Sodium in the structure of Crystal Structure of Environmental Isolated GH11 in Complex With Xylobiose and Feruloyl-Arabino-Xylotriose (pdb 2vgd)

The binding sites of Sodium atom in the structure of Crystal Structure of Environmental Isolated GH11 in Complex With Xylobiose and Feruloyl-Arabino-Xylotriose (pdb code 2vgd). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2vgd structure was solved by M.VARDAKOU, C.DUMON, J.E.FLINT, J.W.MURRAY, P.CHRISTAKOPOULOS, D.P.WEINER, N.JUGE, R.J.LEWIS, H.J.GILBERT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.7-1.8 Space group P41212 a (A) 76.470 b (A) 76.470 c (A) 102.600 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.5 Rfree (%) 20.3 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2vgd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2vgd. 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: Val92, A: Asp94, A: Ser114, A: Asp115, A: Tyr119, A: Arg149, A: Thr153, A: Ile154, A: Thr155, A: His159, A: Hoh2174, conact list: Atom Atom Distance (A) Na CG1 A:Val92 4.14 Na OD1 A:Asp94 4.95 Na O A:Ser114 4.02 Na CB A:Ser114 3.89 Na OG A:Ser114 3.86 Na C A:Ser114 4.29 Na CA A:Ser114 4.75 Na N A:Asp115 4.81 Na CB A:Asp115 3.94 Na OD2 A:Asp115 2.72 Na OD1 A:Asp115 4.81 Na CG A:Asp115 3.68 Na CA A:Asp115 4.99 Na CE2 A:Tyr119 3.48 Na CD2 A:Tyr119 4.49 Na CZ A:Tyr119 3.32 Na CE1 A:Tyr119 4.25 Na OH A:Tyr119 2.98 Na NH2 A:Arg149 4.48 Na O A:Thr153 4.13 Na C A:Thr153 4.90 Na N A:Ile154 4.82 Na CB A:Ile154 4.02 Na CG2 A:Ile154 3.84 Na C A:Ile154 4.49 Na CG1 A:Ile154 3.91 Na CA A:Ile154 3.78 Na N A:Thr155 4.20 Na NE2 A:His159 2.73 Na ND1 A:His159 4.82 Na CD2 A:His159 3.68 Na CE1 A:His159 3.68 Na CG A:His159 4.84 Na O A:Hoh2174 4.53 interactive model: