Chlorine in PDB 7deq: Lysozyme-Sugar Complex in D2O

All present enzymatic activity of Lysozyme-Sugar Complex in D2O:
3.2.1.17;

The structure of Lysozyme-Sugar Complex in D2O, PDB code: 7deq 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)	34.45 / 1.03
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.029, 77.029, 38.285, 90, 90, 90
R / Rfree (%)	13.3 / 14.9

The structure of Lysozyme-Sugar Complex in D2O also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Lysozyme-Sugar Complex in D2O (pdb code 7deq). 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 D2O, PDB code: 7deq:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Lysozyme-Sugar Complex in D2O


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 D2O within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:15.7 occ:1.00 OG A:SER24 3.1 14.8 1.0 N A:GLY26 3.1 9.7 1.0 O A:DOD481 3.2 34.9 1.0 CB A:SER24 3.5 13.3 1.0 CA A:GLN121 3.5 12.5 1.0 CA A:GLY26 3.6 9.5 1.0 CB A:GLN121 3.7 13.7 1.0 N A:GLN121 4.0 12.0 1.0 CG A:GLN121 4.0 14.4 1.0 N A:LEU25 4.1 10.6 1.0 CD1 A:ILE124 4.1 18.3 1.0 C A:SER24 4.2 10.4 1.0 C A:LEU25 4.3 9.5 1.0 C A:VAL120 4.4 11.2 1.0 O A:VAL120 4.4 10.9 1.0 CG2 A:VAL120 4.4 13.8 1.0 CA A:SER24 4.5 11.3 1.0 CG1 A:ILE124 4.5 16.3 1.0 CA A:LEU25 4.6 10.3 1.0 C A:GLY26 4.6 8.6 1.0 N A:ASN27 4.7 8.5 1.0 O A:SER24 4.7 11.2 1.0 C A:GLN121 4.8 11.8 1.0 CB A:LEU25 4.9 11.1 1.0 O A:DOD361 4.9 18.1 0.9 O A:GLN121 5.0 12.1 1.0

Chlorine binding site 2 out of 4 in the Lysozyme-Sugar Complex in D2O


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 D2O within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:13.1 occ:1.00 ND2 A:ASN113 3.4 11.3 1.0 CB A:ASN113 3.6 10.4 1.0 CA A:ALA110 3.8 9.8 1.0 O A:VAL109 3.9 10.1 1.0 CG A:ASN113 4.0 11.2 1.0 CG1 A:VAL109 4.1 16.9 1.0 N A:ALA110 4.2 9.7 1.0 C A:VAL109 4.2 9.2 1.0 CD A:ARG114 4.3 10.5 1.0 CB A:ALA110 4.4 11.1 1.0 CG A:ARG114 4.4 10.4 1.0 C A:ALA110 4.8 9.2 1.0 CA A:ASN113 4.9 9.8 1.0 O A:ALA110 4.9 9.5 1.0 CB A:VAL109 5.0 14.7 1.0

Chlorine binding site 3 out of 4 in the Lysozyme-Sugar Complex in D2O


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 D2O within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:16.4 occ:0.57 O A:DOD391 3.2 13.1 1.0 O A:THR69 3.2 17.8 1.0 N A:THR69 3.3 13.2 1.0 C A:THR69 3.5 16.9 1.0 OD1 A:ASN65 3.5 15.3 1.0 C A:GLY67 3.6 15.1 1.0 N A:ARG68 3.6 13.4 1.0 CA A:GLY67 3.6 15.1 1.0 N A:GLY67 3.7 13.3 1.0 OG A:SER72 3.8 21.1 1.0 CA A:THR69 3.9 14.1 1.0 O A:DOD418 4.0 61.6 1.0 O A:DOD395 4.0 19.6 1.0 O A:GLY67 4.2 17.5 1.0 N A:PRO70 4.2 21.4 1.0 CB A:THR69 4.2 12.1 1.0 C A:ARG68 4.3 14.3 1.0 OD1 A:ASP66 4.3 11.2 1.0 CA A:ARG68 4.4 13.8 1.0 CA A:PRO70 4.5 24.3 1.0 NA A:NA205 4.7 11.5 0.6 CG A:ASN65 4.7 15.4 1.0 C A:ASP66 4.8 12.1 1.0 N A:ASP66 4.8 10.7 1.0 OG1 A:THR69 4.9 12.0 1.0

Chlorine binding site 4 out of 4 in the Lysozyme-Sugar Complex in D2O


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 D2O within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:28.5 occ:1.00 O A:DOD375 2.9 32.0 1.0 O A:DOD473 3.2 41.7 1.0 NZ A:LYS33 3.5 20.9 1.0 CE2 A:PHE38 3.6 11.7 1.0 CE A:LYS33 3.9 19.2 1.0 CD A:LYS33 4.0 16.5 1.0 CZ3 A:TRP123 4.0 16.6 1.0 CD A:ARG5 4.2 12.2 1.0 CZ A:PHE38 4.3 10.3 1.0 CB A:ARG5 4.4 11.7 1.0 O A:DOD381 4.4 48.5 1.0 CD2 A:PHE38 4.5 11.2 1.0 O A:DOD351 4.6 44.2 1.0 O A:DOD488 4.6 39.1 1.0 CG A:ARG5 4.7 11.7 1.0 NE A:ARG5 4.7 13.2 1.0 CE3 A:TRP123 4.8 13.5 1.0 CH2 A:TRP123 4.9 17.0 1.0 O A:DOD397 5.0 23.5 1.0 CG A:LYS33 5.0 14.1 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