Sodium in the structure of Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus With Bound Nadp (pdb 2ehq)

The binding sites of Sodium atom in the structure of Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus With Bound Nadp (pdb code 2ehq). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2ehq 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) 22.1-1.6 Space group H3 a (A) 102.426 b (A) 102.426 c (A) 278.837 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 15.8 Rfree (%) 18 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2ehq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2ehq. 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: Hoh1716, A: Hoh1735, A: Hoh1851, conact list: Atom Atom Distance (A) Na O A:Ser55 4.90 Na CB A:Ser55 4.04 Na OG A:Ser55 2.83 Na C A:Ser55 4.06 Na CA A:Ser55 4.18 Na O A:Leu56 2.58 Na N A:Leu56 3.57 Na CB A:Leu56 4.92 Na C A:Leu56 3.68 Na CA A:Leu56 4.18 Na N A:Asn57 4.84 Na CD A:Pro58 4.49 Na O A:Glu123 2.68 Na CB A:Glu123 4.48 Na OE2 A:Glu123 4.30 Na CD A:Glu123 4.40 Na C A:Glu123 3.75 Na CG A:Glu123 3.44 Na CA A:Glu123 4.23 Na N A:Val124 4.89 Na O A:Asp211 2.69 Na CB A:Asp211 4.30 Na C A:Asp211 3.68 Na OD1 A:Asp211 4.56 Na CG A:Asp211 4.94 Na CA A:Asp211 4.05 Na N A:Ala212 4.85 Na O A:Hoh1716 2.44 Na O A:Hoh1735 4.31 Na O A:Hoh1851 2.36 interactive model: Sodium binding site 2 out of 2 in 2ehq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2ehq. 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: Hoh2790, B: Hoh2818, B: Hoh3019, conact list: Atom Atom Distance (A) Na CB B:Ser55 4.43 Na OG B:Ser55 3.18 Na C B:Ser55 4.40 Na CA B:Ser55 4.58 Na O B:Leu56 2.49 Na N B:Leu56 3.65 Na CB B:Leu56 4.87 Na C B:Leu56 3.62 Na CA B:Leu56 4.19 Na N B:Asn57 4.76 Na CD B:Pro58 4.28 Na CG2 B:Val65 4.96 Na O B:Glu123 2.47 Na CB B:Glu123 4.45 Na OE2 B:Glu123 4.59 Na CD B:Glu123 4.57 Na C B:Glu123 3.59 Na CG B:Glu123 3.51 Na CA B:Glu123 4.13 Na N B:Val124 4.71 Na CG1 B:Val124 4.92 Na CA B:Val124 5.00 Na O B:Asp211 2.90 Na CB B:Asp211 4.42 Na C B:Asp211 3.88 Na OD1 B:Asp211 4.58 Na CA B:Asp211 4.21 Na O B:Val364 4.87 Na O B:Hoh2790 2.35 Na O B:Hoh2818 4.10 Na O B:Hoh3019 2.15 interactive model: