Sodium in the structure of Phosphoketolase From Bifidobacterium Breve Complexed With 2-Acetyl- Thiamine Diphosphate (pdb 3ahd)

The binding sites of Sodium atom in the structure of Phosphoketolase From Bifidobacterium Breve Complexed With 2-Acetyl- Thiamine Diphosphate (pdb code 3ahd). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3ahd structure was solved by R.SUZUKI, T.KATAYAMA, B.-J.KIM, T.WAKAGI, H.SHOUN, H.ASHIDA, K.YAMAMOTO, S.FUSHINOBU, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 34.1-1.9 Space group I422 a (A) 174.448 b (A) 174.448 c (A) 163.847 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.2 Rfree (%) 19.7 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3ahd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3ahd. 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: Tyr721, A: His726, A: Asp727, A: Hoh1563, A: Hoh1589, A: Hoh1605, conact list: Atom Atom Distance (A) Na O A:Tyr721 4.90 Na NE2 A:His726 2.09 Na ND1 A:His726 4.12 Na CD2 A:His726 2.94 Na CE1 A:His726 3.10 Na CG A:His726 4.08 Na N A:Asp727 4.56 Na CB A:Asp727 4.11 Na OD2 A:Asp727 2.98 Na OD1 A:Asp727 1.86 Na CG A:Asp727 2.74 Na CA A:Asp727 4.51 Na O A:Hoh1563 4.95 Na O A:Hoh1589 3.16 Na O A:Hoh1605 3.98 interactive model: