Magnesium in the structure of T. Brucei Farnesyl Diphosphate Synthase Complexed With Bisphosphonate Bph-461 and Isopentyl Diphosphate (pdb 3dyf)

The binding sites of Magnesium atom in the structure of T. Brucei Farnesyl Diphosphate Synthase Complexed With Bisphosphonate Bph-461 and Isopentyl Diphosphate (pdb code 3dyf). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3dyf structure was solved by R.CAO, Y.GAO, H.ROBINSON, A.GODDARD, E.OLDFIELD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.5-2.6 Space group C121 a (A) 133.939 b (A) 117.898 c (A) 63.274 alpha (°) 90.00 beta (°) 111.27 gamma (°) 90.00 Rfactor (%) 20.1 Rfree (%) 26.8 Magnesium Binding Sites: Magnesium binding site 1 out of 6 in 3dyf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3dyf. 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: Thr272, A: Mg3003, A: Mg3004, A: Ni93001, A: Hoh5001, A: Hoh5002, A: Hoh5003, A: Hoh5014, A: Hoh5027, A: Hoh5048, A: Hoh5143, A: Hoh5225, conact list: Atom Atom Distance (A) Mg O A:Asp103 4.21 Mg CB A:Asp103 4.41 Mg OD2 A:Asp103 2.22 Mg C A:Asp103 4.48 Mg OD1 A:Asp103 3.50 Mg CG A:Asp103 3.15 Mg N A:Asp104 4.82 Mg OD1 A:Asp104 3.94 Mg CA A:Asp104 4.91 Mg CB A:Asp107 3.62 Mg OD2 A:Asp107 2.15 Mg OD1 A:Asp107 4.30 Mg CG A:Asp107 3.20 Mg CB A:Ser109 4.98 Mg OG A:Ser109 3.76 Mg NH2 A:Arg112 4.03 Mg OG1 A:Thr272 4.99 Mg MG A:Mg3003 4.91 Mg MG A:Mg3004 4.03 Mg O5 A:Ni93001 4.64 Mg P2 A:Ni93001 3.29 Mg P1 A:Ni93001 3.55 Mg C1 A:Ni93001 3.86 Mg O1 A:Ni93001 3.26 Mg O3 A:Ni93001 2.43 Mg C2 A:Ni93001 4.13 Mg O7 A:Ni93001 2.39 Mg O4 A:Ni93001 4.80 Mg O6 A:Ni93001 4.17 Mg O A:Hoh5001 4.06 Mg O A:Hoh5002 4.95 Mg O A:Hoh5003 4.19 Mg O A:Hoh5014 4.61 Mg O A:Hoh5027 4.95 Mg O A:Hoh5048 4.74 Mg O A:Hoh5143 3.49 Mg O A:Hoh5225 2.03 interactive model: Magnesium binding site 2 out of 6 in 3dyf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3dyf. 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: Gln252, A: Asp255, A: Asp259, A: Lys269, A: Asp273, A: Mg3002, A: Ni93001, A: Hoh5001, A: Hoh5060, A: Hoh5143, A: Hoh5225, conact list: Atom Atom Distance (A) Mg OE1 A:Gln252 4.95 Mg O A:Asp255 4.13 Mg CB A:Asp255 4.49 Mg OD2 A:Asp255 2.40 Mg C A:Asp255 4.51 Mg OD1 A:Asp255 3.49 Mg CG A:Asp255 3.22 Mg CB A:Asp259 4.14 Mg OD2 A:Asp259 4.91 Mg OD1 A:Asp259 3.77 Mg CG A:Asp259 4.10 Mg CE A:Lys269 4.83 Mg NZ A:Lys269 4.75 Mg OD2 A:Asp273 4.37 Mg OD1 A:Asp273 4.57 Mg CG A:Asp273 4.88 Mg MG A:Mg3002 4.91 Mg O5 A:Ni93001 2.75 Mg P2 A:Ni93001 3.04 Mg P1 A:Ni93001 3.60 Mg C1 A:Ni93001 3.61 Mg O1 A:Ni93001 4.53 Mg O3 A:Ni93001 2.66 Mg O2 A:Ni93001 3.61 Mg O7 A:Ni93001 4.41 Mg O4 A:Ni93001 4.83 Mg O6 A:Ni93001 2.55 Mg O A:Hoh5001 2.40 Mg O A:Hoh5060 4.41 Mg O A:Hoh5143 4.44 Mg O A:Hoh5225 4.17 interactive model: Magnesium binding site 3 out of 6 in 3dyf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3dyf. 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: Gln172, A: Asp175, A: Lys212, A: Lys278, A: Mg3002, A: Ni93001, A: Hoh5002, A: Hoh5003, A: Hoh5060, A: Hoh5225, conact list: Atom Atom Distance (A) Mg CB A:Asp103 4.68 Mg OD2 A:Asp103 3.63 Mg OD1 A:Asp103 2.42 Mg CG A:Asp103 3.36 Mg OD2 A:Asp107 3.00 Mg OD1 A:Asp107 3.59 Mg CG A:Asp107 3.69 Mg NE2 A:Gln172 4.01 Mg OE1 A:Gln172 3.92 Mg CD A:Gln172 4.40 Mg CB A:Asp175 4.90 Mg OD2 A:Asp175 3.47 Mg OD1 A:Asp175 4.08 Mg CG A:Asp175 3.91 Mg NZ A:Lys212 4.08 Mg NZ A:Lys278 4.40 Mg MG A:Mg3002 4.03 Mg N A:Ni93001 4.31 Mg P1 A:Ni93001 2.85 Mg C1 A:Ni93001 4.29 Mg C2 A:Ni93001 4.42 Mg C5 A:Ni93001 4.88 Mg C7 A:Ni93001 4.84 Mg C3 A:Ni93001 4.29 Mg O7 A:Ni93001 2.10 Mg O4 A:Ni93001 2.57 Mg O6 A:Ni93001 3.84 Mg O A:Hoh5002 1.76 Mg O A:Hoh5003 2.13 Mg O A:Hoh5060 4.14 Mg O A:Hoh5225 4.35 interactive model: Magnesium binding site 4 out of 6 in 3dyf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3dyf. 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: Asp103, B: Asp104, B: Asp107, B: Ser109, B: Arg112, B: Mg4003, B: Mg4004, B: Ni94001, B: Hoh5015, B: Hoh5067, B: Hoh5116, B: Hoh5117, B: Hoh5122, B: Hoh5161, conact list: Atom Atom Distance (A) Mg O B:Asp103 4.46 Mg CB B:Asp103 4.47 Mg OD2 B:Asp103 3.40 Mg C B:Asp103 4.67 Mg OD1 B:Asp103 2.09 Mg CG B:Asp103 3.09 Mg N B:Asp104 4.98 Mg OD1 B:Asp104 4.50 Mg CB B:Asp107 3.56 Mg OD2 B:Asp107 2.17 Mg OD1 B:Asp107 4.32 Mg CG B:Asp107 3.20 Mg OG B:Ser109 3.91 Mg NH2 B:Arg112 4.47 Mg MG B:Mg4003 4.57 Mg MG B:Mg4004 3.86 Mg O5 B:Ni94001 4.36 Mg P2 B:Ni94001 3.03 Mg P1 B:Ni94001 3.37 Mg C1 B:Ni94001 3.68 Mg O1 B:Ni94001 3.10 Mg O3 B:Ni94001 2.10 Mg C2 B:Ni94001 4.06 Mg O7 B:Ni94001 2.31 Mg O4 B:Ni94001 4.68 Mg O6 B:Ni94001 3.91 Mg O B:Hoh5015 4.51 Mg O B:Hoh5067 4.90 Mg O B:Hoh5116 3.54 Mg O B:Hoh5117 4.92 Mg O B:Hoh5122 4.44 Mg O B:Hoh5161 4.01 interactive model: Magnesium binding site 5 out of 6 in 3dyf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 3dyf. 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: Gln252, B: Asp255, B: Asp256, B: Asp259, B: Lys269, B: Asp273, B: Mg4002, B: Ni94001, B: Hoh5116, B: Hoh5117, B: Hoh5161, B: Hoh5264, conact list: Atom Atom Distance (A) Mg NE2 B:Gln252 4.48 Mg O B:Asp255 4.40 Mg CB B:Asp255 4.50 Mg OD2 B:Asp255 2.39 Mg C B:Asp255 4.72 Mg OD1 B:Asp255 3.11 Mg CG B:Asp255 3.08 Mg OD1 B:Asp256 4.73 Mg CB B:Asp259 4.69 Mg OD1 B:Asp259 4.03 Mg CG B:Asp259 4.62 Mg CE B:Lys269 4.83 Mg NZ B:Lys269 4.60 Mg OD2 B:Asp273 4.36 Mg OD1 B:Asp273 4.66 Mg CG B:Asp273 4.95 Mg MG B:Mg4002 4.57 Mg O5 B:Ni94001 2.75 Mg P2 B:Ni94001 2.95 Mg P1 B:Ni94001 3.23 Mg C1 B:Ni94001 3.29 Mg O1 B:Ni94001 4.47 Mg O3 B:Ni94001 2.69 Mg C2 B:Ni94001 4.83 Mg O2 B:Ni94001 3.24 Mg O7 B:Ni94001 4.16 Mg O4 B:Ni94001 4.38 Mg O6 B:Ni94001 2.16 Mg O B:Hoh5116 4.46 Mg O B:Hoh5117 4.27 Mg O B:Hoh5161 2.40 Mg O B:Hoh5264 2.19 interactive model: Magnesium binding site 6 out of 6 in 3dyf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 3dyf. 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: Asp103, B: Asp107, B: Gln172, B: Asp175, B: Lys212, B: Lys278, B: Mg4002, B: Ni94001, B: Hoh5004, B: Hoh5117, B: Hoh5122, conact list: Atom Atom Distance (A) Mg CB B:Asp103 4.84 Mg OD2 B:Asp103 2.46 Mg OD1 B:Asp103 3.96 Mg CG B:Asp103 3.56 Mg CB B:Asp107 4.50 Mg OD2 B:Asp107 2.40 Mg OD1 B:Asp107 2.95 Mg CG B:Asp107 3.02 Mg NE2 B:Gln172 4.78 Mg OE1 B:Gln172 4.77 Mg CB B:Asp175 4.92 Mg OD2 B:Asp175 3.79 Mg OD1 B:Asp175 3.23 Mg CG B:Asp175 3.74 Mg NZ B:Lys212 4.62 Mg CE B:Lys278 4.45 Mg NZ B:Lys278 4.44 Mg MG B:Mg4002 3.86 Mg P1 B:Ni94001 3.32 Mg C1 B:Ni94001 4.80 Mg O3 B:Ni94001 5.00 Mg O7 B:Ni94001 2.25 Mg O4 B:Ni94001 3.30 Mg O6 B:Ni94001 4.13 Mg O B:Hoh5004 2.27 Mg O B:Hoh5117 3.72 Mg O B:Hoh5122 4.80 interactive model: