Magnesium in the structure of Crystal Structure Of The Y103F Mutant of the Gdp-Mannose Mannosyl Hydrolase in Complex With Gdp-Mannose and Mg+2 (pdb 2gt4)

The binding sites of Magnesium atom in the structure of Crystal Structure Of The Y103F Mutant of the Gdp-Mannose Mannosyl Hydrolase in Complex With Gdp-Mannose and Mg+2 (pdb code 2gt4). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2gt4 structure was solved by S.B.GABELLI, M.A.BIANCHET, H.F.AZURMENDI, A.S.MILDVAN, L.A.AMZEL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 77.6-2.3 Space group C121 a (A) 137.785 b (A) 93.893 c (A) 66.103 alpha (°) 90.00 beta (°) 91.23 gamma (°) 90.00 Rfactor (%) 18.6 Rfree (%) 22.6 Magnesium Binding Sites: Magnesium binding site 1 out of 3 in 2gt4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2gt4. 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: Arg37, A: Gly50, A: Gly51, A: Glu70, A: Gdd201, A: Hoh402, A: Hoh411, A: Hoh455, A: Hoh464, A: Hoh465, A: Hoh476, conact list: Atom Atom Distance (A) Mg NH1 A:Arg37 4.09 Mg O A:Gly50 2.20 Mg N A:Gly50 4.36 Mg C A:Gly50 3.43 Mg CA A:Gly50 4.51 Mg N A:Gly51 4.21 Mg CA A:Gly51 4.07 Mg OE1 A:Glu70 3.33 Mg OE2 A:Glu70 2.36 Mg CD A:Glu70 3.06 Mg CG A:Glu70 4.27 Mg C11 A:Gdd201 4.11 Mg PA A:Gdd201 3.51 Mg O5' A:Gdd201 4.27 Mg O2B A:Gdd201 2.60 Mg O3A A:Gdd201 3.88 Mg O51 A:Gdd201 4.72 Mg O2A A:Gdd201 2.18 Mg O1B A:Gdd201 4.39 Mg PB A:Gdd201 3.77 Mg C5' A:Gdd201 4.53 Mg O1A A:Gdd201 4.72 Mg O A:Hoh402 4.44 Mg O A:Hoh411 2.36 Mg O A:Hoh455 2.32 Mg O A:Hoh464 4.25 Mg O A:Hoh465 4.68 Mg O A:Hoh476 4.02 interactive model: Magnesium binding site 2 out of 3 in 2gt4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2gt4. 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: Gly50, B: Gly51, B: Glu70, B: Bma202, B: Gdd201, B: Hoh402, B: Hoh403, B: Hoh417, B: Hoh468, conact list: Atom Atom Distance (A) Mg O B:Gly50 2.19 Mg N B:Gly50 4.38 Mg C B:Gly50 3.42 Mg CA B:Gly50 4.50 Mg N B:Gly51 4.20 Mg CA B:Gly51 4.09 Mg OE1 B:Glu70 3.51 Mg OE2 B:Glu70 2.17 Mg CD B:Glu70 3.14 Mg CG B:Glu70 4.41 Mg C4 B:Bma202 4.56 Mg C3 B:Bma202 4.76 Mg O3 B:Bma202 4.85 Mg O4 B:Bma202 3.30 Mg O3B B:Gdd201 4.78 Mg C11 B:Gdd201 4.09 Mg PA B:Gdd201 3.48 Mg O5' B:Gdd201 4.35 Mg O2B B:Gdd201 2.20 Mg O3A B:Gdd201 3.77 Mg O51 B:Gdd201 4.83 Mg O2A B:Gdd201 2.18 Mg O1B B:Gdd201 4.25 Mg PB B:Gdd201 3.52 Mg C5' B:Gdd201 4.25 Mg O1A B:Gdd201 4.64 Mg O B:Hoh402 2.29 Mg O B:Hoh403 4.46 Mg O B:Hoh417 1.92 Mg O B:Hoh468 3.41 interactive model: Magnesium binding site 3 out of 3 in 2gt4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2gt4. 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: Gly50, C: Gly51, C: Glu70, C: Bma202, C: Gdd201, C: Hoh402, C: Hoh403, C: Hoh413, C: Hoh425, C: Hoh507, conact list: Atom Atom Distance (A) Mg O C:Gly50 2.17 Mg N C:Gly50 4.31 Mg C C:Gly50 3.36 Mg CA C:Gly50 4.44 Mg N C:Gly51 4.10 Mg CA C:Gly51 3.93 Mg OE1 C:Glu70 3.15 Mg OE2 C:Glu70 2.18 Mg CD C:Glu70 2.91 Mg CG C:Glu70 4.19 Mg C6 C:Bma202 4.84 Mg C4 C:Bma202 4.52 Mg O4 C:Bma202 3.12 Mg O3B C:Gdd201 4.71 Mg C11 C:Gdd201 4.06 Mg PA C:Gdd201 3.48 Mg O5' C:Gdd201 4.31 Mg O2B C:Gdd201 2.17 Mg O3A C:Gdd201 3.82 Mg O51 C:Gdd201 4.89 Mg O2A C:Gdd201 2.19 Mg O1B C:Gdd201 4.18 Mg PB C:Gdd201 3.48 Mg C5' C:Gdd201 4.29 Mg C21 C:Gdd201 4.96 Mg O1A C:Gdd201 4.66 Mg O C:Hoh402 4.50 Mg O C:Hoh403 4.02 Mg O C:Hoh413 2.66 Mg O C:Hoh425 2.37 Mg O C:Hoh507 4.73 interactive model: