Sodium in the structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophirus With Bound Inhibitor Glysine and Nad. (pdb 2j5n)

The binding sites of Sodium atom in the structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophirus With Bound Inhibitor Glysine and Nad. (pdb code 2j5n). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2j5n structure was solved by E.INAGAKI, K.SAKAMOTO, M.NISHIO, S.YOKOYAMA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 92.8-1.6 Space group H3 a (A) 102.589 b (A) 102.589 c (A) 278.637 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 14.6 Rfree (%) 17.4 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2j5n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2j5n. 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: Ser55, A: Leu56, A: Asn57, A: Pro58, A: Glu123, A: Val124, A: Asp211, A: Ala212, A: Hoh2143, A: Hoh2425, A: Hoh2426, conact list: Atom Atom Distance (A) Na O A:Ser55 4.96 Na CB A:Ser55 4.18 Na OG A:Ser55 3.00 Na C A:Ser55 4.12 Na CA A:Ser55 4.27 Na O A:Leu56 2.58 Na N A:Leu56 3.62 Na CB A:Leu56 4.94 Na C A:Leu56 3.69 Na CA A:Leu56 4.21 Na N A:Asn57 4.84 Na CD A:Pro58 4.48 Na O A:Glu123 2.68 Na OE1 A:Glu123 4.45 Na CB A:Glu123 4.55 Na CD A:Glu123 4.52 Na C A:Glu123 3.76 Na CG A:Glu123 3.53 Na CA A:Glu123 4.26 Na N A:Val124 4.89 Na O A:Asp211 2.84 Na CB A:Asp211 4.50 Na C A:Asp211 3.82 Na OD1 A:Asp211 4.68 Na CA A:Asp211 4.22 Na N A:Ala212 4.96 Na O A:Hoh2143 2.51 Na O A:Hoh2425 4.30 Na O A:Hoh2426 2.46 interactive model: Sodium binding site 2 out of 2 in 2j5n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2j5n. 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: B: Ser55, B: Leu56, B: Asn57, B: Pro58, B: Val65, B: Glu123, B: Val124, B: Asp211, B: Val364, B: Hoh2132, B: Hoh2420, B: Hoh2421, conact list: Atom Atom Distance (A) Na CB B:Ser55 4.47 Na OG B:Ser55 3.23 Na C B:Ser55 4.42 Na CA B:Ser55 4.59 Na O B:Leu56 2.52 Na N B:Leu56 3.66 Na CB B:Leu56 4.87 Na C B:Leu56 3.65 Na CA B:Leu56 4.20 Na N B:Asn57 4.78 Na CD B:Pro58 4.27 Na CG2 B:Val65 4.99 Na O B:Glu123 2.49 Na OE1 B:Glu123 4.64 Na CB B:Glu123 4.49 Na CD B:Glu123 4.62 Na C B:Glu123 3.60 Na CG B:Glu123 3.56 Na CA B:Glu123 4.15 Na N B:Val124 4.72 Na CG1 B:Val124 4.96 Na O B:Asp211 3.03 Na CB B:Asp211 4.61 Na C B:Asp211 4.02 Na OD1 B:Asp211 4.65 Na CA B:Asp211 4.41 Na O B:Val364 4.80 Na O B:Hoh2132 2.80 Na O B:Hoh2420 2.37 Na O B:Hoh2421 4.27 interactive model: