Sodium in the structure of Structure and Catalysis of Acylaminoacyl Peptidase (pdb 3o4j)

The binding sites of Sodium atom in the structure of Structure and Catalysis of Acylaminoacyl Peptidase (pdb code 3o4j). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3o4j structure was solved by V.HARMAT, K.DOMOKOS, D.K.MENYHARD, A.PALLO, Z.SZELTNER, I.SZAMOSI, T.BEKE-SOMFAI, G.NARAY-SZABO, L.POLGAR, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.5-2.5 Space group C121 a (A) 184.270 b (A) 227.524 c (A) 110.684 alpha (°) 90.00 beta (°) 100.37 gamma (°) 90.00 Rfactor (%) 19.9 Rfree (%) 23.6 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3o4j Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3o4j. 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: Asn181, B: Ser184, B: Gly185, B: Gly186, conact list: Atom Atom Distance (A) Na N B:Asn181 4.35 Na CB B:Asn181 3.51 Na ND2 B:Asn181 4.72 Na OD1 B:Asn181 3.02 Na CG B:Asn181 3.56 Na CA B:Asn181 4.52 Na O B:Ser184 4.49 Na N B:Ser184 4.38 Na CB B:Ser184 3.32 Na OG B:Ser184 2.07 Na C B:Ser184 4.01 Na CA B:Ser184 4.11 Na O B:Gly185 2.59 Na N B:Gly185 3.96 Na C B:Gly185 3.75 Na CA B:Gly185 4.50 Na N B:Gly186 4.70 Na CA B:Gly186 4.84 interactive model: