Magnesium in the structure of Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp (pdb 2q80)

The binding sites of Magnesium atom in the structure of Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Bound to Ggpp (pdb code 2q80). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2q80 structure was solved by K.L.KAVANAGH, J.E.DUNFORD, G.BUNKOCZI, C.SMEE, F.VONDELFT, C.ARROWSMITH, J.WEIGELT, A.EDWARDS, M.SUNDSTROM, U.OPPERMANN, STRUCTURAL GENOMICSCONSORTIUM (SGC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 47.1-2.7 Space group P41212 a (A) 141.248 b (A) 141.248 c (A) 211.705 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.2 Rfree (%) 25.3 Magnesium Binding Sites: Magnesium binding site 1 out of 12 in 2q80 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2q80. 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: Asp64, A: Asp68, A: Gln126, A: Asp129, A: Lys151, A: Glu210, A: Lys212, A: Mg401, A: Grg500, conact list: Atom Atom Distance (A) Mg O A:Asp64 4.99 Mg CB A:Asp64 4.45 Mg OD2 A:Asp64 3.53 Mg OD1 A:Asp64 2.07 Mg CG A:Asp64 3.14 Mg CB A:Asp68 4.61 Mg OD2 A:Asp68 3.39 Mg OD1 A:Asp68 2.21 Mg CG A:Asp68 3.19 Mg NE2 A:Gln126 4.45 Mg OE1 A:Gln126 3.49 Mg CD A:Gln126 4.36 Mg OD2 A:Asp129 4.32 Mg OD1 A:Asp129 4.67 Mg CG A:Asp129 4.55 Mg NZ A:Lys151 4.27 Mg OE2 A:Glu210 4.25 Mg CE A:Lys212 4.61 Mg NZ A:Lys212 4.48 Mg MG A:Mg401 3.41 Mg C1 A:Grg500 4.05 Mg O1 A:Grg500 3.82 Mg PA A:Grg500 3.25 Mg O2A A:Grg500 3.59 Mg O2B A:Grg500 4.56 Mg O3A A:Grg500 4.52 Mg O1A A:Grg500 2.02 interactive model: Magnesium binding site 2 out of 12 in 2q80 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2q80. 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: Asp64, A: Asp65, A: Asp68, A: Ser70, A: Arg73, A: Lys202, A: Glu210, A: Mg400, A: Grg500, conact list: Atom Atom Distance (A) Mg O A:Asp64 4.32 Mg CB A:Asp64 4.45 Mg OD2 A:Asp64 2.14 Mg C A:Asp64 4.65 Mg OD1 A:Asp64 3.33 Mg CG A:Asp64 3.07 Mg OD1 A:Asp65 4.74 Mg CB A:Asp68 3.38 Mg OD2 A:Asp68 4.21 Mg OD1 A:Asp68 2.18 Mg CG A:Asp68 3.07 Mg CA A:Asp68 4.91 Mg OG A:Ser70 4.13 Mg NH1 A:Arg73 4.42 Mg CE A:Lys202 4.68 Mg NZ A:Lys202 3.64 Mg OE1 A:Glu210 3.81 Mg OE2 A:Glu210 4.40 Mg CD A:Glu210 4.47 Mg MG A:Mg400 3.41 Mg O3B A:Grg500 4.25 Mg C1 A:Grg500 4.74 Mg O1 A:Grg500 4.65 Mg PA A:Grg500 3.55 Mg O2A A:Grg500 4.51 Mg O1B A:Grg500 4.25 Mg PB A:Grg500 3.32 Mg O2B A:Grg500 1.89 Mg O3A A:Grg500 3.59 Mg O1A A:Grg500 2.29 interactive model: Magnesium binding site 3 out of 12 in 2q80 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2q80. 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: Asp64, B: Asp68, B: Gln126, B: Asp129, B: Lys151, B: Glu210, B: Lys212, B: Mg401, B: Grg500, conact list: Atom Atom Distance (A) Mg CB B:Asp64 4.55 Mg OD2 B:Asp64 3.46 Mg OD1 B:Asp64 2.15 Mg CG B:Asp64 3.15 Mg CB B:Asp68 4.47 Mg OD2 B:Asp68 3.25 Mg OD1 B:Asp68 2.14 Mg CG B:Asp68 3.05 Mg NE2 B:Gln126 4.26 Mg OE1 B:Gln126 3.68 Mg CD B:Gln126 4.34 Mg OD2 B:Asp129 3.38 Mg CG B:Asp129 4.49 Mg NZ B:Lys151 4.59 Mg OE2 B:Glu210 4.15 Mg NZ B:Lys212 4.55 Mg MG B:Mg401 3.50 Mg C1 B:Grg500 4.09 Mg O1 B:Grg500 4.10 Mg PA B:Grg500 3.38 Mg O2A B:Grg500 3.69 Mg O2B B:Grg500 4.54 Mg O3A B:Grg500 4.57 Mg O1A B:Grg500 2.13 interactive model: Magnesium binding site 4 out of 12 in 2q80 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 2q80. 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: Asp64, B: Asp65, B: Asp68, B: Ser70, B: Arg73, B: Lys202, B: Glu210, B: Lys212, B: Mg400, B: Grg500, conact list: Atom Atom Distance (A) Mg O B:Asp64 4.39 Mg CB B:Asp64 4.63 Mg OD2 B:Asp64 2.22 Mg C B:Asp64 4.81 Mg OD1 B:Asp64 3.59 Mg CG B:Asp64 3.25 Mg OD1 B:Asp65 4.95 Mg CB B:Asp68 3.26 Mg OD2 B:Asp68 4.25 Mg OD1 B:Asp68 2.19 Mg CG B:Asp68 3.07 Mg CA B:Asp68 4.79 Mg OG B:Ser70 4.05 Mg NH1 B:Arg73 4.64 Mg CE B:Lys202 4.68 Mg NZ B:Lys202 4.73 Mg OE1 B:Glu210 3.70 Mg OE2 B:Glu210 4.13 Mg CD B:Glu210 4.30 Mg NZ B:Lys212 4.98 Mg MG B:Mg400 3.50 Mg O3B B:Grg500 3.98 Mg C1 B:Grg500 4.97 Mg O1 B:Grg500 4.70 Mg PA B:Grg500 3.51 Mg O2A B:Grg500 4.45 Mg O1B B:Grg500 4.52 Mg PB B:Grg500 3.32 Mg O2B B:Grg500 2.13 Mg O3A B:Grg500 3.36 Mg O1A B:Grg500 2.36 interactive model: Magnesium binding site 5 out of 12 in 2q80 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 2q80. 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: Asp64, C: Asp68, C: Gln126, C: Asp129, C: Lys151, C: Glu210, C: Lys212, C: Mg401, C: Grg500, conact list: Atom Atom Distance (A) Mg CB C:Asp64 4.48 Mg OD2 C:Asp64 3.34 Mg OD1 C:Asp64 2.14 Mg CG C:Asp64 3.09 Mg CB C:Asp68 4.58 Mg OD2 C:Asp68 3.22 Mg OD1 C:Asp68 2.23 Mg CG C:Asp68 3.10 Mg NE2 C:Gln126 4.22 Mg OE1 C:Gln126 3.36 Mg CD C:Gln126 4.17 Mg CB C:Asp129 4.98 Mg OD2 C:Asp129 3.30 Mg CG C:Asp129 4.40 Mg NZ C:Lys151 4.29 Mg OE1 C:Glu210 4.98 Mg OE2 C:Glu210 4.01 Mg CD C:Glu210 4.94 Mg NZ C:Lys212 5.00 Mg MG C:Mg401 3.93 Mg C1 C:Grg500 4.08 Mg O1 C:Grg500 3.29 Mg PA C:Grg500 3.14 Mg O2A C:Grg500 3.64 Mg O2B C:Grg500 4.37 Mg O3A C:Grg500 4.54 Mg O1A C:Grg500 2.17 interactive model: Magnesium binding site 6 out of 12 in 2q80 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 2q80. 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: Asp64, C: Asp65, C: Asp68, C: Ser70, C: Arg73, C: Glu210, C: Mg400, C: Grg500, conact list: Atom Atom Distance (A) Mg O C:Asp64 3.93 Mg CB C:Asp64 4.19 Mg OD2 C:Asp64 2.09 Mg C C:Asp64 4.19 Mg OD1 C:Asp64 3.59 Mg CG C:Asp64 3.05 Mg CA C:Asp64 4.79 Mg N C:Asp65 4.57 Mg OD1 C:Asp65 3.99 Mg CA C:Asp65 4.68 Mg CB C:Asp68 3.02 Mg OD2 C:Asp68 4.08 Mg OD1 C:Asp68 2.20 Mg CG C:Asp68 2.90 Mg CA C:Asp68 4.54 Mg CB C:Ser70 4.97 Mg OG C:Ser70 4.07 Mg NH1 C:Arg73 4.13 Mg OE1 C:Glu210 3.76 Mg OE2 C:Glu210 4.61 Mg CD C:Glu210 4.55 Mg MG C:Mg400 3.93 Mg O3B C:Grg500 4.56 Mg PA C:Grg500 4.20 Mg O1B C:Grg500 4.50 Mg PB C:Grg500 3.74 Mg O2B C:Grg500 2.12 Mg O3A C:Grg500 4.37 Mg O1A C:Grg500 2.85 interactive model: Magnesium binding site 7 out of 12 in 2q80 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 2q80. 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: Asp64, D: Glu67, D: Asp68, D: Gln126, D: Asp129, D: Lys151, D: Glu210, D: Lys212, D: Mg401, D: Grg500, conact list: Atom Atom Distance (A) Mg CB D:Asp64 4.54 Mg OD2 D:Asp64 3.58 Mg OD1 D:Asp64 2.17 Mg CG D:Asp64 3.22 Mg OE1 D:Glu67 4.98 Mg CB D:Asp68 4.53 Mg OD2 D:Asp68 3.18 Mg OD1 D:Asp68 2.17 Mg CG D:Asp68 3.05 Mg NE2 D:Gln126 4.17 Mg OE1 D:Gln126 3.64 Mg CD D:Gln126 4.29 Mg CB D:Asp129 4.99 Mg OD2 D:Asp129 3.11 Mg CG D:Asp129 4.32 Mg NZ D:Lys151 4.19 Mg OE2 D:Glu210 4.22 Mg NZ D:Lys212 4.17 Mg MG D:Mg401 3.75 Mg C1 D:Grg500 4.27 Mg O1 D:Grg500 3.84 Mg PA D:Grg500 3.37 Mg O2A D:Grg500 3.66 Mg O2B D:Grg500 4.88 Mg O3A D:Grg500 4.79 Mg O1A D:Grg500 2.20 interactive model: Magnesium binding site 8 out of 12 in 2q80 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Magnesium in the PDB 2q80. 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: Asp64, D: Asp65, D: Asp68, D: Ser70, D: Arg73, D: Lys202, D: Glu210, D: Mg400, D: Grg500, conact list: Atom Atom Distance (A) Mg O D:Asp64 4.25 Mg CB D:Asp64 4.56 Mg OD2 D:Asp64 2.16 Mg C D:Asp64 4.65 Mg OD1 D:Asp64 3.62 Mg CG D:Asp64 3.24 Mg OD1 D:Asp65 4.68 Mg CB D:Asp68 3.20 Mg OD2 D:Asp68 4.17 Mg OD1 D:Asp68 2.15 Mg CG D:Asp68 2.98 Mg CA D:Asp68 4.73 Mg OG D:Ser70 3.78 Mg NH1 D:Arg73 4.33 Mg CE D:Lys202 4.41 Mg NZ D:Lys202 4.49 Mg OE1 D:Glu210 3.84 Mg OE2 D:Glu210 4.50 Mg CD D:Glu210 4.56 Mg MG D:Mg400 3.75 Mg O3B D:Grg500 4.32 Mg C1 D:Grg500 4.95 Mg O1 D:Grg500 4.80 Mg PA D:Grg500 3.65 Mg O2A D:Grg500 4.56 Mg O1B D:Grg500 4.58 Mg PB D:Grg500 3.55 Mg O2B D:Grg500 2.13 Mg O3A D:Grg500 3.85 Mg O1A D:Grg500 2.33 interactive model: Magnesium binding site 9 out of 12 in 2q80 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Magnesium in the PDB 2q80. 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: E: Asp64, E: Asp68, E: Gln126, E: Asp129, E: Lys151, E: Glu210, E: Lys212, E: Mg401, E: Grg500, conact list: Atom Atom Distance (A) Mg CB E:Asp64 4.58 Mg OD2 E:Asp64 3.74 Mg OD1 E:Asp64 2.18 Mg CG E:Asp64 3.29 Mg CB E:Asp68 4.49 Mg OD2 E:Asp68 3.28 Mg OD1 E:Asp68 2.21 Mg CG E:Asp68 3.09 Mg NE2 E:Gln126 4.38 Mg OE1 E:Gln126 4.03 Mg CD E:Gln126 4.64 Mg OD2 E:Asp129 3.78 Mg CG E:Asp129 4.75 Mg NZ E:Lys151 4.44 Mg OE1 E:Glu210 4.89 Mg OE2 E:Glu210 3.99 Mg CD E:Glu210 4.86 Mg CE E:Lys212 4.59 Mg MG E:Mg401 3.46 Mg C1 E:Grg500 4.18 Mg O1 E:Grg500 3.73 Mg PA E:Grg500 3.22 Mg O2A E:Grg500 3.57 Mg O2B E:Grg500 4.64 Mg O3A E:Grg500 4.64 Mg O1A E:Grg500 2.13 interactive model: Magnesium binding site 10 out of 12 in 2q80 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Magnesium in the PDB 2q80. 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: E: Asp64, E: Asp65, E: Asp68, E: Ser70, E: Arg73, E: Lys202, E: Glu210, E: Mg400, E: Grg500, conact list: Atom Atom Distance (A) Mg O E:Asp64 4.30 Mg CB E:Asp64 4.46 Mg OD2 E:Asp64 2.15 Mg C E:Asp64 4.59 Mg OD1 E:Asp64 3.28 Mg CG E:Asp64 3.05 Mg OD1 E:Asp65 4.59 Mg CB E:Asp68 3.13 Mg OD2 E:Asp68 4.06 Mg OD1 E:Asp68 2.07 Mg CG E:Asp68 2.89 Mg CA E:Asp68 4.67 Mg OG E:Ser70 4.07 Mg NH1 E:Arg73 4.56 Mg NZ E:Lys202 4.47 Mg OE1 E:Glu210 3.82 Mg OE2 E:Glu210 4.40 Mg CD E:Glu210 4.40 Mg MG E:Mg400 3.46 Mg O3B E:Grg500 4.63 Mg O1 E:Grg500 4.91 Mg PA E:Grg500 3.71 Mg O2A E:Grg500 4.53 Mg O1B E:Grg500 4.63 Mg PB E:Grg500 3.65 Mg O2B E:Grg500 2.18 Mg O3A E:Grg500 3.98 Mg O1A E:Grg500 2.36 interactive model: Magnesium binding site 11 out of 12 in 2q80 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Magnesium in the PDB 2q80. 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: F: Asp64, F: Glu67, F: Asp68, F: Gln126, F: Asp129, F: Lys151, F: Glu210, F: Mg401, F: Grg500, conact list: Atom Atom Distance (A) Mg O F:Asp64 4.83 Mg CB F:Asp64 4.39 Mg OD2 F:Asp64 3.90 Mg OD1 F:Asp64 2.14 Mg CG F:Asp64 3.28 Mg CA F:Asp64 4.98 Mg OE1 F:Glu67 4.90 Mg CB F:Asp68 4.56 Mg OD2 F:Asp68 3.11 Mg OD1 F:Asp68 2.21 Mg CG F:Asp68 3.05 Mg NE2 F:Gln126 3.93 Mg OE1 F:Gln126 3.57 Mg CD F:Gln126 4.13 Mg CB F:Asp129 4.94 Mg OD2 F:Asp129 3.24 Mg CG F:Asp129 4.36 Mg NZ F:Lys151 4.99 Mg OE2 F:Glu210 4.28 Mg MG F:Mg401 3.55 Mg C1 F:Grg500 4.28 Mg O1 F:Grg500 4.36 Mg PA F:Grg500 3.54 Mg O2A F:Grg500 3.89 Mg O3A F:Grg500 4.73 Mg O1A F:Grg500 2.19 interactive model: Magnesium binding site 12 out of 12 in 2q80 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Magnesium in the PDB 2q80. 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: F: Asp64, F: Asp65, F: Asp68, F: Ser70, F: Arg73, F: Lys202, F: Glu210, F: Mg400, F: Grg500, conact list: Atom Atom Distance (A) Mg O F:Asp64 4.01 Mg CB F:Asp64 4.35 Mg OD2 F:Asp64 2.12 Mg C F:Asp64 4.49 Mg OD1 F:Asp64 2.97 Mg CG F:Asp64 2.89 Mg CA F:Asp64 5.00 Mg OD1 F:Asp65 4.80 Mg CB F:Asp68 3.27 Mg OD2 F:Asp68 4.04 Mg OD1 F:Asp68 2.17 Mg CG F:Asp68 2.95 Mg CA F:Asp68 4.81 Mg OG F:Ser70 4.17 Mg NH1 F:Arg73 4.36 Mg NZ F:Lys202 3.96 Mg OE1 F:Glu210 4.07 Mg OE2 F:Glu210 4.27 Mg CD F:Glu210 4.52 Mg MG F:Mg400 3.55 Mg O3B F:Grg500 4.53 Mg C1 F:Grg500 4.76 Mg O1 F:Grg500 4.31 Mg PA F:Grg500 3.43 Mg O2A F:Grg500 4.62 Mg O1B F:Grg500 4.18 Mg PB F:Grg500 3.35 Mg O2B F:Grg500 2.19 Mg O3A F:Grg500 3.30 Mg O1A F:Grg500 2.26 interactive model: