Magnesium in the structure of Complex With Isocitrate and The Protein Isocitrate Dehydrogenase From the Psychrophilic Bacterium Desulfotalea Psychrophila (pdb 2uxr)

The binding sites of Magnesium atom in the structure of Complex With Isocitrate and The Protein Isocitrate Dehydrogenase From the Psychrophilic Bacterium Desulfotalea Psychrophila (pdb code 2uxr). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2uxr structure was solved by A.-E.FEDOY, N.YANG, A.MARTINEZ, H.-K.S.LEIROS, I.H.STEEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.3 Space group C2221 a (A) 58.560 b (A) 121.740 c (A) 273.770 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.5 Rfree (%) 25.9 Magnesium Binding Sites: Magnesium binding site 1 out of 3 in 2uxr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2uxr. 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: Arg108, A: Arg131, A: Asp272, A: Asp276, A: Ala304, B: Lys209, B: Asp249, A: Ict1403, A: Hoh2102, A: Hoh2103, B: Hoh2053, conact list: Atom Atom Distance (A) Mg NH1 A:Arg108 4.09 Mg NH1 A:Arg131 4.68 Mg O A:Asp272 3.94 Mg CB A:Asp272 4.29 Mg OD2 A:Asp272 3.66 Mg C A:Asp272 4.51 Mg OD1 A:Asp272 2.02 Mg CG A:Asp272 3.14 Mg CA A:Asp272 4.44 Mg OD2 A:Asp276 4.18 Mg OD1 A:Asp276 4.20 Mg CG A:Asp276 4.37 Mg O A:Ala304 3.84 Mg NZ B:Lys209 4.18 Mg CB B:Asp249 3.87 Mg OD2 B:Asp249 2.14 Mg OD1 B:Asp249 4.31 Mg CG B:Asp249 3.30 Mg C6 A:Ict1403 4.15 Mg O5 A:Ict1403 4.44 Mg O2 A:Ict1403 4.13 Mg C1 A:Ict1403 2.95 Mg O1 A:Ict1403 2.02 Mg C3 A:Ict1403 4.27 Mg O7 A:Ict1403 2.34 Mg O6 A:Ict1403 4.36 Mg C2 A:Ict1403 3.21 Mg O A:Hoh2102 2.18 Mg O A:Hoh2103 4.29 Mg O B:Hoh2053 4.87 interactive model: Magnesium binding site 2 out of 3 in 2uxr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2uxr. 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: Gly306, A: Thr307, A: Val308, A: Gln309, A: Ict1404, conact list: Atom Atom Distance (A) Mg O A:Gly306 4.93 Mg N A:Gly306 4.70 Mg C A:Gly306 4.29 Mg CA A:Gly306 4.20 Mg N A:Thr307 4.18 Mg C A:Thr307 4.84 Mg N A:Val308 3.79 Mg C A:Val308 4.74 Mg CA A:Val308 3.97 Mg N A:Gln309 4.33 Mg O2 A:Ict1404 4.01 Mg C1 A:Ict1404 3.65 Mg O1 A:Ict1404 2.55 Mg O6 A:Ict1404 4.41 Mg C2 A:Ict1404 4.90 interactive model: Magnesium binding site 3 out of 3 in 2uxr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2uxr. 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: Lys209, A: Asp249, B: Arg108, B: Arg131, B: Asp272, B: Ser275, B: Asp276, B: Ala304, B: Ict1397, B: Hoh2069, conact list: Atom Atom Distance (A) Mg NZ A:Lys209 4.37 Mg CB A:Asp249 3.72 Mg OD2 A:Asp249 2.32 Mg OD1 A:Asp249 4.46 Mg CG A:Asp249 3.36 Mg CZ B:Arg108 4.91 Mg NH1 B:Arg108 3.76 Mg NH1 B:Arg131 4.57 Mg O B:Asp272 3.51 Mg CB B:Asp272 4.24 Mg OD2 B:Asp272 4.03 Mg C B:Asp272 4.16 Mg OD1 B:Asp272 2.06 Mg CG B:Asp272 3.27 Mg CA B:Asp272 4.18 Mg OG B:Ser275 4.82 Mg CB B:Asp276 4.99 Mg OD2 B:Asp276 3.94 Mg OD1 B:Asp276 3.40 Mg CG B:Asp276 3.88 Mg O B:Ala304 4.01 Mg C6 B:Ict1397 3.23 Mg O5 B:Ict1397 1.97 Mg C5 B:Ict1397 3.48 Mg C4 B:Ict1397 4.17 Mg C3 B:Ict1397 4.26 Mg O7 B:Ict1397 4.86 Mg O3 B:Ict1397 4.49 Mg O4 B:Ict1397 2.36 Mg O6 B:Ict1397 3.96 Mg O B:Hoh2069 4.61 interactive model: