Magnesium in the structure of Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily (pdb 3e84)

The binding sites of Magnesium atom in the structure of Structure-Function Analysis of 2-Keto-3-Deoxy-D-Glycero-D-Galacto- Nononate-9-Phosphate (Kdn) Phosphatase Defines A New Clad Within the Type C0 Had Subfamily (pdb code 3e84). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3e84 structure was solved by Z.LU, L.WANG, D.DUNAWAY-MARIANO, K.N.ALLEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 21.9-1.9 Space group P21212 a (A) 82.086 b (A) 107.336 c (A) 75.310 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.6 Rfree (%) 21.8 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 3e84 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3e84. 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: Asp10, A: Ile11, A: Asp12, A: Gly13, A: Asp103, A: Asp104, A: Asn106, A: Asp107, A: Wo4801, B: Hoh882, B: Hoh1001, conact list: Atom Atom Distance (A) Mg CB A:Asp10 4.33 Mg OD2 A:Asp10 3.39 Mg OD1 A:Asp10 2.01 Mg CG A:Asp10 3.02 Mg C A:Ile11 4.83 Mg O A:Asp12 2.19 Mg N A:Asp12 4.25 Mg CB A:Asp12 4.28 Mg C A:Asp12 3.38 Mg CA A:Asp12 4.14 Mg N A:Gly13 4.40 Mg C A:Gly13 4.99 Mg CA A:Gly13 4.54 Mg N A:Asp103 4.47 Mg CB A:Asp103 4.51 Mg OD2 A:Asp103 3.63 Mg C A:Asp103 4.98 Mg OD1 A:Asp103 2.17 Mg CG A:Asp103 3.23 Mg CA A:Asp103 4.88 Mg N A:Asp104 4.70 Mg CB A:Asp104 4.60 Mg OD1 A:Asn106 4.82 Mg OD2 A:Asp107 3.98 Mg CG A:Asp107 4.99 Mg W A:Wo4801 3.65 Mg O2 A:Wo4801 4.70 Mg O4 A:Wo4801 4.65 Mg O3 A:Wo4801 1.94 Mg O B:Hoh882 2.22 Mg O B:Hoh1001 2.14 interactive model: Magnesium binding site 2 out of 4 in 3e84 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3e84. 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: Asp10, B: Ile11, B: Asp12, B: Gly13, B: Val14, B: Asp103, B: Asp104, B: Asn106, B: Asp107, B: Wo4802, B: Hoh832, B: Hoh900, B: Hoh1038, B: Hoh1143, conact list: Atom Atom Distance (A) Mg CB B:Asp10 4.36 Mg OD2 B:Asp10 2.10 Mg OD1 B:Asp10 3.42 Mg CG B:Asp10 3.07 Mg C B:Ile11 4.94 Mg O B:Asp12 2.18 Mg N B:Asp12 4.30 Mg CB B:Asp12 4.32 Mg C B:Asp12 3.37 Mg CA B:Asp12 4.16 Mg N B:Gly13 4.37 Mg C B:Gly13 4.98 Mg CA B:Gly13 4.52 Mg CG2 B:Val14 4.99 Mg N B:Asp103 4.39 Mg CB B:Asp103 4.47 Mg OD2 B:Asp103 3.67 Mg C B:Asp103 4.91 Mg OD1 B:Asp103 2.18 Mg CG B:Asp103 3.24 Mg CA B:Asp103 4.81 Mg N B:Asp104 4.64 Mg CB B:Asp104 4.50 Mg OD1 B:Asn106 4.86 Mg OD2 B:Asp107 3.96 Mg O1 B:Wo4802 4.60 Mg W B:Wo4802 3.63 Mg O2 B:Wo4802 4.59 Mg O3 B:Wo4802 1.86 Mg O B:Hoh832 2.16 Mg O B:Hoh900 4.60 Mg O B:Hoh1038 4.18 Mg O B:Hoh1143 2.20 interactive model: Magnesium binding site 3 out of 4 in 3e84 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3e84. 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: Asp10, C: Ile11, C: Asp12, C: Gly13, C: Val14, C: Asp103, C: Asp104, C: Asn106, C: Asp107, C: Wo4803, B: Hoh935, B: Hoh936, B: Hoh937, conact list: Atom Atom Distance (A) Mg CB C:Asp10 4.30 Mg OD2 C:Asp10 3.56 Mg OD1 C:Asp10 2.02 Mg CG C:Asp10 3.09 Mg C C:Ile11 4.77 Mg O C:Asp12 2.11 Mg N C:Asp12 4.12 Mg CB C:Asp12 4.17 Mg C C:Asp12 3.27 Mg CA C:Asp12 4.04 Mg N C:Gly13 4.27 Mg C C:Gly13 4.84 Mg CA C:Gly13 4.41 Mg N C:Val14 4.91 Mg CG2 C:Val14 4.99 Mg N C:Asp103 4.42 Mg CB C:Asp103 4.41 Mg OD2 C:Asp103 3.60 Mg C C:Asp103 4.93 Mg OD1 C:Asp103 2.10 Mg CG C:Asp103 3.16 Mg CA C:Asp103 4.81 Mg N C:Asp104 4.76 Mg CB C:Asp104 4.59 Mg OD1 C:Asn106 4.99 Mg OD2 C:Asp107 3.99 Mg O1 C:Wo4803 4.59 Mg W C:Wo4803 3.69 Mg O4 C:Wo4803 4.81 Mg O3 C:Wo4803 1.93 Mg O B:Hoh935 2.23 Mg O B:Hoh936 2.27 Mg O B:Hoh937 4.14 interactive model: Magnesium binding site 4 out of 4 in 3e84 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3e84. 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: Asp10, D: Ile11, D: Asp12, D: Gly13, D: Val14, D: Asp103, D: Asp104, D: Asn106, D: Asp107, D: Wo4804, B: Hoh1086, B: Hoh1093, conact list: Atom Atom Distance (A) Mg CB D:Asp10 4.36 Mg OD2 D:Asp10 2.04 Mg OD1 D:Asp10 3.44 Mg CG D:Asp10 3.06 Mg C D:Ile11 4.82 Mg O D:Asp12 2.19 Mg N D:Asp12 4.21 Mg CB D:Asp12 4.24 Mg C D:Asp12 3.36 Mg CA D:Asp12 4.12 Mg N D:Gly13 4.37 Mg C D:Gly13 4.91 Mg CA D:Gly13 4.49 Mg N D:Val14 4.98 Mg CG2 D:Val14 4.97 Mg N D:Asp103 4.42 Mg CB D:Asp103 4.41 Mg OD2 D:Asp103 3.56 Mg C D:Asp103 4.95 Mg OD1 D:Asp103 2.12 Mg CG D:Asp103 3.15 Mg CA D:Asp103 4.81 Mg N D:Asp104 4.74 Mg CB D:Asp104 4.64 Mg OD1 D:Asn106 4.87 Mg OD2 D:Asp107 4.01 Mg O1 D:Wo4804 4.59 Mg W D:Wo4804 3.64 Mg O4 D:Wo4804 4.59 Mg O3 D:Wo4804 1.90 Mg O B:Hoh1086 2.18 Mg O B:Hoh1093 2.29 interactive model: