Chlorine in PDB 7br5: Lysozyme-Sugar Complex in H2O

All present enzymatic activity of Lysozyme-Sugar Complex in H2O:
3.2.1.17;

The structure of Lysozyme-Sugar Complex in H2O, PDB code: 7br5 was solved by I.Tanaka, T.Chatake, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	16.83 / 1.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.309, 77.309, 38.214, 90, 90, 90
R / Rfree (%)	13.9 / 16.7

The structure of Lysozyme-Sugar Complex in H2O also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Lysozyme-Sugar Complex in H2O (pdb code 7br5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Lysozyme-Sugar Complex in H2O, PDB code: 7br5:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Lysozyme-Sugar Complex in H2O


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Lysozyme-Sugar Complex in H2O within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:13.2 occ:0.85 O A:HOH407 3.2 13.4 0.8 ND2 A:ASN113 3.4 13.4 1.0 CB A:ASN113 3.6 11.7 1.0 CA A:ALA110 3.8 11.0 1.0 O A:VAL109 3.9 11.3 1.0 CG A:ASN113 4.0 12.6 1.0 CG1 A:VAL109 4.0 15.0 0.7 O A:HOH407 4.2 14.6 0.2 N A:ALA110 4.2 10.6 1.0 C A:VAL109 4.2 10.3 1.0 CD A:ARG114 4.2 11.5 1.0 CB A:ALA110 4.4 12.1 1.0 CG A:ARG114 4.4 11.0 1.0 C A:ALA110 4.8 10.3 1.0 CG2 A:VAL109 4.8 13.1 0.3 CB A:VAL109 4.9 15.1 0.7 CA A:ASN113 4.9 11.3 1.0 O A:ALA110 4.9 10.7 1.0 CB A:VAL109 5.0 12.9 0.3

Chlorine binding site 2 out of 4 in the Lysozyme-Sugar Complex in H2O


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Lysozyme-Sugar Complex in H2O within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:33.9 occ:1.00 O A:HOH396 3.0 41.2 1.0 O A:HOH465 3.5 39.4 1.0 NZ A:LYS33 3.6 22.6 1.0 CE2 A:PHE38 3.6 12.9 1.0 CE A:LYS33 3.9 20.5 1.0 CD A:LYS33 4.1 18.2 1.0 CZ3 A:TRP123 4.1 19.0 1.0 CD A:ARG5 4.3 16.0 1.0 CZ A:PHE38 4.3 11.7 1.0 CB A:ARG5 4.4 15.0 1.0 CD2 A:PHE38 4.6 12.8 1.0 CG A:ARG5 4.7 14.9 1.0 NE A:ARG5 4.8 16.6 1.0 CE3 A:TRP123 4.9 15.8 1.0 O A:HOH371 4.9 50.5 1.0 O A:HOH387 5.0 25.9 1.0 CH2 A:TRP123 5.0 18.9 1.0

Chlorine binding site 3 out of 4 in the Lysozyme-Sugar Complex in H2O


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Lysozyme-Sugar Complex in H2O within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:20.1 occ:1.00 OG A:SER24 3.1 17.1 1.0 N A:GLY26 3.1 11.7 1.0 O A:HOH467 3.3 33.0 1.0 CA A:GLN121 3.5 16.6 1.0 CB A:SER24 3.5 15.7 1.0 CA A:GLY26 3.6 11.5 1.0 CB A:GLN121 3.8 18.4 1.0 N A:GLN121 4.0 16.2 1.0 CG A:GLN121 4.0 20.4 1.0 N A:LEU25 4.1 12.4 1.0 CD1 A:ILE124 4.1 21.6 1.0 C A:SER24 4.3 12.2 1.0 C A:LEU25 4.3 10.9 1.0 C A:VAL120 4.4 14.8 1.0 O A:VAL120 4.4 14.0 1.0 CG1 A:ILE124 4.5 19.7 1.0 CG2 A:VAL120 4.5 16.8 1.0 CA A:SER24 4.5 13.0 1.0 CA A:LEU25 4.6 12.2 1.0 C A:GLY26 4.6 10.2 1.0 C A:GLN121 4.7 15.1 1.0 N A:ASN27 4.7 10.3 1.0 O A:SER24 4.8 12.8 1.0 O A:HOH471 4.9 49.9 1.0 CB A:LEU25 4.9 12.9 1.0 O A:GLN121 4.9 16.1 1.0 O A:HOH310 4.9 16.9 1.0

Chlorine binding site 4 out of 4 in the Lysozyme-Sugar Complex in H2O


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Lysozyme-Sugar Complex in H2O within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:16.4 occ:0.75 O A:HOH448 3.1 50.7 1.0 O A:HOH449 3.1 45.9 1.0 O A:HOH376 3.2 14.3 1.0 O A:THR69 3.3 18.5 1.0 N A:THR69 3.3 15.3 1.0 O A:HOH369 3.3 38.6 1.0 C A:THR69 3.5 17.3 1.0 OD1 A:ASN65 3.6 16.9 1.0 C A:GLY67 3.6 16.6 1.0 CA A:GLY67 3.6 16.3 1.0 N A:ARG68 3.7 15.4 1.0 N A:GLY67 3.7 14.2 1.0 OG A:SER72 3.8 17.9 1.0 CA A:THR69 3.9 15.5 1.0 O A:HOH391 4.0 17.1 1.0 N A:PRO70 4.1 20.3 1.0 O A:GLY67 4.2 19.4 1.0 CB A:THR69 4.3 14.2 1.0 C A:ARG68 4.3 15.9 1.0 OD1 A:ASP66 4.4 12.9 1.0 CA A:ARG68 4.4 16.0 0.5 CA A:ARG68 4.5 16.0 0.5 CA A:PRO70 4.5 22.2 1.0 NA A:NA205 4.7 14.2 1.0 C A:ASP66 4.8 13.1 1.0 CG A:ASN65 4.8 15.7 1.0 N A:ASP66 4.9 12.1 1.0 OG1 A:THR69 4.9 13.4 1.0

I.Tanaka, R.Nishinomiya, R.Goto, S.Shimazaki, T.Chatake. Recent Structural Insights Into the Mechanism of Lysozyme Hydrolysis. Acta Crystallogr D Struct V. 77 288 2021BIOL.
ISSN: ISSN 2059-7983
PubMed: 33645532
DOI: 10.1107/S2059798321000346