Magnesium in the structure of Crystal Structure of Ribonuclease II Family Protein From Deinococcus Radiodurans, Triclinic Crystal Form. Northeast Structural Genomics Target DRR63 (pdb 2r7d)

The binding sites of Magnesium atom in the structure of Crystal Structure of Ribonuclease II Family Protein From Deinococcus Radiodurans, Triclinic Crystal Form. Northeast Structural Genomics Target DRR63 (pdb code 2r7d). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2r7d structure was solved by J.SEETHARAMAN, H.NEELY, F.FOROUHAR, D.WANG, Y.FANG, K.CUNNINGHAM, L-C.MA, R.XIA, J.LIU, M.C.BARAN, T.B.ACTON, B.ROST, G.T.MONTELIONE, J.F.HUNT, L.TONG, NORTHEAST STRUCTURALGENOMICS CONSORTIUM (NESG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 36.7-1.8 Space group P1 a (A) 65.762 b (A) 92.205 c (A) 92.345 alpha (°) 60.08 beta (°) 89.57 gamma (°) 71.11 Rfactor (%) 22.1 Rfree (%) 24.3 Magnesium Binding Sites: Magnesium binding site 1 out of 3 in 2r7d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2r7d. 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: Ile92, A: Asp93, A: Pro100, A: Asp101, A: Asp102, A: Hoh1001, A: Hoh1002, A: Hoh1010, A: Hoh1013, A: Hoh1024, A: Hoh1026, A: Hoh1036, A: Hoh1048, A: Hoh1201, A: Hoh1284, A: Hoh1453, conact list: Atom Atom Distance (A) Mg O A:Ile92 4.13 Mg C A:Ile92 4.82 Mg CB A:Asp93 4.45 Mg OD2 A:Asp93 3.48 Mg OD1 A:Asp93 2.16 Mg CG A:Asp93 3.14 Mg CA A:Asp93 4.92 Mg CA A:Pro100 4.99 Mg N A:Asp101 4.50 Mg O A:Asp102 4.30 Mg N A:Asp102 4.21 Mg CB A:Asp102 4.32 Mg OD2 A:Asp102 2.16 Mg C A:Asp102 4.85 Mg OD1 A:Asp102 3.30 Mg CG A:Asp102 3.02 Mg CA A:Asp102 4.69 Mg O A:Hoh1001 2.23 Mg O A:Hoh1002 2.27 Mg O A:Hoh1010 4.91 Mg O A:Hoh1013 4.23 Mg O A:Hoh1024 4.19 Mg O A:Hoh1026 2.38 Mg O A:Hoh1036 4.21 Mg O A:Hoh1048 3.92 Mg O A:Hoh1201 4.93 Mg O A:Hoh1284 4.30 Mg O A:Hoh1453 2.11 interactive model: Magnesium binding site 2 out of 3 in 2r7d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2r7d. 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: Ile92, B: Asp93, B: Pro100, B: Asp101, B: Asp102, B: Hoh2001, B: Hoh2003, B: Hoh2007, B: Hoh2009, B: Hoh2012, B: Hoh2017, B: Hoh2027, B: Hoh2052, B: Hoh2081, B: Hoh2087, B: Hoh2132, B: Hoh2174, conact list: Atom Atom Distance (A) Mg O B:Ile92 4.17 Mg C B:Ile92 4.89 Mg CB B:Asp93 4.50 Mg OD2 B:Asp93 3.46 Mg OD1 B:Asp93 2.21 Mg CG B:Asp93 3.16 Mg CA B:Asp93 4.96 Mg CA B:Pro100 4.87 Mg N B:Asp101 4.30 Mg CB B:Asp101 4.95 Mg O B:Asp102 4.30 Mg N B:Asp102 4.09 Mg CB B:Asp102 4.34 Mg OD2 B:Asp102 2.20 Mg C B:Asp102 4.83 Mg OD1 B:Asp102 3.44 Mg CG B:Asp102 3.09 Mg CA B:Asp102 4.64 Mg O B:Hoh2001 2.37 Mg O B:Hoh2003 2.27 Mg O B:Hoh2007 3.96 Mg O B:Hoh2009 2.28 Mg O B:Hoh2012 4.97 Mg O B:Hoh2017 4.13 Mg O B:Hoh2027 4.40 Mg O B:Hoh2052 4.93 Mg O B:Hoh2081 4.30 Mg O B:Hoh2087 4.22 Mg O B:Hoh2132 2.27 Mg O B:Hoh2174 4.98 interactive model: Magnesium binding site 3 out of 3 in 2r7d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2r7d. 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: Ile92, C: Asp93, C: Pro100, C: Asp101, C: Asp102, C: Hoh3001, C: Hoh3002, C: Hoh3011, C: Hoh3015, C: Hoh3017, C: Hoh3021, C: Hoh3027, C: Hoh3039, C: Hoh3052, C: Hoh3056, C: Hoh3196, conact list: Atom Atom Distance (A) Mg O C:Ile92 4.08 Mg C C:Ile92 4.81 Mg CB C:Asp93 4.41 Mg OD2 C:Asp93 3.42 Mg OD1 C:Asp93 2.11 Mg CG C:Asp93 3.09 Mg CA C:Asp93 4.90 Mg CA C:Pro100 4.83 Mg N C:Asp101 4.41 Mg O C:Asp102 4.31 Mg N C:Asp102 4.22 Mg CB C:Asp102 4.41 Mg OD2 C:Asp102 2.25 Mg C C:Asp102 4.88 Mg OD1 C:Asp102 3.47 Mg CG C:Asp102 3.15 Mg CA C:Asp102 4.74 Mg O C:Hoh3001 2.26 Mg O C:Hoh3002 2.24 Mg O C:Hoh3011 4.93 Mg O C:Hoh3015 4.20 Mg O C:Hoh3017 2.30 Mg O C:Hoh3021 2.26 Mg O C:Hoh3027 4.27 Mg O C:Hoh3039 4.17 Mg O C:Hoh3052 4.08 Mg O C:Hoh3056 4.35 Mg O C:Hoh3196 4.95 interactive model: