Magnesium in the structure of Human Farnesyl Diphosphate Synthase Complexed With Mg and Minodronate (pdb 3b7l)

The binding sites of Magnesium atom in the structure of Human Farnesyl Diphosphate Synthase Complexed With Mg and Minodronate (pdb code 3b7l). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3b7l structure was solved by E.S.PILKA, J.E.DUNFORD, K.GUO, A.C.W.PIKE, K.L.KAVANAGH, F.VON DELFT, F.H.EBETINO, C.H.ARROWSMITH, A.M.EDWARDS, R.G.G.RUSSELL, U.OPPERMANN, STRUCTURAL GENOMICS CONSORTIUM (SGC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.2-1.9 Space group P41212 a (A) 110.922 b (A) 110.922 c (A) 67.308 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.9 Rfree (%) 20.2 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 3b7l Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3b7l. 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: Asp103, A: Asp104, A: Asp107, A: Ser109, A: Arg112, A: Mg908, A: Mg909, A: Mg910, A: M0n901, A: Hoh1008, A: Hoh1059, A: Hoh1128, A: Hoh1131, A: Hoh1132, A: Hoh1134, A: Hoh1135, A: Hoh1136, conact list: Atom Atom Distance (A) Mg O A:Asp103 4.41 Mg CB A:Asp103 4.48 Mg OD2 A:Asp103 2.18 Mg C A:Asp103 4.69 Mg OD1 A:Asp103 3.37 Mg CG A:Asp103 3.11 Mg OD1 A:Asp104 4.65 Mg CB A:Asp107 3.71 Mg OD2 A:Asp107 2.28 Mg OD1 A:Asp107 4.38 Mg CG A:Asp107 3.30 Mg OG A:Ser109 4.31 Mg NH2 A:Arg112 4.20 Mg MG A:Mg908 4.89 Mg MG A:Mg909 3.20 Mg MG A:Mg910 4.38 Mg C9 A:M0n901 3.74 Mg O5 A:M0n901 4.01 Mg P2 A:M0n901 3.34 Mg P1 A:M0n901 3.34 Mg O1 A:M0n901 3.86 Mg O3 A:M0n901 2.11 Mg C8 A:M0n901 4.18 Mg O2 A:M0n901 4.60 Mg O4 A:M0n901 2.08 Mg O6 A:M0n901 4.51 Mg O A:Hoh1008 4.80 Mg O A:Hoh1059 3.80 Mg O A:Hoh1128 4.93 Mg O A:Hoh1131 2.06 Mg O A:Hoh1132 4.27 Mg O A:Hoh1134 4.24 Mg O A:Hoh1135 4.76 Mg O A:Hoh1136 2.14 interactive model: Magnesium binding site 2 out of 4 in 3b7l Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3b7l. 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: Gln240, A: Asp243, A: Asp244, A: Asp247, A: Lys257, A: Asp261, A: Mg907, A: M0n901, A: Hoh937, A: Hoh1059, A: Hoh1084, A: Hoh1129, A: Hoh1130, A: Hoh1131, A: Hoh1132, conact list: Atom Atom Distance (A) Mg NE2 A:Gln240 4.23 Mg O A:Asp243 4.17 Mg CB A:Asp243 4.37 Mg OD2 A:Asp243 2.19 Mg C A:Asp243 4.45 Mg OD1 A:Asp243 3.54 Mg CG A:Asp243 3.14 Mg N A:Asp244 4.82 Mg OD1 A:Asp244 4.36 Mg CB A:Asp247 4.64 Mg OD1 A:Asp247 4.03 Mg CG A:Asp247 4.59 Mg CE A:Lys257 4.72 Mg NZ A:Lys257 4.63 Mg OD2 A:Asp261 4.21 Mg OD1 A:Asp261 4.24 Mg CG A:Asp261 4.66 Mg MG A:Mg907 4.89 Mg C9 A:M0n901 3.56 Mg O5 A:M0n901 2.00 Mg P2 A:M0n901 3.30 Mg P1 A:M0n901 3.33 Mg O1 A:M0n901 2.08 Mg O3 A:M0n901 4.26 Mg O A:M0n901 3.49 Mg O2 A:M0n901 4.38 Mg O4 A:M0n901 4.10 Mg O6 A:M0n901 4.38 Mg O A:Hoh937 3.99 Mg O A:Hoh1059 4.71 Mg O A:Hoh1084 4.08 Mg O A:Hoh1129 2.15 Mg O A:Hoh1130 2.30 Mg O A:Hoh1131 4.12 Mg O A:Hoh1132 2.17 interactive model: Magnesium binding site 3 out of 4 in 3b7l Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3b7l. 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: Asp103, A: Asp107, A: Gln171, A: Asp174, A: Lys200, A: Lys266, A: Mg907, A: Mg910, A: M0n901, A: Hoh937, A: Hoh1128, A: Hoh1131, A: Hoh1134, A: Hoh1135, A: Hoh1136, conact list: Atom Atom Distance (A) Mg CB A:Asp103 4.53 Mg OD2 A:Asp103 3.50 Mg OD1 A:Asp103 2.15 Mg CG A:Asp103 3.16 Mg CB A:Asp107 4.52 Mg OD2 A:Asp107 2.18 Mg OD1 A:Asp107 3.27 Mg CG A:Asp107 3.10 Mg NE2 A:Gln171 4.09 Mg OE1 A:Gln171 4.24 Mg CD A:Gln171 4.62 Mg OD2 A:Asp174 4.24 Mg OD1 A:Asp174 3.85 Mg CG A:Asp174 4.31 Mg NZ A:Lys200 4.67 Mg CE A:Lys266 4.66 Mg NZ A:Lys266 4.60 Mg MG A:Mg907 3.20 Mg MG A:Mg910 4.97 Mg C9 A:M0n901 4.59 Mg N2 A:M0n901 4.93 Mg P1 A:M0n901 3.28 Mg O1 A:M0n901 4.21 Mg O3 A:M0n901 2.11 Mg C8 A:M0n901 4.68 Mg C2 A:M0n901 4.84 Mg O2 A:M0n901 3.46 Mg C3 A:M0n901 4.96 Mg O4 A:M0n901 4.76 Mg O A:Hoh937 4.26 Mg O A:Hoh1128 2.14 Mg O A:Hoh1131 4.23 Mg O A:Hoh1134 2.02 Mg O A:Hoh1135 2.08 Mg O A:Hoh1136 4.97 interactive model: Magnesium binding site 4 out of 4 in 3b7l Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3b7l. 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: Asp107, A: Thr260, A: Asp261, A: Asp264, A: Lys266, A: Mg907, A: Mg909, A: M0n901, A: Hoh937, A: Hoh1008, A: Hoh1131, A: Hoh1132, A: Hoh1134, conact list: Atom Atom Distance (A) Mg O A:Asp107 4.72 Mg CB A:Asp107 3.87 Mg OD2 A:Asp107 3.79 Mg OD1 A:Asp107 4.48 Mg CG A:Asp107 3.85 Mg CA A:Asp107 4.83 Mg O A:Thr260 3.95 Mg N A:Thr260 4.72 Mg CB A:Thr260 3.89 Mg OG1 A:Thr260 2.79 Mg C A:Thr260 3.80 Mg CA A:Thr260 4.36 Mg N A:Asp261 3.81 Mg CB A:Asp261 4.46 Mg OD2 A:Asp261 4.94 Mg OD1 A:Asp261 2.74 Mg CG A:Asp261 3.90 Mg CA A:Asp261 3.83 Mg CB A:Asp264 4.03 Mg OD2 A:Asp264 3.15 Mg CG A:Asp264 3.94 Mg CB A:Lys266 4.96 Mg CE A:Lys266 3.64 Mg CD A:Lys266 4.32 Mg CG A:Lys266 3.79 Mg NZ A:Lys266 4.82 Mg MG A:Mg907 4.38 Mg MG A:Mg909 4.97 Mg O1 A:M0n901 4.93 Mg O3 A:M0n901 4.82 Mg O A:Hoh937 3.77 Mg O A:Hoh1008 4.59 Mg O A:Hoh1131 2.77 Mg O A:Hoh1132 3.72 Mg O A:Hoh1134 4.01 interactive model: