Magnesium in the structure of Crystal Structure of Geranyl Diphosphate C-Methyltransferase From Streptomyces Coelicolor A3(2) in Complex With MG2+, Geranyl Diphosphate, and S-Adenosyl-L-Homocysteine (pdb 3vc2)

The binding sites of Magnesium atom in the structure of Crystal Structure of Geranyl Diphosphate C-Methyltransferase From Streptomyces Coelicolor A3(2) in Complex With MG2+, Geranyl Diphosphate, and S-Adenosyl-L-Homocysteine (pdb code 3vc2). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3vc2 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) 48.9-2.0 Space group P1211 a (A) 98.128 b (A) 103.252 c (A) 204.132 alpha (°) 90.00 beta (°) 99.05 gamma (°) 90.00 Rfactor (%) 18.1 Rfree (%) 22.2 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 3vc2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3vc2. 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: Val36, A: Asn37, A: His48, A: His49, A: His50, A: Tyr51, A: Glu81, A: Tyr256, A: Arg260, A: Gpp303, A: Hoh401, A: Hoh402, A: Hoh403, conact list: Atom Atom Distance (A) Mg O A:Val36 4.85 Mg CG1 A:Val36 4.98 Mg CB A:Asn37 4.69 Mg ND2 A:Asn37 4.37 Mg OD1 A:Asn37 2.47 Mg CG A:Asn37 3.63 Mg CA A:Asn37 4.84 Mg O A:His48 4.61 Mg ND1 A:His49 4.84 Mg C A:His49 4.55 Mg CA A:His49 4.40 Mg O A:His50 4.01 Mg N A:His50 4.32 Mg C A:His50 4.65 Mg CA A:His50 4.97 Mg CD1 A:Tyr51 4.66 Mg CE1 A:Tyr51 4.41 Mg OE1 A:Glu81 4.46 Mg OE2 A:Glu81 3.66 Mg CD A:Glu81 4.38 Mg OH A:Tyr256 4.40 Mg NH1 A:Arg260 3.87 Mg O3B A:Gpp303 4.86 Mg O1 A:Gpp303 4.20 Mg PA A:Gpp303 3.38 Mg O2A A:Gpp303 4.65 Mg O1B A:Gpp303 2.38 Mg PB A:Gpp303 3.48 Mg O2B A:Gpp303 4.04 Mg O3A A:Gpp303 3.82 Mg O1A A:Gpp303 2.21 Mg O A:Hoh401 2.47 Mg O A:Hoh402 2.45 Mg O A:Hoh403 2.30 interactive model: Magnesium binding site 2 out of 4 in 3vc2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3vc2. 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: Val36, D: Asn37, D: His48, D: His49, D: His50, D: Tyr51, D: Glu81, D: Tyr256, D: Arg260, D: Gpp303, D: Hoh401, D: Hoh402, D: Hoh403, conact list: Atom Atom Distance (A) Mg O D:Val36 4.13 Mg C D:Val36 4.76 Mg CG1 D:Val36 4.91 Mg N D:Asn37 4.92 Mg CB D:Asn37 4.45 Mg ND2 D:Asn37 4.27 Mg OD1 D:Asn37 2.24 Mg CG D:Asn37 3.45 Mg CA D:Asn37 4.56 Mg O D:His48 4.23 Mg C D:His48 4.89 Mg N D:His49 4.99 Mg ND1 D:His49 4.88 Mg C D:His49 4.56 Mg CA D:His49 4.23 Mg O D:His50 4.12 Mg N D:His50 4.29 Mg C D:His50 4.86 Mg CD1 D:Tyr51 4.96 Mg CE1 D:Tyr51 4.72 Mg OE1 D:Glu81 4.10 Mg OE2 D:Glu81 3.54 Mg CD D:Glu81 4.19 Mg OH D:Tyr256 4.55 Mg NH1 D:Arg260 4.15 Mg O3B D:Gpp303 4.99 Mg O1 D:Gpp303 4.31 Mg PA D:Gpp303 3.52 Mg O2A D:Gpp303 4.70 Mg O1B D:Gpp303 2.45 Mg PB D:Gpp303 3.64 Mg O2B D:Gpp303 4.21 Mg O3A D:Gpp303 4.05 Mg O1A D:Gpp303 2.21 Mg O D:Hoh401 2.39 Mg O D:Hoh402 2.22 Mg O D:Hoh403 2.33 interactive model: Magnesium binding site 3 out of 4 in 3vc2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3vc2. 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: H: Val36, H: Asn37, H: His48, H: His49, H: His50, H: Tyr51, H: Glu81, H: Tyr256, H: Arg260, H: Gpp303, H: Hoh401, H: Hoh402, H: Hoh403, conact list: Atom Atom Distance (A) Mg O H:Val36 4.11 Mg CG2 H:Val36 4.84 Mg C H:Val36 4.61 Mg CG1 H:Val36 4.50 Mg N H:Asn37 4.82 Mg CB H:Asn37 4.50 Mg ND2 H:Asn37 3.93 Mg OD1 H:Asn37 2.22 Mg CG H:Asn37 3.33 Mg CA H:Asn37 4.57 Mg O H:His48 4.40 Mg ND1 H:His49 4.80 Mg C H:His49 4.55 Mg CA H:His49 4.27 Mg O H:His50 4.31 Mg N H:His50 4.32 Mg C H:His50 4.94 Mg CD1 H:Tyr51 4.99 Mg CE1 H:Tyr51 4.66 Mg OE1 H:Glu81 4.53 Mg OE2 H:Glu81 3.96 Mg CD H:Glu81 4.59 Mg OH H:Tyr256 4.70 Mg NH1 H:Arg260 4.23 Mg O3B H:Gpp303 2.42 Mg O1 H:Gpp303 4.62 Mg PA H:Gpp303 3.31 Mg O2A H:Gpp303 2.16 Mg O1B H:Gpp303 4.85 Mg PB H:Gpp303 3.37 Mg O2B H:Gpp303 3.68 Mg O3A H:Gpp303 3.70 Mg O1A H:Gpp303 4.04 Mg O H:Hoh401 2.47 Mg O H:Hoh402 2.34 Mg O H:Hoh403 2.34 interactive model: Magnesium binding site 4 out of 4 in 3vc2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3vc2. 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: J: Val36, J: Asn37, J: His48, J: His49, J: His50, J: Tyr51, J: Glu81, J: Tyr256, J: Arg260, J: Gpp303, J: Hoh401, J: Hoh402, J: Hoh403, conact list: Atom Atom Distance (A) Mg O J:Val36 4.13 Mg CG2 J:Val36 4.99 Mg C J:Val36 4.61 Mg CG1 J:Val36 4.49 Mg N J:Asn37 4.79 Mg CB J:Asn37 4.53 Mg ND2 J:Asn37 4.23 Mg OD1 J:Asn37 2.27 Mg CG J:Asn37 3.47 Mg CA J:Asn37 4.54 Mg O J:His48 4.46 Mg C J:His49 4.73 Mg CA J:His49 4.46 Mg O J:His50 4.18 Mg N J:His50 4.43 Mg C J:His50 4.85 Mg CD1 J:Tyr51 4.88 Mg CE1 J:Tyr51 4.62 Mg OE1 J:Glu81 4.29 Mg OE2 J:Glu81 3.71 Mg CD J:Glu81 4.36 Mg OH J:Tyr256 4.55 Mg NH1 J:Arg260 4.05 Mg O3B J:Gpp303 4.79 Mg O1 J:Gpp303 4.54 Mg PA J:Gpp303 3.56 Mg O2A J:Gpp303 4.58 Mg O1B J:Gpp303 2.24 Mg PB J:Gpp303 3.46 Mg O2B J:Gpp303 4.10 Mg O3A J:Gpp303 3.93 Mg O1A J:Gpp303 2.29 Mg O J:Hoh401 2.31 Mg O J:Hoh402 2.36 Mg O J:Hoh403 2.26 interactive model: