Sodium in the structure of Structure of Alfa-Galactosidase (MEL1) From Saccharomyces Cerevisiae (pdb 3lrk)

The binding sites of Sodium atom in the structure of Structure of Alfa-Galactosidase (MEL1) From Saccharomyces Cerevisiae (pdb code 3lrk). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3lrk structure was solved by R.FERNANDEZ-LEIRO, A.PEREIRA-RODRIGUEZ, M.E.CERDAN, M.BECERRA, J.SANZ-APARICIO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 111.5-1.9 Space group P4212 a (A) 101.243 b (A) 101.243 c (A) 111.521 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.4 Rfree (%) 23.4 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3lrk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3lrk. 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: Glu46, A: Asn94, A: His98, A: His102, A: Nag1001, A: Btb9001, conact list: Atom Atom Distance (A) Na OE2 A:Glu46 4.14 Na ND2 A:Asn94 4.92 Na NE2 A:His98 2.30 Na ND1 A:His98 4.36 Na CD2 A:His98 3.15 Na CE1 A:His98 3.31 Na CG A:His98 4.32 Na NE2 A:His102 2.29 Na ND1 A:His102 4.39 Na CD2 A:His102 3.21 Na CE1 A:His102 3.29 Na CG A:His102 4.38 Na C8 A:Nag1001 4.71 Na N A:Btb9001 2.32 Na C1 A:Btb9001 3.10 Na O8 A:Btb9001 2.23 Na O1 A:Btb9001 2.25 Na O3 A:Btb9001 2.23 Na C8 A:Btb9001 3.39 Na C2 A:Btb9001 2.94 Na C6 A:Btb9001 3.10 Na C5 A:Btb9001 2.98 Na C7 A:Btb9001 3.40 Na C4 A:Btb9001 4.43 Na C3 A:Btb9001 3.06 Na O6 A:Btb9001 2.24 interactive model: