Sodium in PDB 7vgo: Hen Egg Lysozyme

All present enzymatic activity of Hen Egg Lysozyme:
3.2.1.17;

The structure of Hen Egg Lysozyme, PDB code: 7vgo was solved by M.Oda, T.Ikura, N.Ito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.49 / 1.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.816, 78.816, 36.917, 90, 90, 90
R / Rfree (%)	14.5 / 16.2

The structure of Hen Egg Lysozyme also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Hen Egg Lysozyme (pdb code 7vgo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Hen Egg Lysozyme, PDB code: 7vgo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hen Egg Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hen Egg Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:30.6 occ:1.00 O A:HOH335 2.6 43.4 1.0 OE1 A:GLU35 2.7 10.8 1.0 O A:HOH328 2.7 16.3 1.0 O A:HOH398 2.7 31.5 1.0 O A:HOH303 3.1 16.6 1.0 OD2 A:ASP52 3.2 17.1 1.0 CD A:GLU35 3.6 10.1 1.0 OE2 A:GLU35 3.9 10.6 1.0 CB A:GLN57 4.0 9.2 1.0 O A:HOH318 4.0 40.3 1.0 O A:HOH338 4.2 33.5 1.0 O A:HOH400 4.2 37.5 1.0 O A:HOH355 4.3 22.4 1.0 CG A:ASP52 4.4 13.4 1.0 CG A:GLN57 4.5 9.4 1.0 O A:HOH337 4.6 16.6 1.0 O A:GLN57 4.7 10.8 1.0 OE1 A:GLN57 4.9 10.5 1.0 CB A:ASP52 5.0 10.9 1.0

Sodium binding site 2 out of 2 in the Hen Egg Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hen Egg Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:12.9 occ:1.00 O A:SER60 2.3 12.9 1.0 O A:HOH375 2.4 15.9 1.0 O A:ARG73 2.4 15.5 1.0 O A:CYS64 2.4 10.8 1.0 O A:HOH351 2.5 12.4 1.0 OG A:SER72 2.5 15.5 1.0 CB A:SER72 3.2 15.5 1.0 C A:SER60 3.5 12.1 1.0 C A:ARG73 3.5 15.0 1.0 C A:CYS64 3.5 11.0 1.0 N A:ARG73 3.9 15.9 1.0 CA A:ASN65 3.9 10.8 1.0 CA A:SER60 4.0 10.6 1.0 N A:ASN65 4.2 10.5 1.0 C A:SER72 4.2 15.7 1.0 CB A:SER60 4.2 10.6 1.0 CA A:ARG73 4.3 15.4 1.0 CA A:SER72 4.3 15.7 1.0 N A:ASN74 4.4 14.6 1.0 N A:CYS64 4.5 11.0 1.0 N A:ARG61 4.6 13.4 1.0 C A:ARG61 4.6 14.8 1.0 CA A:ASN74 4.6 13.7 1.0 O A:ARG61 4.6 16.1 1.0 N A:ASP66 4.7 10.0 1.0 CB A:THR69 4.7 12.3 1.0 CA A:CYS64 4.7 10.9 1.0 OD1 A:ASN65 4.7 14.1 1.0 CL A:CL205 4.7 15.4 1.0 CB A:ASN74 4.7 14.0 1.0 O A:SER72 4.8 17.5 1.0 C A:ASN65 4.8 9.7 1.0 CA A:ARG61 4.8 16.5 1.0 CB A:ASN65 4.9 12.3 1.0 N A:TRP62 4.9 13.6 1.0

M.Oda, T.Sano, Y.O.Kamatari, Y.Abe, T.Ikura, N.Ito. Structural Analysis of Hen Egg Lysozyme Refolded After Denaturation at Acidic pH. Protein J. V. 41 71 2022.
ISSN: ISSN 1572-3887
PubMed: 35094218
DOI: 10.1007/S10930-021-10036-3