Asp165 2.00 Fe OD1 D:Asp165 3.53 Fe CG D:Asp165 3.09 Fe CB D:Trp167 4.54 Fe CD1 D:Trp167 4.91 Fe CG D:Trp167 4.65 Fe NE2 D:His169 2.18 Fe ND1 D:His169 4.25 Fe CD2 D:His169 3.20 Fe CE1 D:His169 3.11 Fe CG D:His169 4.33 Fe O D:Hoh219 2.04 Fe O D:Hoh267 2.23 interactive model: