Iron in the structure of Malonate-Bound Structure Of The Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) and Characterization of the Native FE2+ Metal Ion Preference (pdb 2zo9)

The binding sites of Iron atom in the structure of Malonate-Bound Structure Of The Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) and Characterization of the Native FE2+ Metal Ion Preference (pdb code 2zo9). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2zo9 structure was solved by C.J.JACKSON, P.D.CARR, D.L.OLLIS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.0-2.2 Space group P213 a (A) 164.159 b (A) 164.159 c (A) 164.159 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17 Rfree (%) 18.9 Iron Binding Sites: Iron binding site 1 out of 4 in 2zo9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2zo9. 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: Asp8, B: His10, B: Asp50, B: His81, B: His156, B: His195, B: His197, B: Fe2276, B: Mli277, conact list: Atom Atom Distance (A) Fe CB B:Asp8 3.75 Fe OD2 B:Asp8 4.17 Fe OD1 B:Asp8 2.07 Fe CG B:Asp8 3.16 Fe CA B:Asp8 4.56 Fe NE2 B:His10 2.36 Fe ND1 B:His10 4.36 Fe CD2 B:His10 3.46 Fe CE1 B:His10 3.17 Fe CG B:His10 4.53 Fe CB B:Asp50 3.39 Fe OD2 B:Asp50 2.30 Fe OD1 B:Asp50 4.38 Fe CG B:Asp50 3.21 Fe CA B:Asp50 4.91 Fe NE2 B:His81 4.85 Fe CD2 B:His81 4.50 Fe NE2 B:His156 4.70 Fe CE1 B:His156 4.51 Fe O B:His195 4.32 Fe C B:His195 4.93 Fe CA B:His195 4.77 Fe NE2 B:His197 2.37 Fe ND1 B:His197 4.40 Fe CD2 B:His197 3.41 Fe CE1 B:His197 3.24 Fe CG B:His197 4.51 Fe FE B:Fe2276 3.54 Fe O9 B:Mli277 2.62 Fe C1 B:Mli277 4.36 Fe O8 B:Mli277 2.38 Fe C3 B:Mli277 2.85 Fe O7 B:Mli277 4.89 interactive model: Iron binding site 2 out of 4 in 2zo9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2zo9. 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: Asp8, B: Asp50, B: Asn80, B: His81, B: His156, B: His195, B: Fe2275, B: Mli277, conact list: Atom Atom Distance (A) Fe OD1 B:Asp8 4.07 Fe CB B:Asp50 4.37 Fe OD2 B:Asp50 2.34 Fe OD1 B:Asp50 3.41 Fe CG B:Asp50 3.14 Fe N B:Asn80 4.38 Fe CB B:Asn80 4.62 Fe ND2 B:Asn80 3.69 Fe OD1 B:Asn80 2.27 Fe CG B:Asn80 3.29 Fe NE2 B:His81 4.90 Fe CD2 B:His81 4.19 Fe NE2 B:His156 2.36 Fe ND1 B:His156 4.41 Fe CD2 B:His156 3.42 Fe CE1 B:His156 3.24 Fe CG B:His156 4.53 Fe O B:His195 4.29 Fe NE2 B:His195 4.46 Fe N B:His195 4.67 Fe CB B:His195 4.13 Fe ND1 B:His195 2.51 Fe CD2 B:His195 4.70 Fe C B:His195 4.58 Fe CE1 B:His195 3.23 Fe CG B:His195 3.68 Fe CA B:His195 3.81 Fe FE B:Fe2275 3.54 Fe O9 B:Mli277 4.11 Fe C1 B:Mli277 4.09 Fe O8 B:Mli277 2.52 Fe C3 B:Mli277 3.36 Fe O7 B:Mli277 3.28 Fe C2 B:Mli277 4.13 interactive model: Iron binding site 3 out of 4 in 2zo9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2zo9. 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: Asp8, C: His10, C: Asp50, C: His81, C: His156, C: His195, C: His197, C: Fe2276, C: Mli277, conact list: Atom Atom Distance (A) Fe CB C:Asp8 3.70 Fe OD2 C:Asp8 4.27 Fe OD1 C:Asp8 2.25 Fe CG C:Asp8 3.23 Fe CA C:Asp8 4.52 Fe NE2 C:His10 2.42 Fe ND1 C:His10 4.38 Fe CD2 C:His10 3.56 Fe CE1 C:His10 3.17 Fe CG C:His10 4.59 Fe CB C:Asp50 3.56 Fe OD2 C:Asp50 2.28 Fe OD1 C:Asp50 4.44 Fe CG C:Asp50 3.29 Fe NE2 C:His81 4.91 Fe CD2 C:His81 4.63 Fe NE2 C:His156 4.70 Fe CE1 C:His156 4.50 Fe O C:His195 4.29 Fe C C:His195 4.86 Fe CA C:His195 4.66 Fe NE2 C:His197 2.31 Fe ND1 C:His197 4.41 Fe CD2 C:His197 3.23 Fe CE1 C:His197 3.32 Fe CG C:His197 4.40 Fe FE C:Fe2276 3.56 Fe O9 C:Mli277 2.66 Fe C1 C:Mli277 4.31 Fe O8 C:Mli277 2.32 Fe C3 C:Mli277 2.82 interactive model: Iron binding site 4 out of 4 in 2zo9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2zo9. 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: Asp8, C: Asp50, C: Asn80, C: His81, C: His156, C: His195, C: Fe2275, C: Mli277, conact list: Atom Atom Distance (A) Fe OD1 C:Asp8 4.09 Fe CB C:Asp50 4.42 Fe OD2 C:Asp50 2.37 Fe OD1 C:Asp50 3.29 Fe CG C:Asp50 3.11 Fe N C:Asn80 4.36 Fe CB C:Asn80 4.63 Fe ND2 C:Asn80 3.66 Fe OD1 C:Asn80 2.29 Fe CG C:Asn80 3.29 Fe NE2 C:His81 4.89 Fe CD2 C:His81 4.20 Fe NE2 C:His156 2.26 Fe ND1 C:His156 4.31 Fe CD2 C:His156 3.33 Fe CE1 C:His156 3.14 Fe CG C:His156 4.43 Fe O C:His195 4.35 Fe NE2 C:His195 4.55 Fe N C:His195 4.60 Fe CB C:His195 3.93 Fe ND1 C:His195 2.55 Fe CD2 C:His195 4.68 Fe C C:His195 4.59 Fe CE1 C:His195 3.38 Fe CG C:His195 3.60 Fe CA C:His195 3.75 Fe FE C:Fe2275 3.56 Fe O9 C:Mli277 4.09 Fe C1 C:Mli277 4.10 Fe O8 C:Mli277 2.51 Fe C3 C:Mli277 3.35 Fe O7 C:Mli277 3.75 Fe C2 C:Mli277 4.41 interactive model: