Sodium in the structure of Glycine Ethyl Ester Shielding on the Aromatic Surfaces Of Lysozyme: Implication For Suppression of Protein Aggregation (pdb 3ato)

The binding sites of Sodium atom in the structure of Glycine Ethyl Ester Shielding on the Aromatic Surfaces Of Lysozyme: Implication For Suppression of Protein Aggregation (pdb code 3ato). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3ato structure was solved by L.ITO, K.SHIRAKI, K.HASEGAWA, T.KUMASAKA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.6-1.2 Space group P43212 a (A) 77.171 b (A) 77.171 c (A) 36.898 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 15.4 Rfree (%) 17.5 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3ato Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3ato. 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: Ser60, A: Arg61, A: Trp62, A: Cys64, A: Asn65, A: Asp66, A: Thr69, A: Ser72, A: Arg73, A: Asn74, A: Cl211, A: Hoh304, A: Hoh335, A: Hoh346, conact list: Atom Atom Distance (A) Na O A:Ser60 2.22 Na CB A:Ser60 4.22 Na OG A:Ser60 4.95 Na C A:Ser60 3.31 Na CA A:Ser60 3.96 Na O A:Arg61 4.58 Na N A:Arg61 4.40 Na C A:Arg61 4.47 Na CA A:Arg61 4.74 Na N A:Trp62 4.74 Na O A:Cys64 2.69 Na N A:Cys64 4.65 Na C A:Cys64 3.78 Na CA A:Cys64 4.87 Na N A:Asn65 4.41 Na OD1 A:Asn65 4.79 Na CA A:Asn65 4.14 Na N A:Asp66 4.77 Na O A:Thr69 4.78 Na CB A:Thr69 4.45 Na CG2 A:Thr69 4.91 Na OG1 A:Thr69 4.94 Na O A:Ser72 4.79 Na CB A:Ser72 3.26 Na OG A:Ser72 2.59 Na C A:Ser72 4.16 Na CA A:Ser72 4.31 Na O A:Arg73 2.41 Na N A:Arg73 3.88 Na C A:Arg73 3.42 Na CA A:Arg73 4.20 Na N A:Asn74 4.36 Na CB A:Asn74 4.92 Na CA A:Asn74 4.71 Na CL A:Cl211 4.75 Na O A:Hoh304 2.43 Na O A:Hoh335 4.73 Na O A:Hoh346 2.34 interactive model: