Magnesium in the structure of The Crystal Structure of REM1 in Complex With Gdp (pdb 2nzj)

The binding sites of Magnesium atom in the structure of The Crystal Structure of REM1 in Complex With Gdp (pdb code 2nzj). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2nzj structure was solved by A.P.TURNBULL, E.PAPAGRIGORIOU, E.UGOCHUKWU, J.M.ELKINS, M.SOUNDARARAJAN, X.YANG, F.GORREC, C.UMEANO, E.SALAH, N.BURGESS, C.JOHANSSON, G.BERRIDGE, O.GILEADI, J.BRAY, B.MARSDEN, S.WATTS, F.VON DELFT, J.WEIGELT, A.EDWARDS, C.H.ARROWSMITH, M.SUNDSTROM, D.DOYLE, STRUCTURAL GENOMICS CONSORTIUM(SGC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.0-2.5 Space group P212121 a (A) 43.640 b (A) 102.284 c (A) 165.565 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.5 Rfree (%) 28 Magnesium Binding Sites: Magnesium binding site 1 out of 4 in 2nzj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2nzj. 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: Thr94, A: Asp134, A: Gdp1001, A: Hoh1, A: Hoh2, A: Hoh3, A: Hoh4, conact list: Atom Atom Distance (A) Mg N A:Thr94 3.95 Mg CB A:Thr94 3.11 Mg CG2 A:Thr94 4.22 Mg OG1 A:Thr94 2.16 Mg CA A:Thr94 4.12 Mg OD2 A:Asp134 4.15 Mg OD1 A:Asp134 4.45 Mg CG A:Asp134 4.73 Mg O3B A:Gdp1001 3.24 Mg PA A:Gdp1001 4.38 Mg O2A A:Gdp1001 4.61 Mg O1B A:Gdp1001 4.33 Mg PB A:Gdp1001 3.22 Mg O2B A:Gdp1001 2.13 Mg O3A A:Gdp1001 4.29 Mg O1A A:Gdp1001 3.68 Mg O A:Hoh1 2.05 Mg O A:Hoh2 2.04 Mg O A:Hoh3 1.81 Mg O A:Hoh4 1.88 interactive model: Magnesium binding site 2 out of 4 in 2nzj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2nzj. 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: Lys93, B: Thr94, B: Asp134, B: Gdp1002, B: Hoh5, B: Hoh6, B: Hoh7, B: Hoh8, conact list: Atom Atom Distance (A) Mg CB B:Lys93 4.95 Mg N B:Thr94 4.05 Mg CB B:Thr94 3.36 Mg CG2 B:Thr94 4.50 Mg OG1 B:Thr94 2.35 Mg CA B:Thr94 4.29 Mg OD2 B:Asp134 4.34 Mg OD1 B:Asp134 4.51 Mg CG B:Asp134 4.88 Mg O3B B:Gdp1002 3.15 Mg PA B:Gdp1002 4.34 Mg O2A B:Gdp1002 4.57 Mg O1B B:Gdp1002 4.10 Mg PB B:Gdp1002 3.14 Mg O2B B:Gdp1002 2.07 Mg O3A B:Gdp1002 4.23 Mg O1A B:Gdp1002 3.78 Mg O B:Hoh5 2.16 Mg O B:Hoh6 1.98 Mg O B:Hoh7 2.02 Mg O B:Hoh8 1.96 interactive model: Magnesium binding site 3 out of 4 in 2nzj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2nzj. 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: Lys93, C: Thr94, C: Asp134, C: Gdp1003, C: Hoh9, C: Hoh10, C: Hoh11, C: Hoh12, conact list: Atom Atom Distance (A) Mg CB C:Lys93 4.69 Mg CE C:Lys93 4.97 Mg C C:Lys93 4.77 Mg NZ C:Lys93 4.92 Mg N C:Thr94 3.68 Mg CB C:Thr94 2.92 Mg CG2 C:Thr94 4.07 Mg OG1 C:Thr94 1.84 Mg CA C:Thr94 3.82 Mg OD2 C:Asp134 3.72 Mg OD1 C:Asp134 4.01 Mg CG C:Asp134 4.29 Mg O3B C:Gdp1003 3.83 Mg PA C:Gdp1003 4.65 Mg O2A C:Gdp1003 4.81 Mg O1B C:Gdp1003 4.41 Mg PB C:Gdp1003 3.51 Mg O2B C:Gdp1003 2.16 Mg O3A C:Gdp1003 4.53 Mg O1A C:Gdp1003 4.15 Mg O C:Hoh9 1.97 Mg O C:Hoh10 1.96 Mg O C:Hoh11 2.12 Mg O C:Hoh12 2.04 interactive model: Magnesium binding site 4 out of 4 in 2nzj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 2nzj. 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: Lys93, D: Thr94, D: Asp134, D: Gdp1004, D: Hoh13, D: Hoh14, D: Hoh15, D: Hoh16, conact list: Atom Atom Distance (A) Mg CB D:Lys93 4.69 Mg CE D:Lys93 4.91 Mg C D:Lys93 4.94 Mg NZ D:Lys93 4.44 Mg N D:Thr94 3.89 Mg CB D:Thr94 3.27 Mg CG2 D:Thr94 4.39 Mg OG1 D:Thr94 2.17 Mg CA D:Thr94 4.14 Mg OD2 D:Asp134 3.72 Mg OD1 D:Asp134 4.13 Mg CG D:Asp134 4.36 Mg O3B D:Gdp1004 3.34 Mg PA D:Gdp1004 4.56 Mg O2A D:Gdp1004 4.81 Mg O1B D:Gdp1004 4.18 Mg PB D:Gdp1004 3.20 Mg O2B D:Gdp1004 1.97 Mg O3A D:Gdp1004 4.32 Mg O1A D:Gdp1004 4.14 Mg O D:Hoh13 1.81 Mg O D:Hoh14 1.84 Mg O D:Hoh15 1.80 Mg O D:Hoh16 2.03 interactive model: