Magnesium in the structure of Structure of Inorganic Pyrophosphatase (pdb 1obw)

The binding sites of Magnesium atom in the structure of Structure of Inorganic Pyrophosphatase (pdb code 1obw). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1obw structure was solved by V.YU.OGANESSYAN, E.H.HARUTYUNYAN, S.M.AVAEVA, N.N.OGANESSYAN, T.MATHER, R.HUBER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 15.0-1.9 Space group P3221 a (A) 110.300 b (A) 110.300 c (A) 78.200 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 17.6 Rfree (%) 22 Magnesium Binding Sites: Magnesium binding site 1 out of 7 in 1obw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1obw. 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: Ser63, A: Asp65, A: Pro68, A: Asp70, A: Asp102, A: Ala103, A: Lys104, A: Mg178, A: Hoh198, A: Hoh200, A: Hoh202, A: Hoh208, A: Hoh225, A: Hoh265, conact list: Atom Atom Distance (A) Mg OG A:Ser63 4.44 Mg CB A:Asp65 4.31 Mg OD2 A:Asp65 1.98 Mg OD1 A:Asp65 3.43 Mg CG A:Asp65 3.03 Mg O A:Pro68 4.54 Mg N A:Asp70 4.78 Mg CB A:Asp70 4.31 Mg OD2 A:Asp70 2.20 Mg OD1 A:Asp70 3.76 Mg CG A:Asp70 3.20 Mg O A:Asp102 4.75 Mg CB A:Asp102 4.09 Mg OD2 A:Asp102 3.76 Mg C A:Asp102 4.36 Mg OD1 A:Asp102 1.97 Mg CG A:Asp102 3.05 Mg CA A:Asp102 4.06 Mg O A:Ala103 4.41 Mg N A:Ala103 4.79 Mg CE A:Lys104 4.90 Mg NZ A:Lys104 3.88 Mg MG A:Mg178 4.97 Mg O A:Hoh198 2.14 Mg O A:Hoh200 2.15 Mg O A:Hoh202 2.01 Mg O A:Hoh208 4.73 Mg O A:Hoh225 3.92 Mg O A:Hoh265 4.36 interactive model: Magnesium binding site 2 out of 7 in 1obw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1obw. 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: Asn24, A: Ala25, A: Asp26, A: Hoh201, A: Hoh203, A: Hoh209, A: Hoh234, conact list: Atom Atom Distance (A) Mg O A:Asn24 4.14 Mg ND2 A:Asn24 4.93 Mg C A:Asn24 4.57 Mg OD1 A:Asn24 3.88 Mg CG A:Asn24 4.59 Mg O A:Ala25 4.23 Mg N A:Ala25 4.99 Mg C A:Ala25 4.50 Mg N A:Asp26 4.95 Mg OD1 A:Asp26 4.52 Mg O A:Hoh201 2.18 Mg O A:Hoh203 2.13 Mg O A:Hoh209 2.12 Mg O A:Hoh234 4.82 interactive model: Magnesium binding site 3 out of 7 in 1obw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1obw. 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: Glu20, A: Tyr55, A: Gly56, A: Tyr57, A: Asp67, A: Pro68, A: Asp70, A: Mg176, A: Hoh200, A: Hoh202, A: Hoh211, A: Hoh213, A: Hoh217, A: Hoh224, A: Hoh225, A: Hoh242, conact list: Atom Atom Distance (A) Mg OE1 A:Glu20 4.28 Mg OE2 A:Glu20 4.94 Mg CE2 A:Tyr55 4.69 Mg CZ A:Tyr55 4.79 Mg OH A:Tyr55 4.20 Mg O A:Gly56 4.88 Mg CB A:Tyr57 4.58 Mg CB A:Asp67 4.70 Mg O A:Pro68 4.12 Mg CB A:Asp70 4.38 Mg OD2 A:Asp70 3.89 Mg OD1 A:Asp70 2.06 Mg CG A:Asp70 3.24 Mg CA A:Asp70 4.69 Mg MG A:Mg176 4.97 Mg O A:Hoh200 4.39 Mg O A:Hoh202 4.34 Mg O A:Hoh211 4.79 Mg O A:Hoh213 2.13 Mg O A:Hoh217 2.67 Mg O A:Hoh224 1.98 Mg O A:Hoh225 1.95 Mg O A:Hoh242 2.20 interactive model: Magnesium binding site 4 out of 7 in 1obw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1obw. 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: Ser63, B: Asp65, B: Asp67, B: Pro68, B: Asp70, B: Asp102, B: Ala103, B: Lys104, B: Mg177, B: Hoh209, B: Hoh232, B: Hoh233, B: Hoh242, B: Hoh253, conact list: Atom Atom Distance (A) Mg OG B:Ser63 4.50 Mg CB B:Asp65 4.46 Mg OD2 B:Asp65 2.13 Mg OD1 B:Asp65 3.55 Mg CG B:Asp65 3.19 Mg CB B:Asp67 4.97 Mg O B:Pro68 4.56 Mg N B:Asp70 4.75 Mg CB B:Asp70 4.27 Mg OD2 B:Asp70 2.15 Mg OD1 B:Asp70 3.76 Mg CG B:Asp70 3.17 Mg O B:Asp102 4.93 Mg CB B:Asp102 4.11 Mg OD2 B:Asp102 3.87 Mg C B:Asp102 4.52 Mg OD1 B:Asp102 1.97 Mg CG B:Asp102 3.10 Mg CA B:Asp102 4.11 Mg O B:Ala103 4.37 Mg N B:Ala103 4.96 Mg CE B:Lys104 4.94 Mg NZ B:Lys104 3.95 Mg MG B:Mg177 4.85 Mg O B:Hoh209 2.13 Mg O B:Hoh232 4.43 Mg O B:Hoh233 3.86 Mg O B:Hoh242 2.09 Mg O B:Hoh253 1.94 interactive model: Magnesium binding site 5 out of 7 in 1obw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 1obw. 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: Glu20, B: Tyr55, B: Tyr57, B: Asp67, B: Pro68, B: Asp70, B: Mg176, B: Hoh206, B: Hoh209, B: Hoh211, B: Hoh233, B: Hoh237, B: Hoh239, B: Hoh253, conact list: Atom Atom Distance (A) Mg OE1 B:Glu20 4.40 Mg CE2 B:Tyr55 4.54 Mg CZ B:Tyr55 4.55 Mg OH B:Tyr55 3.88 Mg CB B:Tyr57 4.84 Mg CB B:Asp67 4.71 Mg OD2 B:Asp67 4.54 Mg O B:Pro68 4.35 Mg CB B:Asp70 4.24 Mg OD2 B:Asp70 3.68 Mg OD1 B:Asp70 2.06 Mg CG B:Asp70 3.12 Mg CA B:Asp70 4.73 Mg MG B:Mg176 4.85 Mg O B:Hoh206 2.20 Mg O B:Hoh209 4.54 Mg O B:Hoh211 2.10 Mg O B:Hoh233 2.03 Mg O B:Hoh237 2.26 Mg O B:Hoh239 2.30 Mg O B:Hoh253 4.09 interactive model: Magnesium binding site 6 out of 7 in 1obw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 1obw. 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: Asn24, C: Ala25, C: Asp26, C: Hoh187, C: Hoh200, C: Hoh232, conact list: Atom Atom Distance (A) Mg O C:Asn24 4.19 Mg C C:Asn24 4.64 Mg OD1 C:Asn24 3.82 Mg CG C:Asn24 4.64 Mg O C:Ala25 4.14 Mg C C:Ala25 4.55 Mg N C:Asp26 5.00 Mg OD1 C:Asp26 4.56 Mg O C:Hoh187 2.16 Mg O C:Hoh200 2.12 Mg O C:Hoh232 2.09 interactive model: Magnesium binding site 7 out of 7 in 1obw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 1obw. 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: Ser63, C: Asp65, C: Asp67, C: Pro68, C: Asp70, C: Asp102, C: Ala103, C: Lys104, C: Hoh195, C: Hoh218, C: Hoh222, C: Hoh227, C: Hoh254, conact list: Atom Atom Distance (A) Mg OG C:Ser63 4.47 Mg CB C:Asp65 4.42 Mg OD2 C:Asp65 2.08 Mg OD1 C:Asp65 3.43 Mg CG C:Asp65 3.11 Mg CB C:Asp67 4.91 Mg OD2 C:Asp67 4.99 Mg O C:Pro68 4.49 Mg N C:Asp70 4.76 Mg CB C:Asp70 4.24 Mg OD2 C:Asp70 2.21 Mg OD1 C:Asp70 3.64 Mg CG C:Asp70 3.10 Mg CB C:Asp102 4.18 Mg OD2 C:Asp102 3.99 Mg C C:Asp102 4.75 Mg OD1 C:Asp102 2.10 Mg CG C:Asp102 3.21 Mg CA C:Asp102 4.32 Mg O C:Ala103 4.49 Mg CE C:Lys104 5.00 Mg NZ C:Lys104 4.04 Mg O C:Hoh195 2.03 Mg O C:Hoh218 1.74 Mg O C:Hoh222 4.00 Mg O C:Hoh227 4.12 Mg O C:Hoh254 1.83 interactive model: