Sodium in PDB 7vgp: Hen Egg Lysozyme Refolded After Denaturation at Acidic pH

All present enzymatic activity of Hen Egg Lysozyme Refolded After Denaturation at Acidic pH:
3.2.1.17;

The structure of Hen Egg Lysozyme Refolded After Denaturation at Acidic pH, PDB code: 7vgp 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)	31.17 / 1.91
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	31.543, 53.445, 71.219, 90, 98.82, 90
R / Rfree (%)	20.2 / 25.5

The binding sites of Sodium atom in the Hen Egg Lysozyme Refolded After Denaturation at Acidic pH (pdb code 7vgp). 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 Refolded After Denaturation at Acidic pH, PDB code: 7vgp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hen Egg Lysozyme Refolded After Denaturation at Acidic pH


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 Refolded After Denaturation at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:25.0 occ:1.00 O A:CYS64 2.3 17.1 1.0 O A:ARG73 2.4 26.7 1.0 O A:SER60 2.4 21.3 1.0 O A:HOH305 2.4 22.0 1.0 O A:HOH311 2.7 16.3 1.0 OG A:SER72 2.7 31.8 1.0 CB A:SER72 3.3 24.9 1.0 C A:CYS64 3.3 19.2 1.0 C A:ARG73 3.4 23.6 1.0 C A:SER60 3.5 20.2 1.0 CA A:ASN65 3.8 17.5 1.0 N A:ARG73 3.9 23.5 1.0 N A:ASN65 3.9 18.9 1.0 CA A:SER60 4.1 14.6 1.0 C A:SER72 4.2 28.1 1.0 N A:ASN74 4.2 19.5 1.0 N A:CYS64 4.3 17.5 1.0 CA A:ARG73 4.3 20.6 1.0 CA A:SER72 4.3 29.3 1.0 CA A:ASN74 4.4 16.3 1.0 C A:ARG61 4.4 22.6 1.0 O A:ARG61 4.4 24.9 1.0 CB A:SER60 4.4 18.4 1.0 CA A:CYS64 4.4 17.2 1.0 OD1 A:ASN65 4.5 24.2 1.0 CB A:ASN74 4.5 18.1 1.0 N A:ARG61 4.5 16.5 1.0 CB A:ASN65 4.6 17.8 1.0 N A:ASP66 4.7 19.4 1.0 O A:HOH313 4.7 24.7 1.0 CA A:ARG61 4.7 22.1 1.0 C A:ASN65 4.7 16.2 1.0 N A:TRP62 4.8 18.6 1.0 O A:SER72 4.8 21.7 1.0 N A:TRP63 4.9 15.1 1.0 C A:TRP62 4.9 17.6 1.0

Sodium binding site 2 out of 2 in the Hen Egg Lysozyme Refolded After Denaturation at Acidic pH


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 Refolded After Denaturation at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:20.9 occ:1.00 O B:CYS64 2.3 20.5 1.0 O B:SER60 2.4 21.2 1.0 O B:HOH309 2.5 22.7 1.0 O B:ARG73 2.5 20.7 1.0 OG B:SER72 2.6 19.1 1.0 O B:HOH304 2.6 22.0 1.0 C B:CYS64 3.4 21.1 1.0 CB B:SER72 3.4 22.2 1.0 C B:SER60 3.5 19.1 1.0 C B:ARG73 3.5 17.6 1.0 CA B:ASN65 3.9 20.8 1.0 N B:ARG73 4.0 18.1 1.0 N B:ASN65 4.0 19.0 1.0 CA B:SER60 4.0 16.9 1.0 CB B:SER60 4.1 16.9 1.0 C B:SER72 4.2 22.3 1.0 N B:CYS64 4.3 19.3 1.0 CA B:ARG73 4.4 19.0 1.0 N B:ASN74 4.4 14.1 1.0 CA B:SER72 4.4 21.9 1.0 CA B:CYS64 4.5 21.0 1.0 C B:ARG61 4.6 22.4 1.0 O B:ARG61 4.6 21.7 1.0 CA B:ASN74 4.6 20.9 1.0 N B:ARG61 4.6 18.0 1.0 OD1 B:ASN65 4.6 23.1 1.0 O B:HOH314 4.7 16.2 1.0 O B:SER72 4.7 22.9 1.0 N B:ASP66 4.7 17.8 1.0 CB B:ASN74 4.7 20.2 1.0 C B:ASN65 4.8 18.5 1.0 CB B:THR69 4.8 21.5 1.0 N B:TRP62 4.8 18.9 1.0 CB B:ASN65 4.9 20.9 1.0 CA B:ARG61 4.9 21.4 1.0 OG B:SER60 5.0 16.7 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