Chlorine 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:

Sodium

(Na)

2 atoms

The binding sites of Chlorine atom in the Hen Egg Lysozyme (pdb code 7vgo). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Hen Egg Lysozyme, PDB code: 7vgo:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Hen Egg Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hen Egg Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:15.6 occ:1.00 OH A:TYR23 3.0 12.0 1.0 O A:HOH372 3.2 31.5 1.0 O A:HOH339 3.2 15.9 1.0 CZ A:TYR23 3.7 11.2 1.0 CE2 A:TYR23 3.7 11.0 1.0 CA A:GLY104 4.1 11.8 1.0 O A:ARG21 4.6 14.4 1.0 N A:GLY104 4.7 13.0 1.0 CE1 A:TYR23 4.9 10.7 1.0 CD2 A:TYR23 4.9 10.9 1.0

Chlorine binding site 2 out of 4 in the Hen Egg Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hen Egg Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:21.7 occ:1.00 OG A:SER24 3.0 17.2 1.0 N A:GLY26 3.1 11.5 1.0 CB A:SER24 3.5 15.5 1.0 CA A:GLY26 3.5 12.0 1.0 CA A:GLN121 3.6 17.5 1.0 CD1 A:ILE124 3.9 22.4 1.0 CB A:GLN121 3.9 22.6 1.0 N A:GLN121 4.0 15.6 1.0 N A:LEU25 4.1 13.4 1.0 CG1 A:ILE124 4.3 20.6 1.0 C A:VAL120 4.3 14.2 1.0 O A:VAL120 4.3 13.8 1.0 CG A:GLN121 4.3 28.6 1.0 C A:LEU25 4.3 12.5 1.0 CG2 A:VAL120 4.3 15.2 1.0 C A:SER24 4.3 13.0 1.0 C A:GLY26 4.5 10.1 1.0 CA A:SER24 4.5 13.1 1.0 N A:ASN27 4.6 10.2 1.0 CA A:LEU25 4.7 13.9 1.0 O A:SER24 4.8 12.9 1.0 C A:GLN121 4.8 15.3 1.0

Chlorine binding site 3 out of 4 in the Hen Egg Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hen Egg Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl205 b:15.4 occ:1.00 O A:HOH351 3.2 12.4 1.0 O A:HOH395 3.2 38.2 1.0 N A:THR69 3.2 12.3 1.0 O A:HOH396 3.2 25.9 1.0 O A:THR69 3.3 14.2 1.0 N A:ARG68 3.5 12.1 1.0 C A:GLY67 3.6 13.2 1.0 O A:HOH369 3.6 32.8 1.0 CA A:GLY67 3.6 13.5 1.0 C A:THR69 3.7 12.9 1.0 OG A:SER72 3.7 15.5 1.0 N A:GLY67 3.7 11.6 1.0 OD1 A:ASN65 3.7 14.1 1.0 CA A:THR69 3.8 12.1 1.0 O A:HOH375 4.0 15.9 1.0 O A:GLY67 4.2 15.0 1.0 CB A:THR69 4.2 12.3 1.0 C A:ARG68 4.2 14.1 1.0 OD1 A:ASP66 4.2 10.3 1.0 CA A:ARG68 4.3 13.0 1.0 N A:PRO70 4.5 14.2 1.0 O A:HOH408 4.6 32.2 1.0 NA A:NA202 4.7 12.9 1.0 O A:HOH360 4.8 21.1 0.5 C A:ASP66 4.8 10.6 1.0 OG1 A:THR69 4.8 11.8 1.0 N A:ASP66 4.9 10.0 1.0 CB A:SER72 4.9 15.5 1.0 CG A:ASN65 4.9 13.9 1.0

Chlorine binding site 4 out of 4 in the Hen Egg Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hen Egg Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl206 b:27.3 occ:1.00 NZ A:LYS33 3.6 18.6 1.0 CE2 A:PHE38 3.6 11.3 1.0 CZ3 A:TRP123 3.9 17.6 1.0 CE A:LYS33 4.0 16.6 1.0 CD A:LYS33 4.2 14.3 1.0 CB A:ARG5 4.3 15.9 1.0 CD A:ARG5 4.3 16.6 1.0 CZ A:PHE38 4.3 10.6 1.0 O A:HOH378 4.3 35.0 1.0 CD2 A:PHE38 4.6 10.3 1.0 CG A:ARG5 4.7 16.3 1.0 CE3 A:TRP123 4.8 15.2 1.0 CH2 A:TRP123 4.8 18.3 1.0 NE A:ARG5 4.9 18.3 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