Magnesium in the structure of Crystal Structure of the Hypothetical Protein TTHB029 From Thermus Thermophilus HB8 (pdb 2e67)

The binding sites of Magnesium atom in the structure of Crystal Structure of the Hypothetical Protein TTHB029 From Thermus Thermophilus HB8 (pdb code 2e67). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2e67 structure was solved by T.IMAGAWA, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.9 Space group H321 a (A) 202.006 b (A) 202.006 c (A) 345.294 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 21.9 Rfree (%) 25.9 Magnesium Binding Sites: Magnesium binding site 1 out of 6 in 2e67 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2e67. 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: Asp20, A: Asp21, A: Met43, A: His60, A: His127, A: Gln128, A: His215, conact list: Atom Atom Distance (A) Mg CB A:Asp20 4.40 Mg OD2 A:Asp20 3.46 Mg CG A:Asp20 4.25 Mg N A:Asp21 4.55 Mg CB A:Asp21 4.44 Mg OD2 A:Asp21 1.99 Mg OD1 A:Asp21 3.48 Mg CG A:Asp21 3.07 Mg CA A:Asp21 4.71 Mg CE A:Met43 4.32 Mg NE2 A:His60 2.11 Mg ND1 A:His60 4.19 Mg CD2 A:His60 3.14 Mg CE1 A:His60 3.05 Mg CG A:His60 4.27 Mg NE2 A:His127 4.00 Mg N A:His127 4.73 Mg CB A:His127 3.57 Mg ND1 A:His127 1.98 Mg CD2 A:His127 4.15 Mg C A:His127 4.60 Mg CE1 A:His127 2.83 Mg CG A:His127 3.10 Mg CA A:His127 3.67 Mg N A:Gln128 4.48 Mg NE2 A:His215 4.57 Mg CD2 A:His215 4.92 interactive model: Magnesium binding site 2 out of 6 in 2e67 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2e67. 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: Asp20, B: Asp21, B: Met43, B: His60, B: His127, B: Gln128, B: His215, B: Hoh328, B: Hoh331, conact list: Atom Atom Distance (A) Mg CB B:Asp20 4.56 Mg OD2 B:Asp20 3.36 Mg CG B:Asp20 4.27 Mg N B:Asp21 4.55 Mg CB B:Asp21 4.59 Mg OD2 B:Asp21 2.18 Mg OD1 B:Asp21 3.79 Mg CG B:Asp21 3.30 Mg CA B:Asp21 4.84 Mg CE B:Met43 4.57 Mg NE2 B:His60 2.31 Mg ND1 B:His60 4.34 Mg CD2 B:His60 3.34 Mg CE1 B:His60 3.19 Mg CG B:His60 4.44 Mg NE2 B:His127 4.21 Mg N B:His127 4.96 Mg CB B:His127 3.69 Mg ND1 B:His127 2.18 Mg CD2 B:His127 4.35 Mg C B:His127 4.56 Mg CE1 B:His127 3.03 Mg CG B:His127 3.28 Mg CA B:His127 3.80 Mg N B:Gln128 4.24 Mg NE2 B:His215 4.58 Mg CD2 B:His215 4.85 Mg O B:Hoh328 2.81 Mg O B:Hoh331 4.21 interactive model: Magnesium binding site 3 out of 6 in 2e67 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2e67. 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: Asp20, C: Asp21, C: Met43, C: His60, C: His127, C: Gln128, C: His215, conact list: Atom Atom Distance (A) Mg CB C:Asp20 4.82 Mg OD2 C:Asp20 4.05 Mg OD1 C:Asp20 4.98 Mg CG C:Asp20 4.44 Mg N C:Asp21 4.78 Mg CB C:Asp21 4.58 Mg OD2 C:Asp21 2.21 Mg OD1 C:Asp21 3.62 Mg CG C:Asp21 3.25 Mg CA C:Asp21 4.84 Mg SD C:Met43 4.75 Mg NE2 C:His60 2.53 Mg ND1 C:His60 4.60 Mg CD2 C:His60 3.30 Mg CE1 C:His60 3.58 Mg CG C:His60 4.50 Mg NE2 C:His127 4.16 Mg N C:His127 4.94 Mg CB C:His127 3.54 Mg ND1 C:His127 2.10 Mg CD2 C:His127 4.26 Mg C C:His127 4.55 Mg CE1 C:His127 3.00 Mg CG C:His127 3.17 Mg CA C:His127 3.77 Mg N C:Gln128 4.38 Mg NE2 C:His215 4.51 Mg CD2 C:His215 4.91 interactive model: Magnesium binding site 4 out of 6 in 2e67 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 2e67. 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: Asp20, D: Asp21, D: His60, D: His127, D: Gln128, D: His215, conact list: Atom Atom Distance (A) Mg CB D:Asp20 4.54 Mg OD2 D:Asp20 3.36 Mg CG D:Asp20 4.13 Mg N D:Asp21 4.70 Mg CB D:Asp21 4.63 Mg OD2 D:Asp21 2.25 Mg OD1 D:Asp21 3.61 Mg CG D:Asp21 3.27 Mg CA D:Asp21 4.89 Mg NE2 D:His60 2.30 Mg ND1 D:His60 4.30 Mg CD2 D:His60 3.39 Mg CE1 D:His60 3.13 Mg CG D:His60 4.46 Mg NE2 D:His127 4.09 Mg N D:His127 4.76 Mg CB D:His127 3.74 Mg ND1 D:His127 2.09 Mg CD2 D:His127 4.28 Mg C D:His127 4.50 Mg CE1 D:His127 2.88 Mg CG D:His127 3.25 Mg CA D:His127 3.71 Mg N D:Gln128 4.14 Mg NE2 D:His215 4.61 Mg CD2 D:His215 4.89 interactive model: Magnesium binding site 5 out of 6 in 2e67 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 2e67. 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: Asp20, E: Asp21, E: Met43, E: His60, E: His127, E: Gln128, E: His215, conact list: Atom Atom Distance (A) Mg CB E:Asp20 4.22 Mg OD2 E:Asp20 3.64 Mg C E:Asp20 4.98 Mg OD1 E:Asp20 4.63 Mg CG E:Asp20 3.96 Mg N E:Asp21 4.25 Mg CB E:Asp21 4.35 Mg OD2 E:Asp21 1.97 Mg OD1 E:Asp21 3.58 Mg CG E:Asp21 3.09 Mg CA E:Asp21 4.51 Mg CE E:Met43 4.65 Mg NE2 E:His60 2.30 Mg ND1 E:His60 4.44 Mg CD2 E:His60 3.14 Mg CE1 E:His60 3.38 Mg CG E:His60 4.36 Mg NE2 E:His127 4.14 Mg CB E:His127 3.86 Mg ND1 E:His127 2.19 Mg CD2 E:His127 4.36 Mg C E:His127 4.82 Mg CE1 E:His127 2.93 Mg CG E:His127 3.36 Mg CA E:His127 3.97 Mg N E:Gln128 4.56 Mg NE2 E:His215 4.39 Mg CD2 E:His215 4.79 interactive model: Magnesium binding site 6 out of 6 in 2e67 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 2e67. 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: Asp20, F: Asp21, F: Met43, F: His60, F: His127, F: Gln128, F: His215, conact list: Atom Atom Distance (A) Mg CB F:Asp20 4.15 Mg OD2 F:Asp20 3.15 Mg OD1 F:Asp20 4.93 Mg CG F:Asp20 3.91 Mg N F:Asp21 4.47 Mg CB F:Asp21 4.33 Mg OD2 F:Asp21 1.89 Mg OD1 F:Asp21 3.37 Mg CG F:Asp21 2.97 Mg CA F:Asp21 4.63 Mg CE F:Met43 4.52 Mg NE2 F:His60 2.15 Mg ND1 F:His60 4.25 Mg CD2 F:His60 3.16 Mg CE1 F:His60 3.11 Mg CG F:His60 4.30 Mg NE2 F:His127 4.07 Mg N F:His127 4.63 Mg CB F:His127 3.56 Mg ND1 F:His127 2.05 Mg CD2 F:His127 4.20 Mg C F:His127 4.54 Mg CE1 F:His127 2.91 Mg CG F:His127 3.14 Mg CA F:His127 3.62 Mg N F:Gln128 4.37 Mg NE2 F:His215 4.75 interactive model: