Sodium in the structure of X-Ray Crystal Structure of The Wbpe (Wlbe) Aminotransferase From Pseudomonas Aeruginosa As the Plp Internal Aldimine Adduct With Lysine 185 (pdb 3nyu)

The binding sites of Sodium atom in the structure of X-Ray Crystal Structure of The Wbpe (Wlbe) Aminotransferase From Pseudomonas Aeruginosa As the Plp Internal Aldimine Adduct With Lysine 185 (pdb code 3nyu). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3nyu structure was solved by H.M.HOLDEN, J.B.THODEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.5 Space group P1 a (A) 47.628 b (A) 54.068 c (A) 150.903 alpha (°) 84.26 beta (°) 82.43 gamma (°) 64.93 Rfactor (%) 18.1 Rfree (%) 21.9 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3nyu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3nyu. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ala57, A: Asp192, A: Arg229, A: Asp231, B: Ala57, B: Asp192, B: Arg229, B: Asp231, A: Hoh383, A: Hoh408, A: Hoh426, A: Hoh1038, A: Hoh1039, B: Hoh378, B: Hoh388, B: Hoh1035, B: Hoh1036, B: Hoh1037, conact list: Atom Atom Distance (A) Na O A:Ala57 4.71 Na O A:Asp192 4.14 Na CB A:Asp192 4.72 Na C A:Asp192 4.92 Na O A:Arg229 4.69 Na OD2 A:Asp231 4.00 Na OD1 A:Asp231 4.19 Na CG A:Asp231 4.38 Na O B:Ala57 4.73 Na CB B:Ala57 4.94 Na O B:Asp192 4.15 Na CB B:Asp192 4.72 Na C B:Asp192 4.93 Na O B:Arg229 4.80 Na OD2 B:Asp231 4.03 Na OD1 B:Asp231 4.19 Na CG B:Asp231 4.43 Na O A:Hoh383 2.07 Na O A:Hoh408 4.00 Na O A:Hoh426 4.23 Na O A:Hoh1038 2.04 Na O A:Hoh1039 2.10 Na O B:Hoh378 4.21 Na O B:Hoh388 4.02 Na O B:Hoh1035 2.07 Na O B:Hoh1036 2.12 Na O B:Hoh1037 2.14 interactive model: Sodium binding site 2 out of 2 in 3nyu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3nyu. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Ala57, C: Asp192, C: Arg229, C: Asp231, D: Ala57, D: Asp192, D: Arg229, D: Asp231, C: Hoh403, C: Hoh409, C: Hoh436, C: Hoh1040, C: Hoh1043, C: Hoh1044, D: Hoh374, D: Hoh397, D: Hoh1041, D: Hoh1042, conact list: Atom Atom Distance (A) Na O C:Ala57 4.73 Na CB C:Ala57 4.88 Na O C:Asp192 4.20 Na CB C:Asp192 4.73 Na C C:Asp192 4.98 Na O C:Arg229 4.76 Na OD2 C:Asp231 3.97 Na OD1 C:Asp231 4.15 Na CG C:Asp231 4.34 Na O D:Ala57 4.63 Na CB D:Ala57 4.93 Na O D:Asp192 4.11 Na CB D:Asp192 4.70 Na C D:Asp192 4.91 Na O D:Arg229 4.72 Na OD2 D:Asp231 4.05 Na OD1 D:Asp231 4.17 Na CG D:Asp231 4.37 Na O C:Hoh403 4.22 Na O C:Hoh409 2.10 Na O C:Hoh436 4.04 Na O C:Hoh1040 2.12 Na O C:Hoh1043 2.02 Na O C:Hoh1044 2.09 Na O D:Hoh374 3.97 Na O D:Hoh397 4.21 Na O D:Hoh1041 2.13 Na O D:Hoh1042 2.00 interactive model: