Sodium in PDB 1h6m: Covalent Glycosyl-Enzyme Intermediate of Hen Egg White Lysozyme

All present enzymatic activity of Covalent Glycosyl-Enzyme Intermediate of Hen Egg White Lysozyme:
3.2.1.17;

The structure of Covalent Glycosyl-Enzyme Intermediate of Hen Egg White Lysozyme, PDB code: 1h6m was solved by D.J.Vocadlo, G.J.Davies, R.Laine, S.G.Withers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.00 / 1.64
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.632, 78.632, 36.700, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 22.2

The structure of Covalent Glycosyl-Enzyme Intermediate of Hen Egg White Lysozyme also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Sodium atom in the Covalent Glycosyl-Enzyme Intermediate of Hen Egg White Lysozyme (pdb code 1h6m). 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 Covalent Glycosyl-Enzyme Intermediate of Hen Egg White Lysozyme, PDB code: 1h6m:

Sodium binding site 1 out of 1 in the Covalent Glycosyl-Enzyme Intermediate of Hen Egg White Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Covalent Glycosyl-Enzyme Intermediate of Hen Egg White Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1130 b:20.1 occ:1.00 O A:SER60 2.3 15.2 1.0 O A:CYS64 2.3 13.5 1.0 O A:HOH2116 2.4 14.3 1.0 O A:HOH2112 2.5 19.4 1.0 O A:ARG73 2.5 19.7 1.0 OG A:SER72 2.5 21.7 1.0 CB A:SER72 3.3 21.8 1.0 C A:SER60 3.4 15.2 1.0 C A:CYS64 3.4 12.5 1.0 C A:ARG73 3.5 18.6 1.0 CA A:ASN65 3.8 13.3 1.0 N A:ARG73 4.0 20.2 1.0 CA A:SER60 4.0 12.4 1.0 N A:ASN65 4.1 13.2 1.0 C A:SER72 4.2 23.6 1.0 CB A:SER60 4.2 13.8 1.0 CA A:ARG73 4.3 19.3 1.0 CA A:SER72 4.4 22.9 1.0 N A:ASN74 4.4 18.3 1.0 N A:CYS64 4.4 14.2 1.0 N A:ARG61 4.5 17.6 1.0 N A:ASP66 4.6 12.0 1.0 CA A:ASN74 4.6 16.3 1.0 O A:HOH2127 4.6 34.1 1.0 CA A:CYS64 4.6 15.2 1.0 C A:ARG61 4.6 20.5 1.0 CB A:THR69 4.6 16.3 1.0 O A:ARG61 4.6 19.8 1.0 OD1 A:ASN65 4.6 17.4 1.0 O A:HOH2122 4.7 11.2 1.0 CB A:ASN74 4.7 15.2 1.0 C A:ASN65 4.7 12.7 1.0 CB A:ASN65 4.8 14.3 1.0 O A:SER72 4.8 24.9 1.0 CA A:ARG61 4.8 20.5 1.0 N A:TRP62 4.9 18.3 1.0

D.J.Vocadlo, G.J.Davies, R.Laine, S.G.Withers. Catalysis By Hen Egg-White Lysozyme Proceeds Via A Covalent Intermediate Nature V. 412 835 2001.
ISSN: ISSN 0028-0836
PubMed: 11518970
DOI: 10.1038/35090602