Magnesium in the structure of Crystal Structure of Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex With Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate (pdb 3n0g)

The binding sites of Magnesium atom in the structure of Crystal Structure of Isoprene Synthase From Grey Poplar Leaves (Populus X Canescens) in Complex With Three MG2+ Ions and Dimethylallyl-S-Thiolodiphosphate (pdb code 3n0g). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3n0g structure was solved by M.KOKSAL, D.W.CHRISTIANSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 46.4-2.8 Space group P43212 a (A) 155.014 b (A) 155.014 c (A) 143.744 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.8 Rfree (%) 24.6 Magnesium Binding Sites: Magnesium binding site 1 out of 6 in 3n0g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3n0g. 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: Asp345, A: Tyr348, A: Asp349, A: Phe420, A: Glu423, A: Dst601, A: Mg623, conact list: Atom Atom Distance (A) Mg O A:Asp345 3.50 Mg CB A:Asp345 4.39 Mg OD2 A:Asp345 4.14 Mg C A:Asp345 4.22 Mg OD1 A:Asp345 2.41 Mg CG A:Asp345 3.45 Mg CA A:Asp345 4.27 Mg CB A:Tyr348 4.44 Mg N A:Asp349 4.40 Mg CB A:Asp349 3.90 Mg OD2 A:Asp349 3.84 Mg OD1 A:Asp349 4.70 Mg CG A:Asp349 3.97 Mg CA A:Asp349 4.79 Mg CB A:Phe420 4.78 Mg CD1 A:Phe420 3.29 Mg CZ A:Phe420 4.61 Mg CE1 A:Phe420 3.52 Mg CG A:Phe420 4.27 Mg CA A:Phe420 4.95 Mg OE2 A:Glu423 3.27 Mg CD A:Glu423 4.53 Mg O5 A:Dst601 4.24 Mg P1 A:Dst601 3.04 Mg O2 A:Dst601 3.93 Mg O4 A:Dst601 2.29 Mg O6 A:Dst601 2.66 Mg MG A:Mg623 4.59 interactive model: Magnesium binding site 2 out of 6 in 3n0g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3n0g. 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: Tyr438, A: Arg486, A: Asp490, A: Ser493, A: Glu497, A: Ala504, A: Dst601, A: Hoh733, conact list: Atom Atom Distance (A) Mg OH A:Tyr438 4.65 Mg NH1 A:Arg486 4.20 Mg OD1 A:Asp490 4.10 Mg CG A:Asp490 4.79 Mg OG A:Ser493 4.68 Mg OE1 A:Glu497 4.12 Mg OE2 A:Glu497 3.28 Mg CD A:Glu497 4.11 Mg O A:Ala504 3.55 Mg C A:Ala504 4.75 Mg O5 A:Dst601 3.36 Mg P1 A:Dst601 4.49 Mg O8 A:Dst601 2.61 Mg P3 A:Dst601 3.88 Mg O2 A:Dst601 4.53 Mg O7 A:Dst601 4.04 Mg O A:Hoh733 3.46 interactive model: Magnesium binding site 3 out of 6 in 3n0g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3n0g. 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: Arg308, A: Asp345, A: Asp346, A: Asp349, A: Dst601, A: Mg621, conact list: Atom Atom Distance (A) Mg NH2 A:Arg308 4.65 Mg CB A:Asp345 5.00 Mg OD2 A:Asp345 2.67 Mg OD1 A:Asp345 3.73 Mg CG A:Asp345 3.58 Mg OD1 A:Asp346 4.65 Mg CB A:Asp349 4.97 Mg OD2 A:Asp349 3.68 Mg OD1 A:Asp349 3.26 Mg CG A:Asp349 3.72 Mg O5 A:Dst601 4.41 Mg S9 A:Dst601 3.32 Mg P1 A:Dst601 3.41 Mg O8 A:Dst601 3.36 Mg P3 A:Dst601 3.09 Mg O2 A:Dst601 2.37 Mg C10 A:Dst601 3.81 Mg O7 A:Dst601 4.51 Mg O4 A:Dst601 3.26 Mg O6 A:Dst601 4.52 Mg MG A:Mg621 4.59 interactive model: Magnesium binding site 4 out of 6 in 3n0g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3n0g. 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: Asp345, B: Tyr348, B: Asp349, B: Phe420, B: Glu423, B: Dst612, B: Mg633, conact list: Atom Atom Distance (A) Mg O B:Asp345 3.61 Mg CB B:Asp345 4.36 Mg OD2 B:Asp345 4.17 Mg C B:Asp345 4.31 Mg OD1 B:Asp345 2.31 Mg CG B:Asp345 3.43 Mg CA B:Asp345 4.36 Mg CB B:Tyr348 4.72 Mg N B:Asp349 4.61 Mg CB B:Asp349 3.89 Mg OD2 B:Asp349 4.82 Mg OD1 B:Asp349 3.08 Mg CG B:Asp349 3.77 Mg CA B:Asp349 4.88 Mg CD1 B:Phe420 3.48 Mg CZ B:Phe420 4.56 Mg CE1 B:Phe420 3.52 Mg CG B:Phe420 4.49 Mg OE2 B:Glu423 3.84 Mg O5 B:Dst612 4.28 Mg P1 B:Dst612 3.09 Mg O2 B:Dst612 4.01 Mg O4 B:Dst612 2.33 Mg O6 B:Dst612 2.68 Mg MG B:Mg633 3.79 interactive model: Magnesium binding site 5 out of 6 in 3n0g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 3n0g. 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: Arg486, B: Asn489, B: Asp490, B: Glu497, B: Ala504, B: Dst612, B: Mg633, B: Hoh610, B: Hoh727, conact list: Atom Atom Distance (A) Mg NH1 B:Arg486 3.95 Mg OD1 B:Asn489 4.55 Mg OD1 B:Asp490 4.38 Mg OE1 B:Glu497 4.96 Mg OE2 B:Glu497 4.30 Mg O B:Ala504 4.72 Mg O5 B:Dst612 2.61 Mg S9 B:Dst612 4.93 Mg P1 B:Dst612 3.61 Mg O8 B:Dst612 2.96 Mg P3 B:Dst612 3.11 Mg O2 B:Dst612 3.73 Mg O7 B:Dst612 2.39 Mg O4 B:Dst612 4.24 Mg MG B:Mg633 4.89 Mg O B:Hoh610 4.02 Mg O B:Hoh727 2.36 interactive model: Magnesium binding site 6 out of 6 in 3n0g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 3n0g. 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: Arg308, B: Asp345, B: Asp346, B: Asp349, B: Dst612, B: Mg631, B: Mg632, conact list: Atom Atom Distance (A) Mg NH2 B:Arg308 4.68 Mg O B:Asp345 4.69 Mg CB B:Asp345 4.67 Mg OD2 B:Asp345 2.57 Mg C B:Asp345 4.91 Mg OD1 B:Asp345 3.06 Mg CG B:Asp345 3.18 Mg OD1 B:Asp346 4.77 Mg CB B:Asp349 4.61 Mg OD2 B:Asp349 3.44 Mg OD1 B:Asp349 2.99 Mg CG B:Asp349 3.41 Mg O5 B:Dst612 4.27 Mg S9 B:Dst612 3.84 Mg P1 B:Dst612 3.20 Mg O8 B:Dst612 2.38 Mg P3 B:Dst612 3.04 Mg O2 B:Dst612 2.78 Mg C10 B:Dst612 3.83 Mg O7 B:Dst612 4.44 Mg O4 B:Dst612 2.45 Mg O6 B:Dst612 4.28 Mg MG B:Mg631 3.79 Mg MG B:Mg632 4.89 interactive model: