Magnesium in the structure of E. Coli Glucarate Dehydratase Bound to Product 2,3- Dihydroxy-5-Oxo-Hexanedioate (pdb 1ec8)

The binding sites of Magnesium atom in the structure of E. Coli Glucarate Dehydratase Bound to Product 2,3- Dihydroxy-5-Oxo-Hexanedioate (pdb code 1ec8). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1ec8 structure was solved by A.M.GULICK, B.K.HUBBARD, J.A.GERLT, I.RAYMENT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.9 Space group P1 a (A) 71.090 b (A) 84.606 c (A) 98.858 alpha (°) 103.42 beta (°) 93.99 gamma (°) 113.06 Rfactor (%) n/a Rfree (%) n/a Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 1ec8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1ec8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Tyr150, A: Lys205, A: Lys207, A: Asp235, A: Asn237, A: Glu260, A: Asp261, A: Asn289, A: His339, A: Glr499, A: Hoh1583, conact list: Atom Atom Distance (A) Mg OH A:Tyr150 4.99 Mg CE A:Lys205 4.77 Mg NZ A:Lys205 3.98 Mg NZ A:Lys207 3.97 Mg CB A:Asp235 4.33 Mg OD2 A:Asp235 3.54 Mg OD1 A:Asp235 2.09 Mg CG A:Asp235 3.04 Mg ND2 A:Asn237 3.87 Mg OD1 A:Asn237 4.80 Mg CG A:Asn237 4.63 Mg OE1 A:Glu260 4.23 Mg CB A:Glu260 4.93 Mg OE2 A:Glu260 2.13 Mg CD A:Glu260 3.24 Mg CG A:Glu260 3.66 Mg OD2 A:Asp261 3.99 Mg N A:Asn289 4.83 Mg CB A:Asn289 4.22 Mg ND2 A:Asn289 3.56 Mg OD1 A:Asn289 1.85 Mg CG A:Asn289 2.98 Mg CA A:Asn289 4.98 Mg NE2 A:His339 4.95 Mg CD2 A:His339 4.24 Mg C6 A:Glr499 2.52 Mg O5 A:Glr499 4.80 Mg C5 A:Glr499 4.02 Mg O6B A:Glr499 2.10 Mg C4 A:Glr499 4.87 Mg O6A A:Glr499 2.30 Mg O A:Hoh1583 1.84 interactive model: Magnesium binding site 2 out of 4 in 1ec8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1ec8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Tyr150, B: Lys205, B: Lys207, B: Asp235, B: Asn237, B: Glu260, B: Asp261, B: Asn289, B: Leu311, B: His339, B: Glr500, B: Hoh1689, conact list: Atom Atom Distance (A) Mg OH B:Tyr150 4.75 Mg CE B:Lys205 4.47 Mg NZ B:Lys205 3.79 Mg NZ B:Lys207 3.81 Mg CB B:Asp235 4.34 Mg OD2 B:Asp235 3.58 Mg OD1 B:Asp235 2.21 Mg CG B:Asp235 3.11 Mg ND2 B:Asn237 3.89 Mg OD1 B:Asn237 4.84 Mg CG B:Asn237 4.64 Mg OE1 B:Glu260 4.22 Mg OE2 B:Glu260 2.08 Mg CD B:Glu260 3.24 Mg CG B:Glu260 3.74 Mg OD2 B:Asp261 4.30 Mg CB B:Asn289 4.46 Mg ND2 B:Asn289 3.60 Mg OD1 B:Asn289 2.11 Mg CG B:Asn289 3.14 Mg CD1 B:Leu311 4.82 Mg CD2 B:His339 4.40 Mg C6 B:Glr500 2.34 Mg O5 B:Glr500 4.47 Mg C5 B:Glr500 3.78 Mg O6B B:Glr500 1.86 Mg C4 B:Glr500 4.70 Mg O6A B:Glr500 2.23 Mg O B:Hoh1689 1.98 interactive model: Magnesium binding site 3 out of 4 in 1ec8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1ec8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Tyr150, C: Lys205, C: Lys207, C: Asp235, C: Asn237, C: Glu260, C: Asp261, C: Asn289, C: Leu311, C: His339, C: Glr501, C: Hoh1874, conact list: Atom Atom Distance (A) Mg OH C:Tyr150 4.82 Mg CE C:Lys205 4.75 Mg NZ C:Lys205 3.76 Mg NZ C:Lys207 3.91 Mg CB C:Asp235 4.35 Mg OD2 C:Asp235 3.52 Mg OD1 C:Asp235 2.22 Mg CG C:Asp235 3.10 Mg ND2 C:Asn237 3.92 Mg OD1 C:Asn237 4.82 Mg CG C:Asn237 4.64 Mg OE1 C:Glu260 4.12 Mg OE2 C:Glu260 2.01 Mg CD C:Glu260 3.18 Mg CG C:Glu260 3.74 Mg OD2 C:Asp261 4.14 Mg N C:Asn289 4.93 Mg CB C:Asn289 4.32 Mg ND2 C:Asn289 3.43 Mg OD1 C:Asn289 1.95 Mg CG C:Asn289 2.99 Mg CD1 C:Leu311 4.89 Mg CD2 C:His339 4.23 Mg C6 C:Glr501 2.31 Mg O5 C:Glr501 4.43 Mg C5 C:Glr501 3.76 Mg O6B C:Glr501 1.91 Mg C4 C:Glr501 4.74 Mg O6A C:Glr501 2.15 Mg O C:Hoh1874 2.10 interactive model: Magnesium binding site 4 out of 4 in 1ec8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1ec8. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Tyr150, D: Lys205, D: Lys207, D: Asp235, D: Asn237, D: Glu260, D: Asp261, D: Asn289, D: Leu311, D: His339, D: Glr502, D: Hoh1907, conact list: Atom Atom Distance (A) Mg OH D:Tyr150 4.96 Mg CE D:Lys205 4.50 Mg NZ D:Lys205 3.91 Mg NZ D:Lys207 3.97 Mg CB D:Asp235 4.22 Mg OD2 D:Asp235 3.38 Mg OD1 D:Asp235 1.99 Mg CG D:Asp235 2.93 Mg ND2 D:Asn237 3.81 Mg OD1 D:Asn237 4.85 Mg CG D:Asn237 4.63 Mg OE1 D:Glu260 4.18 Mg CB D:Glu260 4.91 Mg OE2 D:Glu260 2.13 Mg CD D:Glu260 3.16 Mg CG D:Glu260 3.55 Mg OD2 D:Asp261 4.17 Mg N D:Asn289 4.95 Mg CB D:Asn289 4.28 Mg ND2 D:Asn289 3.42 Mg OD1 D:Asn289 1.90 Mg CG D:Asn289 2.96 Mg CD1 D:Leu311 4.91 Mg CD2 D:His339 4.49 Mg C6 D:Glr502 2.50 Mg O5 D:Glr502 4.68 Mg C5 D:Glr502 3.97 Mg O6B D:Glr502 2.12 Mg C4 D:Glr502 4.89 Mg O6A D:Glr502 2.26 Mg O D:Hoh1907 1.88 interactive model: