Magnesium in the structure of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and The Benzoxaborole AN2679 in the Editing Conformation (pdb 4ari)

The binding sites of Magnesium atom in the structure of Ternary Complex of E. Coli Leucyl-Trna Synthetase, Trna(Leu) and The Benzoxaborole AN2679 in the Editing Conformation (pdb code 4ari). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 4ari structure was solved by A.PALENCIA, T.CREPIN, M.T.VU, T.L.LINCECUM JR, S.A.MARTINIS, S.CUSACK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 90.9-2.1 Space group P212121 a (A) 76.180 b (A) 118.940 c (A) 141.030 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.879 Rfree (%) 24.436 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 4ari Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 4ari. 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: Val236, A: Asn237, A: Asp238, A: Tyr239, A: Asp240, A: Asn241, A: Hoh2108, conact list: Atom Atom Distance (A) Mg O A:Val236 2.56 Mg N A:Val236 4.28 Mg C A:Val236 3.74 Mg CA A:Val236 4.56 Mg N A:Asn237 4.71 Mg C A:Asn237 4.85 Mg CA A:Asn237 4.83 Mg N A:Asp238 4.58 Mg O A:Tyr239 2.02 Mg N A:Tyr239 3.85 Mg CB A:Tyr239 4.48 Mg C A:Tyr239 3.23 Mg CA A:Tyr239 4.09 Mg N A:Asp240 4.19 Mg C A:Asp240 4.78 Mg OD1 A:Asp240 4.96 Mg CA A:Asp240 4.32 Mg O A:Asn241 3.87 Mg N A:Asn241 4.29 Mg C A:Asn241 4.75 Mg O A:Hoh2108 2.50 interactive model: Magnesium binding site 2 out of 2 in 4ari Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 4ari. 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: A7, B: U8, B: G9, B: U11, B: Hoh2003, B: Hoh2005, B: Hoh2006, conact list: Atom Atom Distance (A) Mg O3' B:A7 4.46 Mg OP1 B:U8 4.21 Mg P B:U8 3.39 Mg O3' B:U8 4.77 Mg OP2 B:U8 1.99 Mg C5' B:U8 4.37 Mg O5' B:U8 3.95 Mg OP1 B:G9 4.22 Mg P B:G9 3.62 Mg OP2 B:G9 2.25 Mg C5' B:G9 4.50 Mg O5' B:G9 4.39 Mg OP1 B:U11 4.98 Mg O B:Hoh2003 2.45 Mg O B:Hoh2005 1.81 Mg O B:Hoh2006 4.56 interactive model: