Sodium in the structure of Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378 (pdb 2die)

The binding sites of Sodium atom in the structure of Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378 (pdb code 2die). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2die structure was solved by T.SHIRAI, K.IGARASHI, T.OZAWA, H.HAGIHARA, T.KOBAYASHI, K.OZAKI, S.ITO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-2.1 Space group C121 a (A) 174.577 b (A) 41.467 c (A) 74.855 alpha (°) 90.00 beta (°) 92.24 gamma (°) 90.00 Rfactor (%) 17.7 Rfree (%) 23.1 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2die Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2die. 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: Asp163, A: Trp187, A: Asp188, A: Asp199, A: Asp205, A: Ile206, A: Asp207, A: Met208, A: Ca778, A: Ca779, A: Hoh611, A: Hoh707, conact list: Atom Atom Distance (A) Na N A:Asp163 4.97 Na CB A:Asp163 3.65 Na OD2 A:Asp163 2.29 Na OD1 A:Asp163 4.42 Na CG A:Asp163 3.29 Na CA A:Asp163 4.94 Na CE3 A:Trp187 4.77 Na N A:Asp188 4.25 Na CB A:Asp188 4.07 Na OD2 A:Asp188 3.75 Na OD1 A:Asp188 2.70 Na CG A:Asp188 3.25 Na CA A:Asp188 4.83 Na CB A:Asp199 4.44 Na OD2 A:Asp199 2.46 Na OD1 A:Asp199 2.79 Na CG A:Asp199 2.96 Na O A:Asp205 4.77 Na CB A:Asp205 4.54 Na OD2 A:Asp205 4.02 Na C A:Asp205 4.64 Na OD1 A:Asp205 2.26 Na CG A:Asp205 3.42 Na O A:Ile206 2.65 Na N A:Ile206 4.55 Na C A:Ile206 3.56 Na CA A:Ile206 4.66 Na N A:Asp207 4.12 Na C A:Asp207 4.68 Na CA A:Asp207 3.95 Na N A:Met208 4.29 Na CA A:Ca778 4.42 Na CA A:Ca779 4.08 Na O A:Hoh611 3.85 Na O A:Hoh707 3.54 interactive model: