Sodium in PDB 3a34: Effect of Ariginine on Lysozyme

All present enzymatic activity of Effect of Ariginine on Lysozyme:
3.2.1.17;

The structure of Effect of Ariginine on Lysozyme, PDB code: 3a34 was solved by L.Ito, K.Shiraki, T.Matsuura, H.Yamaguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.69 / 1.65
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.357, 78.357, 37.312, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 22.6

The structure of Effect of Ariginine on Lysozyme also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Effect of Ariginine on Lysozyme (pdb code 3a34). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Effect of Ariginine on Lysozyme, PDB code: 3a34:

Sodium binding site 1 out of 1 in the Effect of Ariginine on Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Effect of Ariginine on Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na137 b:12.9 occ:1.00 O A:HOH167 2.3 9.6 1.0 O A:SER60 2.4 10.1 1.0 O A:HOH158 2.5 10.7 1.0 O A:CYS64 2.5 8.7 1.0 O A:ARG73 2.5 13.4 1.0 OG A:SER72 2.5 15.1 1.0 CB A:SER72 3.4 15.4 1.0 C A:ARG73 3.5 13.8 1.0 C A:SER60 3.5 10.2 1.0 C A:CYS64 3.5 8.8 1.0 CA A:ASN65 3.9 9.4 1.0 N A:ARG73 4.0 14.8 1.0 C A:SER72 4.1 15.3 1.0 N A:ASN65 4.2 9.1 1.0 CA A:SER60 4.2 9.6 1.0 CA A:ARG73 4.3 14.5 1.0 CB A:SER60 4.4 9.7 1.0 N A:ASN74 4.4 13.2 1.0 CA A:SER72 4.4 15.4 1.0 N A:CYS64 4.5 9.1 1.0 CA A:ASN74 4.6 12.6 1.0 O A:SER72 4.6 15.6 1.0 N A:ARG61 4.6 10.6 1.0 OD1 A:ASN65 4.6 11.3 1.0 C A:ARG61 4.6 11.3 1.0 N A:ASP66 4.6 9.8 1.0 CA A:CYS64 4.7 8.9 1.0 CL A:CL136 4.7 13.3 1.0 CB A:ASN74 4.7 12.6 1.0 CB A:THR69 4.7 12.9 1.0 O A:ARG61 4.7 11.4 1.0 CB A:ASN65 4.8 9.8 1.0 C A:ASN65 4.8 9.6 1.0 N A:TRP62 4.9 11.3 1.0 CA A:ARG61 4.9 11.3 0.7 CA A:ARG61 4.9 11.0 0.3 O A:THR69 5.0 12.9 1.0

L.Ito, K.Shiraki, T.Matsuura, H.Yamaguchi. Implication of Arg Bindings on Aromatic Surfaces of Lysozyme For Additives That Prevent Protein Aggregation To Be Published.