Iron in the structure of R2F From Corynebacterium Ammoniagenes in Its Reduced, Fe Containing, Form (pdb 1kgo)

The binding sites of Iron atom in the structure of R2F From Corynebacterium Ammoniagenes in Its Reduced, Fe Containing, Form (pdb code 1kgo). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1kgo structure was solved by M.HOGBOM, Y.HUQUE, B.M.SJOBERG, P.NORDLUND, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 25.0-2.2 Space group P1211 a (A) 49.951 b (A) 91.154 c (A) 137.270 alpha (°) 90.00 beta (°) 91.27 gamma (°) 90.00 Rfactor (%) 16.3 Rfree (%) 23.8 Iron Binding Sites: Iron binding site 1 out of 8 in 1kgo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1kgo. 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: Asp77, A: Glu108, A: His111, A: Glu168, A: Phe172, A: Ile198, A: Glu202, A: Fe21002, A: Hoh1062, conact list: Atom Atom Distance (A) Fe CB A:Asp77 4.12 Fe OD2 A:Asp77 3.54 Fe OD1 A:Asp77 1.80 Fe CG A:Asp77 2.95 Fe CA A:Asp77 4.67 Fe O A:Glu108 4.89 Fe OE1 A:Glu108 2.29 Fe CB A:Glu108 4.67 Fe OE2 A:Glu108 3.00 Fe CD A:Glu108 2.95 Fe CG A:Glu108 4.34 Fe CA A:Glu108 4.38 Fe NE2 A:His111 4.26 Fe CB A:His111 3.50 Fe ND1 A:His111 2.18 Fe CD2 A:His111 4.31 Fe CE1 A:His111 3.12 Fe CG A:His111 3.19 Fe OE1 A:Glu168 4.97 Fe CE2 A:Phe172 4.14 Fe CZ A:Phe172 3.60 Fe CE1 A:Phe172 4.32 Fe CG2 A:Ile198 4.15 Fe OE1 A:Glu202 2.85 Fe OE2 A:Glu202 1.90 Fe CD A:Glu202 2.65 Fe CG A:Glu202 4.01 Fe FE A:Fe21002 3.85 Fe O A:Hoh1062 3.73 interactive model: Iron binding site 2 out of 8 in 1kgo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1kgo. 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: Gln80, A: Ile104, A: Glu108, A: His111, A: Glu168, A: Phe172, A: Glu202, A: His205, A: Fe21001, conact list: Atom Atom Distance (A) Fe CG A:Gln80 4.39 Fe CG2 A:Ile104 4.60 Fe OE1 A:Glu108 3.50 Fe OE2 A:Glu108 1.96 Fe CD A:Glu108 2.93 Fe CG A:Glu108 4.04 Fe ND1 A:His111 4.83 Fe CE1 A:His111 4.69 Fe OE1 A:Glu168 1.99 Fe CB A:Glu168 4.67 Fe OE2 A:Glu168 2.29 Fe CD A:Glu168 2.42 Fe CG A:Glu168 3.93 Fe CE2 A:Phe172 4.51 Fe CZ A:Phe172 4.94 Fe N A:Glu202 4.61 Fe OE1 A:Glu202 1.94 Fe CB A:Glu202 4.23 Fe OE2 A:Glu202 3.85 Fe CD A:Glu202 3.14 Fe CG A:Glu202 4.22 Fe CA A:Glu202 3.99 Fe NE2 A:His205 4.48 Fe CB A:His205 3.73 Fe ND1 A:His205 2.43 Fe CD2 A:His205 4.57 Fe CE1 A:His205 3.33 Fe CG A:His205 3.45 Fe FE A:Fe21001 3.85 interactive model: Iron binding site 3 out of 8 in 1kgo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1kgo. 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: Asp77, B: Glu108, B: His111, B: Glu168, B: Phe172, B: Ile198, B: Glu202, B: Fe21004, B: Hoh1034, conact list: Atom Atom Distance (A) Fe CB B:Asp77 3.83 Fe OD2 B:Asp77 3.33 Fe OD1 B:Asp77 1.66 Fe CG B:Asp77 2.71 Fe CA B:Asp77 4.46 Fe O B:Glu108 4.77 Fe OE1 B:Glu108 2.03 Fe CB B:Glu108 4.62 Fe OE2 B:Glu108 3.60 Fe CD B:Glu108 3.14 Fe CG B:Glu108 4.42 Fe CA B:Glu108 4.29 Fe NE2 B:His111 4.20 Fe CB B:His111 3.42 Fe ND1 B:His111 2.12 Fe CD2 B:His111 4.24 Fe CE1 B:His111 3.09 Fe CG B:His111 3.11 Fe CA B:His111 4.95 Fe OE2 B:Glu168 4.53 Fe CE2 B:Phe172 4.27 Fe CZ B:Phe172 3.64 Fe CE1 B:Phe172 4.27 Fe CG2 B:Ile198 4.25 Fe OE1 B:Glu202 3.15 Fe OE2 B:Glu202 1.74 Fe CD B:Glu202 2.73 Fe CG B:Glu202 4.00 Fe FE B:Fe21004 3.82 Fe O B:Hoh1034 4.26 interactive model: Iron binding site 4 out of 8 in 1kgo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1kgo. 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: Asp77, B: Gln80, B: Ile104, B: Glu108, B: His111, B: Glu168, B: Phe172, B: Glu202, B: His205, B: Fe21003, conact list: Atom Atom Distance (A) Fe OD1 B:Asp77 4.91 Fe CG B:Gln80 4.50 Fe CG2 B:Ile104 4.54 Fe OE1 B:Glu108 3.31 Fe OE2 B:Glu108 1.77 Fe CD B:Glu108 2.84 Fe CG B:Glu108 4.12 Fe ND1 B:His111 4.70 Fe CE1 B:His111 4.59 Fe OE1 B:Glu168 3.03 Fe CB B:Glu168 4.98 Fe OE2 B:Glu168 1.60 Fe CD B:Glu168 2.52 Fe CG B:Glu168 3.69 Fe CE2 B:Phe172 4.58 Fe CZ B:Phe172 4.96 Fe N B:Glu202 4.58 Fe OE1 B:Glu202 1.72 Fe CB B:Glu202 4.24 Fe OE2 B:Glu202 3.44 Fe CD B:Glu202 2.86 Fe CG B:Glu202 4.07 Fe CA B:Glu202 4.03 Fe NE2 B:His205 4.20 Fe CB B:His205 3.71 Fe ND1 B:His205 2.19 Fe CD2 B:His205 4.35 Fe CE1 B:His205 3.02 Fe CG B:His205 3.29 Fe FE B:Fe21003 3.82 interactive model: Iron binding site 5 out of 8 in 1kgo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1kgo. 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: Asp77, C: Met107, C: Glu108, C: His111, C: Glu168, C: Phe172, C: Ile198, C: Glu202, C: Fe22002, C: Hoh2037, conact list: Atom Atom Distance (A) Fe CB C:Asp77 4.26 Fe OD2 C:Asp77 3.81 Fe OD1 C:Asp77 1.99 Fe CG C:Asp77 3.15 Fe CA C:Asp77 4.73 Fe O C:Met107 4.87 Fe O C:Glu108 4.76 Fe N C:Glu108 4.93 Fe OE1 C:Glu108 2.71 Fe CB C:Glu108 4.42 Fe OE2 C:Glu108 2.34 Fe CD C:Glu108 2.77 Fe C C:Glu108 4.96 Fe CG C:Glu108 4.10 Fe CA C:Glu108 4.08 Fe NE2 C:His111 4.16 Fe CB C:His111 3.46 Fe ND1 C:His111 2.11 Fe CD2 C:His111 4.22 Fe CE1 C:His111 3.04 Fe CG C:His111 3.12 Fe CA C:His111 4.98 Fe OE1 C:Glu168 4.93 Fe CE2 C:Phe172 3.96 Fe CD2 C:Phe172 4.83 Fe CZ C:Phe172 3.78 Fe CE1 C:Phe172 4.54 Fe CG2 C:Ile198 4.60 Fe OE1 C:Glu202 1.79 Fe OE2 C:Glu202 2.90 Fe CD C:Glu202 2.66 Fe CG C:Glu202 4.08 Fe FE C:Fe22002 3.63 Fe O C:Hoh2037 4.32 interactive model: Iron binding site 6 out of 8 in 1kgo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1kgo. 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: Gln80, C: Ile104, C: Glu108, C: His111, C: Glu168, C: Phe172, C: Glu202, C: His205, C: Fe22001, conact list: Atom Atom Distance (A) Fe NE2 C:Gln80 4.90 Fe CG C:Gln80 4.42 Fe CG2 C:Ile104 4.62 Fe OE1 C:Glu108 3.23 Fe OE2 C:Glu108 2.47 Fe CD C:Glu108 2.99 Fe CG C:Glu108 4.13 Fe ND1 C:His111 4.88 Fe CE1 C:His111 4.82 Fe OE1 C:Glu168 1.99 Fe CB C:Glu168 4.68 Fe OE2 C:Glu168 2.13 Fe CD C:Glu168 2.34 Fe CG C:Glu168 3.87 Fe CE2 C:Phe172 4.05 Fe CD2 C:Phe172 4.79 Fe CZ C:Phe172 4.85 Fe N C:Glu202 4.82 Fe OE1 C:Glu202 3.70 Fe CB C:Glu202 4.40 Fe OE2 C:Glu202 1.96 Fe CD C:Glu202 3.10 Fe CG C:Glu202 4.30 Fe CA C:Glu202 4.18 Fe NE2 C:His205 4.46 Fe CB C:His205 3.68 Fe ND1 C:His205 2.39 Fe CD2 C:His205 4.53 Fe CE1 C:His205 3.30 Fe CG C:His205 3.40 Fe FE C:Fe22001 3.63 interactive model: Iron binding site 7 out of 8 in 1kgo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1kgo. 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: Asp77, D: Glu108, D: His111, D: Phe172, D: Ile198, D: Glu202, D: Fe22004, D: Hoh2050, conact list: Atom Atom Distance (A) Fe CB D:Asp77 4.00 Fe OD2 D:Asp77 3.60 Fe OD1 D:Asp77 1.80 Fe CG D:Asp77 2.93 Fe CA D:Asp77 4.44 Fe O D:Glu108 4.89 Fe OE1 D:Glu108 1.98 Fe CB D:Glu108 4.67 Fe OE2 D:Glu108 3.54 Fe CD D:Glu108 3.09 Fe CG D:Glu108 4.42 Fe CA D:Glu108 4.32 Fe NE2 D:His111 4.20 Fe CB D:His111 3.49 Fe ND1 D:His111 2.14 Fe CD2 D:His111 4.26 Fe CE1 D:His111 3.07 Fe CG D:His111 3.15 Fe CE2 D:Phe172 4.06 Fe CZ D:Phe172 3.46 Fe CE1 D:Phe172 4.14 Fe CG2 D:Ile198 4.17 Fe OE1 D:Glu202 3.02 Fe OE2 D:Glu202 1.81 Fe CD D:Glu202 2.70 Fe CG D:Glu202 4.02 Fe FE D:Fe22004 3.90 Fe O D:Hoh2050 3.93 interactive model: Iron binding site 8 out of 8 in 1kgo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 1kgo. 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: Gln80, D: Ile104, D: Glu108, D: His111, D: Glu168, D: Phe172, D: Glu202, D: His205, D: Fe22003, conact list: Atom Atom Distance (A) Fe CG D:Gln80 4.51 Fe CG2 D:Ile104 4.53 Fe OE1 D:Glu108 3.45 Fe OE2 D:Glu108 1.91 Fe CD D:Glu108 3.01 Fe CG D:Glu108 4.31 Fe ND1 D:His111 4.80 Fe CE1 D:His111 4.63 Fe OE1 D:Glu168 2.37 Fe CB D:Glu168 4.64 Fe OE2 D:Glu168 1.92 Fe CD D:Glu168 2.43 Fe CG D:Glu168 3.94 Fe CE2 D:Phe172 4.25 Fe CZ D:Phe172 4.70 Fe O D:Glu202 5.00 Fe N D:Glu202 4.59 Fe OE1 D:Glu202 2.05 Fe CB D:Glu202 4.27 Fe OE2 D:Glu202 3.55 Fe CD D:Glu202 3.03 Fe C D:Glu202 5.00 Fe CG D:Glu202 4.20 Fe CA D:Glu202 3.96 Fe NE2 D:His205 4.17 Fe CB D:His205 3.46 Fe ND1 D:His205 2.09 Fe CD2 D:His205 4.23 Fe CE1 D:His205 3.03 Fe CG D:His205 3.12 Fe CA D:His205 4.99 Fe FE D:Fe22003 3.90 interactive model: