Chlorine in PDB 7der: Lysozyme Alone in H2O

All present enzymatic activity of Lysozyme Alone in H2O:
3.2.1.17;

The structure of Lysozyme Alone in H2O, PDB code: 7der 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)	33.56 / 1.03
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.777, 78.777, 37.093, 90, 90, 90
R / Rfree (%)	14.9 / 17.3

The structure of Lysozyme Alone in H2O also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Lysozyme Alone in H2O (pdb code 7der). 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 Alone in H2O, PDB code: 7der:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Lysozyme Alone 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 Alone in H2O within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:13.6 occ:1.00 ND2 A:ASN113 3.4 13.1 1.0 CB A:ASN113 3.6 11.5 1.0 CA A:ALA110 3.8 15.4 1.0 CG A:ASN113 4.0 12.5 1.0 CD A:ARG114 4.2 10.8 1.0 CB A:ALA110 4.2 17.7 1.0 O A:VAL109 4.2 16.8 1.0 N A:ALA110 4.2 16.7 1.0 CG A:ARG114 4.4 11.4 1.0 C A:VAL109 4.4 17.3 1.0 CG1 A:VAL109 4.5 21.9 1.0 O A:HOH464 4.6 19.8 1.0 C A:ALA110 4.8 13.1 1.0 O A:ALA110 4.9 12.2 1.0 CA A:ASN113 4.9 11.6 1.0

Chlorine binding site 2 out of 4 in the Lysozyme Alone 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 Alone in H2O within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:22.5 occ:1.00 O A:HOH435 3.2 28.2 0.6 O A:HOH394 3.3 42.2 1.0 CE2 A:PHE38 3.6 12.2 1.0 NZ A:LYS33 3.8 20.4 1.0 CZ3 A:TRP123 3.9 15.8 1.0 CD A:ARG5 4.2 16.4 1.0 CB A:ARG5 4.3 16.1 1.0 CE A:LYS33 4.3 18.2 1.0 CD A:LYS33 4.3 15.1 1.0 CZ A:PHE38 4.3 11.8 1.0 CD2 A:PHE38 4.6 11.6 1.0 CG A:ARG5 4.6 15.4 1.0 CE3 A:TRP123 4.7 14.9 1.0 NE A:ARG5 4.7 17.6 1.0 O A:HOH435 4.7 31.4 0.4 O A:HOH449 4.7 33.9 1.0 CH2 A:TRP123 4.8 16.4 1.0

Chlorine binding site 3 out of 4 in the Lysozyme Alone 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 Alone in H2O within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:17.6 occ:1.00 O A:HOH443 2.7 32.2 1.0 OG A:SER24 3.0 15.2 1.0 O A:HOH501 3.1 34.1 1.0 N A:GLY26 3.1 11.3 1.0 CA A:GLY26 3.4 10.7 1.0 CB A:SER24 3.5 14.0 1.0 CA A:GLN121 3.6 16.1 1.0 CD1 A:ILE124 3.8 23.6 1.0 N A:GLN121 3.9 14.5 1.0 CB A:GLN121 4.0 19.3 1.0 CG A:GLN121 4.2 21.1 1.0 O A:VAL120 4.2 13.1 1.0 C A:VAL120 4.2 13.3 1.0 CG2 A:VAL120 4.3 14.9 1.0 CG1 A:ILE124 4.3 20.8 1.0 N A:LEU25 4.3 13.0 1.0 C A:LEU25 4.4 11.9 1.0 O A:HOH505 4.4 39.2 1.0 C A:SER24 4.4 12.6 1.0 C A:GLY26 4.5 10.1 1.0 N A:ASN27 4.6 10.2 1.0 CA A:SER24 4.6 12.5 1.0 CA A:LEU25 4.8 12.9 1.0 C A:GLN121 4.8 14.4 1.0 O A:SER24 4.9 12.7 1.0

Chlorine binding site 4 out of 4 in the Lysozyme Alone 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 Alone in H2O within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:16.4 occ:1.00 N A:THR69 3.0 13.3 1.0 O A:HOH460 3.1 26.6 1.0 O A:THR69 3.1 16.3 1.0 O A:HOH391 3.3 13.9 1.0 N A:ARG68 3.5 12.6 1.0 C A:THR69 3.5 15.2 1.0 C A:GLY67 3.5 13.4 1.0 CA A:GLY67 3.6 13.3 1.0 CA A:THR69 3.7 13.6 1.0 N A:GLY67 3.7 12.6 1.0 O A:HOH419 3.8 38.1 1.0 OD1 A:ASN65 3.8 16.6 1.0 OG A:SER72 3.8 18.1 1.0 C A:ARG68 4.1 14.7 1.0 O A:HOH438 4.1 18.7 1.0 CB A:THR69 4.1 13.7 1.0 O A:GLY67 4.1 16.1 1.0 CA A:ARG68 4.2 14.1 1.0 OD1 A:ASP66 4.3 10.2 1.0 N A:PRO70 4.3 17.9 1.0 O A:HOH463 4.6 52.1 1.0 NA A:NA205 4.7 15.3 1.0 OG1 A:THR69 4.7 12.7 1.0 C A:ASP66 4.8 11.0 1.0 O A:HOH369 4.8 15.4 0.5 CA A:PRO70 4.9 20.0 1.0 N A:ASP66 5.0 10.5 1.0 CG A:ASN65 5.0 15.9 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