Magnesium in the structure of Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant E145Q From Methanocaldococcus Jannaschii in Complex With Pyrophosphate and Magnesium (pdb 3gf0)

The binding sites of Magnesium atom in the structure of Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant E145Q From Methanocaldococcus Jannaschii in Complex With Pyrophosphate and Magnesium (pdb code 3gf0). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3gf0 structure was solved by J.H.B.SIGGAARD, E.JOHANSSON, T.VOGNSEN, S.S.HELT, P.HARRIS, M.WILLEMOES, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.3-2.6 Space group I432 a (A) 171.569 b (A) 171.569 c (A) 171.569 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.1 Rfree (%) 22.9 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 3gf0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3gf0. 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: Asp135, A: Tyr177, A: Pop277, A: Hoh307, A: Hoh340, conact list: Atom Atom Distance (A) Mg OD2 A:Asp135 4.60 Mg OD1 A:Asp135 4.54 Mg CG A:Asp135 4.97 Mg CE1 A:Tyr177 4.64 Mg O A:Pop277 3.05 Mg O5 A:Pop277 2.25 Mg P2 A:Pop277 2.95 Mg O2 A:Pop277 2.41 Mg P1 A:Pop277 3.12 Mg O1 A:Pop277 4.09 Mg O3 A:Pop277 4.12 Mg O4 A:Pop277 3.36 Mg O6 A:Pop277 4.33 Mg O A:Hoh307 4.72 Mg O A:Hoh340 4.65 interactive model: Magnesium binding site 2 out of 4 in 3gf0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3gf0. 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: Ile42, A: Glu93, A: Gly94, A: Gly95, A: Val96, A: Hoh299, A: Hoh314, A: Hoh337, conact list: Atom Atom Distance (A) Mg CD1 A:Ile42 4.78 Mg CG2 A:Ile42 3.77 Mg O A:Glu93 2.57 Mg N A:Glu93 4.76 Mg C A:Glu93 3.79 Mg CA A:Glu93 4.88 Mg O A:Gly94 4.56 Mg N A:Gly94 4.50 Mg C A:Gly94 3.94 Mg CA A:Gly94 4.23 Mg O A:Gly95 2.52 Mg N A:Gly95 3.60 Mg C A:Gly95 3.57 Mg CA A:Gly95 4.04 Mg N A:Val96 4.72 Mg O A:Hoh299 3.12 Mg O A:Hoh314 3.98 Mg O A:Hoh337 4.40 interactive model: Magnesium binding site 3 out of 4 in 3gf0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3gf0. 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: His128, A: Hoh348, conact list: Atom Atom Distance (A) Mg NE2 A:His128 4.62 Mg CE1 A:His128 4.40 Mg O A:Hoh348 3.87 interactive model: Magnesium binding site 4 out of 4 in 3gf0 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3gf0. 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: Tyr114, A: Gln115, A: Gly116, A: His128, A: Hoh348, A: Hoh349, conact list: Atom Atom Distance (A) Mg O A:Tyr114 4.17 Mg C A:Tyr114 4.81 Mg O A:Gln115 4.93 Mg N A:Gln115 4.55 Mg OE1 A:Gln115 4.85 Mg CB A:Gln115 3.46 Mg C A:Gln115 3.73 Mg CG A:Gln115 4.75 Mg CA A:Gln115 3.31 Mg O A:Gly116 4.93 Mg N A:Gly116 3.17 Mg CA A:Gly116 4.31 Mg NE2 A:His128 2.66 Mg CB A:His128 4.68 Mg CB A:His128 4.82 Mg ND1 A:His128 4.35 Mg CD2 A:His128 2.61 Mg CE1 A:His128 3.80 Mg CG A:His128 3.77 Mg O A:Hoh348 3.04 Mg O A:Hoh349 3.93 interactive model: