Magnesium in the structure of Yeast Enolase Complexed With An Equilibrium Mixture of 2'- Phosphoglyceate and Phosphoenolpyruvate (pdb 1one)

The binding sites of Magnesium atom in the structure of Yeast Enolase Complexed With An Equilibrium Mixture of 2'- Phosphoglyceate and Phosphoenolpyruvate (pdb code 1one). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1one structure was solved by T.M.LARSEN, J.E.WEDEKIND, I.RAYMENT, G.H.REED, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 60.0-1.8 Space group C121 a (A) 121.900 b (A) 73.200 c (A) 93.900 alpha (°) 90.00 beta (°) 93.30 gamma (°) 90.00 Rfactor (%) 17.7 Rfree (%) n/a Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 1one Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1one. 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: Gln167, A: Glu168, A: Asp246, A: Glu295, A: Asp296, A: Asp320, A: Leu343, A: Lys345, A: Lys396, A: Mg439, A: Pep440, A: 2pg441, A: Hoh948, A: Hoh949, A: Hoh1091, conact list: Atom Atom Distance (A) Mg NE2 A:Gln167 4.23 Mg OE2 A:Glu168 4.60 Mg CB A:Asp246 4.24 Mg OD2 A:Asp246 2.04 Mg OD1 A:Asp246 3.12 Mg CG A:Asp246 2.91 Mg OE1 A:Glu295 3.83 Mg OE2 A:Glu295 1.88 Mg CD A:Glu295 3.06 Mg CG A:Glu295 3.90 Mg OD2 A:Asp296 3.99 Mg CG A:Asp296 4.83 Mg CB A:Asp320 3.47 Mg OD2 A:Asp320 2.07 Mg OD1 A:Asp320 4.13 Mg CG A:Asp320 3.11 Mg CD2 A:Leu343 4.16 Mg NZ A:Lys345 4.04 Mg CE A:Lys396 4.77 Mg NZ A:Lys396 3.73 Mg MG A:Mg439 4.19 Mg O2 A:Pep440 4.99 Mg C1 A:Pep440 2.71 Mg O1 A:Pep440 2.37 Mg O2' A:Pep440 2.41 Mg C2 A:Pep440 4.19 Mg O2 A:2pg441 2.32 Mg C1 A:2pg441 2.70 Mg O1 A:2pg441 2.42 Mg C2 A:2pg441 4.26 Mg O A:Hoh948 1.97 Mg O A:Hoh949 3.75 Mg O A:Hoh1091 4.08 interactive model: Magnesium binding site 2 out of 4 in 1one Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1one. 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: Ser39, A: Thr40, A: Gln167, A: Asp320, A: Asp321, A: Lys345, A: Arg374, A: Mg438, A: Pep440, A: 2pg441, A: Hoh948, A: Hoh949, A: Hoh1091, conact list: Atom Atom Distance (A) Mg O A:Ser39 2.10 Mg N A:Ser39 3.98 Mg CB A:Ser39 3.09 Mg OG A:Ser39 2.20 Mg C A:Ser39 3.10 Mg CA A:Ser39 3.57 Mg N A:Thr40 4.27 Mg CA A:Thr40 4.71 Mg NE2 A:Gln167 4.23 Mg OE1 A:Gln167 4.32 Mg CD A:Gln167 4.72 Mg OD2 A:Asp320 3.84 Mg CG A:Asp320 4.93 Mg OD2 A:Asp321 4.20 Mg OD1 A:Asp321 4.11 Mg CG A:Asp321 4.55 Mg NZ A:Lys345 3.86 Mg NH2 A:Arg374 4.08 Mg MG A:Mg438 4.19 Mg O2 A:Pep440 3.18 Mg P A:Pep440 3.16 Mg O3P A:Pep440 4.33 Mg C1 A:Pep440 3.11 Mg O1 A:Pep440 4.20 Mg O1P A:Pep440 2.05 Mg C3 A:Pep440 4.94 Mg O2' A:Pep440 2.20 Mg C2 A:Pep440 3.65 Mg O2P A:Pep440 3.84 Mg O2 A:2pg441 4.30 Mg P A:2pg441 3.19 Mg O3P A:2pg441 2.19 Mg C1 A:2pg441 3.19 Mg O1 A:2pg441 2.20 Mg O1P A:2pg441 3.22 Mg O4P A:2pg441 3.94 Mg C2 A:2pg441 3.52 Mg O2P A:2pg441 4.45 Mg O A:Hoh948 4.21 Mg O A:Hoh949 2.13 Mg O A:Hoh1091 2.08 interactive model: Magnesium binding site 3 out of 4 in 1one Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1one. 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: Gln167, B: Glu168, B: Asp246, B: Glu295, B: Asp296, B: Asp320, B: Leu343, B: Lys345, B: Lys396, B: Mg439, B: Pep440, B: 2pg441, B: Hoh945, B: Hoh1114, B: Hoh1276, conact list: Atom Atom Distance (A) Mg NE2 B:Gln167 4.17 Mg OE2 B:Glu168 4.58 Mg CB B:Asp246 4.24 Mg OD2 B:Asp246 1.99 Mg OD1 B:Asp246 3.17 Mg CG B:Asp246 2.93 Mg OE1 B:Glu295 3.70 Mg OE2 B:Glu295 1.89 Mg CD B:Glu295 2.99 Mg CG B:Glu295 3.91 Mg OD2 B:Asp296 4.03 Mg CG B:Asp296 4.88 Mg CB B:Asp320 3.50 Mg OD2 B:Asp320 1.92 Mg OD1 B:Asp320 4.11 Mg CG B:Asp320 3.07 Mg CD2 B:Leu343 4.07 Mg NZ B:Lys345 4.08 Mg CE B:Lys396 4.71 Mg NZ B:Lys396 3.57 Mg MG B:Mg439 4.26 Mg C1 B:Pep440 2.76 Mg O1 B:Pep440 2.36 Mg O2' B:Pep440 2.50 Mg C2 B:Pep440 4.23 Mg O2 B:2pg441 2.30 Mg C1 B:2pg441 2.74 Mg O1 B:2pg441 2.50 Mg C2 B:2pg441 4.30 Mg O B:Hoh945 4.00 Mg O B:Hoh1114 2.16 Mg O B:Hoh1276 3.87 interactive model: Magnesium binding site 4 out of 4 in 1one Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1one. 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: Ser39, B: Thr40, B: Gln167, B: Asp320, B: Asp321, B: Lys345, B: Arg374, B: Mg438, B: Pep440, B: 2pg441, B: Hoh945, B: Hoh1114, B: Hoh1276, conact list: Atom Atom Distance (A) Mg O B:Ser39 1.98 Mg N B:Ser39 4.01 Mg CB B:Ser39 3.11 Mg OG B:Ser39 2.03 Mg C B:Ser39 2.96 Mg CA B:Ser39 3.51 Mg N B:Thr40 4.07 Mg CA B:Thr40 4.57 Mg NE2 B:Gln167 4.22 Mg OE1 B:Gln167 4.39 Mg CD B:Gln167 4.78 Mg OD2 B:Asp320 3.97 Mg OD2 B:Asp321 4.13 Mg OD1 B:Asp321 4.18 Mg CG B:Asp321 4.56 Mg NZ B:Lys345 3.93 Mg NH2 B:Arg374 4.18 Mg MG B:Mg438 4.26 Mg O2 B:Pep440 3.27 Mg P B:Pep440 3.28 Mg O3P B:Pep440 4.45 Mg C1 B:Pep440 3.15 Mg O1 B:Pep440 4.23 Mg O1P B:Pep440 2.18 Mg O2' B:Pep440 2.20 Mg C2 B:Pep440 3.73 Mg O2P B:Pep440 3.94 Mg O2 B:2pg441 4.33 Mg P B:2pg441 3.31 Mg O3P B:2pg441 2.31 Mg C1 B:2pg441 3.23 Mg O1 B:2pg441 2.20 Mg O1P B:2pg441 3.32 Mg O4P B:2pg441 4.03 Mg C2 B:2pg441 3.61 Mg O2P B:2pg441 4.57 Mg O B:Hoh945 1.98 Mg O B:Hoh1114 4.35 Mg O B:Hoh1276 2.18 interactive model: