Sodium in the structure of Pyruvate Oxidase Variant F479W in Complex With Reaction Intermediate 2-Lactyl-Thiamin Diphosphate (pdb 2ez8)

The binding sites of Sodium atom in the structure of Pyruvate Oxidase Variant F479W in Complex With Reaction Intermediate 2-Lactyl-Thiamin Diphosphate (pdb code 2ez8). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2ez8 structure was solved by G.WILLE, D.MEYER, A.STEINMETZ, E.HINZE, R.GOLBIK, K.TITTMANN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 25.0-2.0 Space group C2221 a (A) 118.133 b (A) 154.462 c (A) 165.656 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 14.9 Rfree (%) 17.2 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2ez8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2ez8. 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: His58, A: Glu60, A: Ser451, A: Met452, A: Thr453, A: Gln455, A: Hoh1689, conact list: Atom Atom Distance (A) Na NE2 A:His58 4.82 Na CD2 A:His58 4.19 Na CG A:His58 4.95 Na OE2 A:Glu60 4.98 Na O A:Ser451 4.60 Na O A:Met452 2.71 Na C A:Met452 3.78 Na CA A:Met452 4.62 Na N A:Thr453 4.61 Na CA A:Thr453 4.63 Na NE2 A:Gln455 4.14 Na OE1 A:Gln455 2.77 Na CD A:Gln455 3.70 Na CG A:Gln455 4.90 Na O A:Hoh1689 2.96 interactive model: Sodium binding site 2 out of 2 in 2ez8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2ez8. 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: His58, B: Glu60, B: Ser451, B: Met452, B: Thr453, B: Gln455, B: Hoh1686, conact list: Atom Atom Distance (A) Na NE2 B:His58 4.73 Na CD2 B:His58 4.11 Na CG B:His58 4.83 Na OE2 B:Glu60 4.95 Na O B:Ser451 4.62 Na O B:Met452 2.76 Na C B:Met452 3.80 Na CA B:Met452 4.68 Na N B:Thr453 4.63 Na CA B:Thr453 4.61 Na NE2 B:Gln455 3.98 Na OE1 B:Gln455 2.75 Na CD B:Gln455 3.60 Na CG B:Gln455 4.80 Na O B:Hoh1686 3.02 interactive model: