Magnesium in the structure of VPS54 C-Terminal Domain (pdb 3n1e)

The binding sites of Magnesium atom in the structure of VPS54 C-Terminal Domain (pdb code 3n1e). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3n1e structure was solved by F.J.PEREZ-VICTORIA, G.ABASCAL-PALACIOS, I.TASCON, A.KAJAVA, E.P.PIORO, J.S.BONIFACINO, A.HIERRO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 47.4-1.7 Space group P212121 a (A) 29.760 b (A) 77.064 c (A) 120.057 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.6 Rfree (%) 21.1 Magnesium Binding Sites: Magnesium binding site 1 out of 5 in 3n1e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3n1e. 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: Gly939, A: Pro940, A: Gln941, A: Asn942, A: Hoh13, A: Hoh20, A: Hoh102, A: Hoh279, conact list: Atom Atom Distance (A) Mg O A:Gly939 4.82 Mg C A:Gly939 4.12 Mg CA A:Gly939 4.33 Mg N A:Pro940 3.74 Mg CB A:Pro940 4.33 Mg CD A:Pro940 3.60 Mg C A:Pro940 4.24 Mg CG A:Pro940 4.14 Mg CA A:Pro940 4.34 Mg N A:Gln941 3.26 Mg OE1 A:Gln941 4.70 Mg CB A:Gln941 3.47 Mg CB A:Gln941 3.56 Mg CD A:Gln941 4.92 Mg CG A:Gln941 4.72 Mg CG A:Gln941 3.68 Mg CA A:Gln941 3.98 Mg CA A:Gln941 4.00 Mg N A:Asn942 4.89 Mg O A:Hoh13 3.06 Mg O A:Hoh20 4.52 Mg O A:Hoh102 4.04 Mg O A:Hoh279 2.95 interactive model: Magnesium binding site 2 out of 5 in 3n1e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3n1e. 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: Asn942, B: Val945, B: Thr946, B: Val949, B: Ile972, B: Trp973, B: Hoh3, B: Hoh239, B: Hoh245, B: Hoh265, B: Hoh270, B: Hoh271, conact list: Atom Atom Distance (A) Mg OD1 B:Asn942 4.75 Mg O B:Val945 4.92 Mg C B:Val945 4.84 Mg CG1 B:Val945 4.97 Mg O B:Thr946 4.86 Mg N B:Thr946 4.26 Mg CB B:Thr946 3.76 Mg CG2 B:Thr946 4.08 Mg OG1 B:Thr946 3.01 Mg C B:Thr946 4.79 Mg CA B:Thr946 3.64 Mg CB B:Val949 4.67 Mg CG2 B:Val949 4.85 Mg CG1 B:Val949 4.82 Mg CD1 B:Ile972 4.41 Mg CD1 B:Trp973 4.42 Mg CZ2 B:Trp973 3.97 Mg CE2 B:Trp973 3.98 Mg NE1 B:Trp973 3.28 Mg O B:Hoh3 4.25 Mg O B:Hoh239 3.57 Mg O B:Hoh245 2.71 Mg O B:Hoh265 4.79 Mg O B:Hoh270 3.23 Mg O B:Hoh271 4.83 interactive model: Magnesium binding site 3 out of 5 in 3n1e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3n1e. 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: Hoh30, B: Hoh292, conact list: Atom Atom Distance (A) Mg O B:Hoh30 4.21 Mg O B:Hoh292 3.06 interactive model: Magnesium binding site 4 out of 5 in 3n1e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3n1e. 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: Asp835, B: Gln836, B: Trp837, B: Hoh88, B: Hoh235, conact list: Atom Atom Distance (A) Mg CB B:Asp835 3.54 Mg OD2 B:Asp835 4.79 Mg C B:Asp835 4.16 Mg CG B:Asp835 4.42 Mg CA B:Asp835 4.14 Mg NE2 B:Gln836 4.45 Mg N B:Gln836 3.23 Mg CB B:Gln836 3.66 Mg CD B:Gln836 4.42 Mg CG B:Gln836 3.71 Mg CA B:Gln836 4.05 Mg N B:Trp837 4.97 Mg O B:Hoh88 4.74 Mg O B:Hoh235 3.41 interactive model: Magnesium binding site 5 out of 5 in 3n1e Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 3n1e. 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: Asp937, B: Gly939, B: Pro940, B: Gln941, B: Asn942, B: Hoh31, B: Hoh67, B: Hoh148, conact list: Atom Atom Distance (A) Mg OD1 B:Asp937 4.77 Mg O B:Gly939 4.74 Mg C B:Gly939 3.96 Mg CA B:Gly939 4.05 Mg N B:Pro940 3.59 Mg CB B:Pro940 4.48 Mg CD B:Pro940 3.52 Mg C B:Pro940 4.23 Mg CG B:Pro940 3.64 Mg CA B:Pro940 4.29 Mg N B:Gln941 3.26 Mg OE1 B:Gln941 4.30 Mg CB B:Gln941 3.62 Mg CD B:Gln941 4.32 Mg CG B:Gln941 3.56 Mg CA B:Gln941 4.03 Mg N B:Asn942 4.82 Mg O B:Hoh31 2.93 Mg O B:Hoh67 4.10 Mg O B:Hoh148 3.85 interactive model: