Sodium in the structure of Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure (pdb 3ecq)

The binding sites of Sodium atom in the structure of Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure (pdb code 3ecq). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3ecq structure was solved by M.E.C.CAINES, H.ZHU, M.VUCKOVIC, N.C.J.STRYNADKA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 112.5-2.9 Space group P21212 a (A) 210.611 b (A) 158.209 c (A) 112.436 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19 Rfree (%) 23.5 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3ecq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3ecq. 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: Glu703, A: Asp728, A: His1258, A: Leu1259, A: Ser1260, A: Glu1261, conact list: Atom Atom Distance (A) Na OE1 A:Glu703 1.94 Na CB A:Glu703 4.51 Na OE2 A:Glu703 3.73 Na CD A:Glu703 3.13 Na CG A:Glu703 4.33 Na CB A:Asp728 4.85 Na OD2 A:Asp728 2.86 Na OD1 A:Asp728 3.08 Na CG A:Asp728 3.34 Na NE2 A:His1258 2.48 Na ND1 A:His1258 4.60 Na CD2 A:His1258 3.29 Na CE1 A:His1258 3.55 Na CG A:His1258 4.51 Na O A:Leu1259 4.35 Na CB A:Ser1260 4.49 Na C A:Ser1260 4.99 Na CA A:Ser1260 4.17 Na N A:Glu1261 4.67 interactive model: Sodium binding site 2 out of 2 in 3ecq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3ecq. 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: Glu703, B: Asp728, B: His1258, B: Leu1259, B: Ser1260, B: Glu1261, conact list: Atom Atom Distance (A) Na OE1 B:Glu703 2.32 Na CB B:Glu703 4.62 Na OE2 B:Glu703 3.24 Na CD B:Glu703 2.91 Na CG B:Glu703 4.02 Na CB B:Asp728 4.84 Na OD2 B:Asp728 2.53 Na OD1 B:Asp728 3.60 Na CG B:Asp728 3.44 Na NE2 B:His1258 2.42 Na ND1 B:His1258 4.54 Na CD2 B:His1258 3.24 Na CE1 B:His1258 3.49 Na CG B:His1258 4.45 Na O B:Leu1259 4.60 Na CB B:Ser1260 4.67 Na CA B:Ser1260 4.37 Na N B:Glu1261 4.90 interactive model: