Sodium in the structure of Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus With Bound L-Alanine (pdb 2ejd)

The binding sites of Sodium atom in the structure of Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus With Bound L-Alanine (pdb code 2ejd). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2ejd structure was solved by E.INAGAKI, K.SAKAMOTO, S.YOKOYAMA, RIKEN STRUCTURAL GENOMICS/PROTEOMICSINITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.5-1.9 Space group H3 a (A) 101.661 b (A) 101.661 c (A) 279.261 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 15.3 Rfree (%) 19 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2ejd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2ejd. 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: Hoh2578, A: Hoh2790, A: Hoh2857, conact list: Atom Atom Distance (A) Na CB A:Ser55 4.29 Na OG A:Ser55 3.07 Na C A:Ser55 4.22 Na CA A:Ser55 4.39 Na O A:Leu56 2.65 Na N A:Leu56 3.67 Na CB A:Leu56 4.99 Na C A:Leu56 3.76 Na CA A:Leu56 4.26 Na N A:Asn57 4.91 Na CD A:Pro58 4.54 Na O A:Glu123 2.72 Na OE1 A:Glu123 4.41 Na CB A:Glu123 4.49 Na CD A:Glu123 4.47 Na C A:Glu123 3.78 Na CG A:Glu123 3.47 Na CA A:Glu123 4.23 Na N A:Val124 4.92 Na O A:Asp211 2.82 Na CB A:Asp211 4.43 Na C A:Asp211 3.78 Na OD1 A:Asp211 4.64 Na CA A:Asp211 4.15 Na N A:Ala212 4.93 Na O A:Hoh2578 2.34 Na O A:Hoh2790 3.16 Na O A:Hoh2857 4.38 interactive model: Sodium binding site 2 out of 2 in 2ejd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2ejd. 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: Glu123, B: Val124, B: Asp211, B: Val364, B: Hoh2788, B: Hoh2923, B: Hoh2933, conact list: Atom Atom Distance (A) Na CB B:Ser55 4.68 Na OG B:Ser55 3.48 Na C B:Ser55 4.60 Na CA B:Ser55 4.77 Na O B:Leu56 2.66 Na N B:Leu56 3.89 Na C B:Leu56 3.81 Na CA B:Leu56 4.40 Na N B:Asn57 4.92 Na CD B:Pro58 4.18 Na O B:Glu123 2.45 Na OE1 B:Glu123 4.58 Na CB B:Glu123 4.40 Na CD B:Glu123 4.59 Na C B:Glu123 3.55 Na CG B:Glu123 3.52 Na CA B:Glu123 4.08 Na N B:Val124 4.66 Na CG1 B:Val124 4.98 Na CA B:Val124 4.96 Na O B:Asp211 2.88 Na CB B:Asp211 4.49 Na C B:Asp211 3.91 Na OD1 B:Asp211 4.70 Na CA B:Asp211 4.29 Na O B:Val364 4.78 Na O B:Hoh2788 2.31 Na O B:Hoh2923 1.98 Na O B:Hoh2933 4.09 interactive model: