Magnesium in the structure of E. Coli Glucarate Dehydratase Bound to Xylarohydroxamate (pdb 1ec9)

The binding sites of Magnesium atom in the structure of E. Coli Glucarate Dehydratase Bound to Xylarohydroxamate (pdb code 1ec9). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1ec9 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) 30.0-2.0 Space group P1 a (A) 71.294 b (A) 84.836 c (A) 98.987 alpha (°) 103.14 beta (°) 94.31 gamma (°) 113.20 Rfactor (%) n/a Rfree (%) n/a Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 1ec9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1ec9. 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: Xyh499, A: Hoh1212, A: Hoh1760, conact list: Atom Atom Distance (A) Mg OH A:Tyr150 4.82 Mg CE A:Lys205 4.58 Mg NZ A:Lys205 3.76 Mg CE A:Lys207 4.96 Mg NZ A:Lys207 3.74 Mg CB A:Asp235 4.33 Mg OD2 A:Asp235 3.58 Mg OD1 A:Asp235 2.12 Mg CG A:Asp235 3.09 Mg ND2 A:Asn237 4.06 Mg OD1 A:Asn237 4.87 Mg CG A:Asn237 4.76 Mg OE1 A:Glu260 4.13 Mg OE2 A:Glu260 2.04 Mg CD A:Glu260 3.20 Mg CG A:Glu260 3.74 Mg OD2 A:Asp261 4.28 Mg CB A:Asn289 4.29 Mg ND2 A:Asn289 3.59 Mg OD1 A:Asn289 1.92 Mg CG A:Asn289 3.04 Mg CD2 A:His339 4.41 Mg N6 A:Xyh499 2.94 Mg C5 A:Xyh499 2.97 Mg OH5 A:Xyh499 2.21 Mg OH6 A:Xyh499 2.17 Mg C4 A:Xyh499 4.45 Mg OH4 A:Xyh499 4.28 Mg O A:Hoh1212 4.97 Mg O A:Hoh1760 2.09 interactive model: Magnesium binding site 2 out of 4 in 1ec9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1ec9. 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: His339, B: Xyh500, B: Hoh1755, B: Hoh1758, conact list: Atom Atom Distance (A) Mg OH B:Tyr150 4.76 Mg CE B:Lys205 4.49 Mg NZ B:Lys205 3.71 Mg CE B:Lys207 4.88 Mg NZ B:Lys207 3.55 Mg CB B:Asp235 4.40 Mg OD2 B:Asp235 3.77 Mg OD1 B:Asp235 2.15 Mg CG B:Asp235 3.20 Mg ND2 B:Asn237 4.03 Mg OD1 B:Asn237 4.82 Mg CG B:Asn237 4.75 Mg OE1 B:Glu260 4.06 Mg OE2 B:Glu260 2.00 Mg CD B:Glu260 3.17 Mg CG B:Glu260 3.85 Mg OD2 B:Asp261 4.59 Mg CB B:Asn289 4.47 Mg ND2 B:Asn289 3.51 Mg OD1 B:Asn289 2.10 Mg CG B:Asn289 3.12 Mg CD2 B:His339 4.38 Mg N6 B:Xyh500 2.84 Mg C5 B:Xyh500 2.88 Mg OH5 B:Xyh500 2.11 Mg OH6 B:Xyh500 1.97 Mg C4 B:Xyh500 4.39 Mg OH4 B:Xyh500 4.45 Mg O B:Hoh1755 2.25 Mg O B:Hoh1758 4.97 interactive model: Magnesium binding site 3 out of 4 in 1ec9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1ec9. 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: Xyh501, C: Hoh1564, C: Hoh1856, conact list: Atom Atom Distance (A) Mg OH C:Tyr150 5.00 Mg CE C:Lys205 4.74 Mg NZ C:Lys205 3.67 Mg NZ C:Lys207 3.88 Mg CB C:Asp235 4.37 Mg OD2 C:Asp235 3.55 Mg OD1 C:Asp235 2.18 Mg CG C:Asp235 3.11 Mg ND2 C:Asn237 4.02 Mg OD1 C:Asn237 4.92 Mg CG C:Asn237 4.77 Mg OE1 C:Glu260 4.12 Mg OE2 C:Glu260 1.98 Mg CD C:Glu260 3.19 Mg CG C:Glu260 3.81 Mg OD2 C:Asp261 4.21 Mg N C:Asn289 4.92 Mg CB C:Asn289 4.29 Mg ND2 C:Asn289 3.40 Mg OD1 C:Asn289 1.94 Mg CG C:Asn289 2.96 Mg CD1 C:Leu311 4.88 Mg CD2 C:His339 4.37 Mg N6 C:Xyh501 3.06 Mg C5 C:Xyh501 3.04 Mg OH5 C:Xyh501 2.20 Mg OH6 C:Xyh501 2.27 Mg C4 C:Xyh501 4.53 Mg OH4 C:Xyh501 4.24 Mg O C:Hoh1564 4.91 Mg O C:Hoh1856 2.02 interactive model: Magnesium binding site 4 out of 4 in 1ec9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1ec9. 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: His339, D: Xyh502, D: Hoh1066, D: Hoh1757, conact list: Atom Atom Distance (A) Mg OH D:Tyr150 4.86 Mg CE D:Lys205 4.45 Mg NZ D:Lys205 3.66 Mg NZ D:Lys207 3.79 Mg CB D:Asp235 4.36 Mg OD2 D:Asp235 3.65 Mg OD1 D:Asp235 2.09 Mg CG D:Asp235 3.12 Mg ND2 D:Asn237 4.03 Mg OD1 D:Asn237 4.92 Mg CG D:Asn237 4.79 Mg OE1 D:Glu260 4.12 Mg OE2 D:Glu260 2.14 Mg CD D:Glu260 3.24 Mg CG D:Glu260 3.82 Mg OD2 D:Asp261 4.46 Mg CB D:Asn289 4.35 Mg ND2 D:Asn289 3.44 Mg OD1 D:Asn289 1.94 Mg CG D:Asn289 3.00 Mg CD2 D:His339 4.35 Mg N6 D:Xyh502 2.85 Mg C5 D:Xyh502 2.88 Mg OH5 D:Xyh502 2.20 Mg OH6 D:Xyh502 2.05 Mg C4 D:Xyh502 4.39 Mg OH4 D:Xyh502 4.51 Mg O D:Hoh1066 4.74 Mg O D:Hoh1757 2.06 interactive model: