Chlorine in PDB 8dct: Lysozyme Cluster 3 Dual Apo Structure

All present enzymatic activity of Lysozyme Cluster 3 Dual Apo Structure:
3.2.1.17;

The structure of Lysozyme Cluster 3 Dual Apo Structure, PDB code: 8dct was solved by A.S.Soares, Y.Yamada, J.Jakoncic, D.K.Schneider, H.J.Bernstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.65 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.23, 79.23, 37.52, 90, 90, 90
R / Rfree (%)	20.6 / 26.5

The structure of Lysozyme Cluster 3 Dual Apo Structure also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Lysozyme Cluster 3 Dual Apo Structure (pdb code 8dct). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Lysozyme Cluster 3 Dual Apo Structure, PDB code: 8dct:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Lysozyme Cluster 3 Dual Apo Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Lysozyme Cluster 3 Dual Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:64.1 occ:1.00 O A:HOH377 3.3 48.5 1.0 N A:ILE88 3.4 35.4 1.0 O A:HOH317 3.4 46.8 1.0 OD1 A:ASP87 3.5 54.4 1.0 O A:HOH457 3.5 45.0 1.0 CA A:ASP87 3.7 39.0 1.0 CG1 A:ILE88 3.9 34.7 1.0 O A:SER86 3.9 35.3 1.0 O A:HOH380 3.9 21.8 0.5 NE2 A:HIS15 4.0 43.1 1.0 C A:ASP87 4.0 38.1 1.0 CG A:ASP87 4.2 47.1 1.0 CG2 A:ILE88 4.4 36.9 1.0 CB A:ILE88 4.4 34.8 1.0 CA A:ILE88 4.4 34.0 1.0 CZ A:PHE3 4.4 24.5 1.0 CB A:ASP87 4.5 43.2 1.0 CB A:ALA11 4.6 26.8 1.0 N A:ASP87 4.6 34.5 1.0 CD2 A:HIS15 4.6 41.7 1.0 C A:SER86 4.7 32.6 1.0 O A:HOH402 4.7 52.5 1.0 CD1 A:ILE88 4.9 36.0 1.0 CE1 A:HIS15 5.0 42.1 1.0 N A:THR89 5.0 28.4 1.0

Chlorine binding site 2 out of 5 in the Lysozyme Cluster 3 Dual Apo Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Lysozyme Cluster 3 Dual Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:32.5 occ:1.00 OH A:TYR23 3.0 21.0 1.0 O A:HOH373 3.7 31.2 1.0 CE2 A:TYR23 3.7 19.7 1.0 CZ A:TYR23 3.8 19.8 1.0 CA A:GLY104 4.1 20.5 1.0 O A:ARG21 4.6 31.6 1.0 N A:GLY104 4.7 20.9 1.0 O A:HOH365 4.8 32.7 1.0 CD2 A:TYR23 5.0 19.4 1.0 CE1 A:TYR23 5.0 19.8 1.0

Chlorine binding site 3 out of 5 in the Lysozyme Cluster 3 Dual Apo Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Lysozyme Cluster 3 Dual Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:37.5 occ:1.00 O A:HOH349 2.7 45.2 1.0 OG A:SER24 2.9 22.7 1.0 N A:GLY26 3.1 22.9 1.0 CB A:SER24 3.3 22.8 1.0 CD1 A:ILE124 3.4 31.0 1.0 CA A:GLY26 3.5 22.6 1.0 CA A:GLN121 3.7 31.1 1.0 O A:HOH352 4.0 62.1 1.0 N A:GLN121 4.0 29.0 1.0 N A:LEU25 4.0 24.5 1.0 CG1 A:ILE124 4.1 30.1 1.0 CB A:GLN121 4.1 37.7 1.0 C A:SER24 4.2 23.5 1.0 CG A:GLN121 4.2 43.9 1.0 C A:LEU25 4.3 24.1 1.0 CA A:SER24 4.3 22.6 1.0 CG2 A:VAL120 4.4 29.9 1.0 C A:VAL120 4.4 29.4 1.0 O A:VAL120 4.5 28.0 1.0 CA A:LEU25 4.6 24.7 1.0 C A:GLY26 4.7 21.3 1.0 O A:SER24 4.7 21.7 1.0 CB A:LEU25 4.8 24.7 1.0 N A:ASN27 4.8 20.9 1.0 C A:GLN121 4.9 29.5 1.0

Chlorine binding site 4 out of 5 in the Lysozyme Cluster 3 Dual Apo Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Lysozyme Cluster 3 Dual Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl205 b:53.0 occ:1.00 O A:HOH412 3.5 50.5 1.0 CE2 A:PHE38 3.8 23.4 1.0 CZ3 A:TRP123 4.0 29.4 1.0 NZ A:LYS33 4.1 23.3 1.0 CE A:LYS33 4.1 22.4 1.0 CD A:ARG5 4.2 30.8 1.0 CB A:ARG5 4.2 30.6 1.0 O A:HOH381 4.3 41.0 1.0 CD A:LYS33 4.4 20.8 1.0 CZ A:PHE38 4.4 23.9 1.0 CG A:ARG5 4.7 29.9 1.0 CD2 A:PHE38 4.7 24.1 1.0 CE3 A:TRP123 4.7 29.3 1.0 NE A:ARG5 4.8 29.9 1.0 CH2 A:TRP123 5.0 28.9 1.0

Chlorine binding site 5 out of 5 in the Lysozyme Cluster 3 Dual Apo Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Lysozyme Cluster 3 Dual Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl206 b:31.5 occ:1.00 O A:HOH340 2.8 15.7 1.0 O A:THR69 3.1 31.4 1.0 N A:THR69 3.3 26.4 1.0 OG A:SER72 3.4 35.5 1.0 O A:HOH444 3.5 51.5 1.0 C A:THR69 3.6 29.0 1.0 O A:HOH406 3.6 53.0 1.0 O A:HOH382 3.7 35.1 1.0 N A:ARG68 3.7 27.5 1.0 O A:HOH477 3.7 42.1 1.0 CA A:GLY67 3.7 21.8 1.0 OD1 A:ASN65 3.7 25.2 1.0 C A:GLY67 3.7 25.2 1.0 CA A:THR69 3.8 27.4 1.0 N A:GLY67 3.8 20.9 1.0 O A:HOH400 4.1 24.1 1.0 CB A:THR69 4.2 26.5 1.0 C A:ARG68 4.3 26.2 1.0 OD1 A:ASP66 4.3 26.6 1.0 N A:PRO70 4.4 31.6 1.0 O A:GLY67 4.5 26.2 1.0 CA A:ARG68 4.5 27.5 1.0 NA A:NA201 4.7 23.1 1.0 CB A:SER72 4.7 34.3 1.0 CA A:PRO70 4.9 31.5 1.0 CG A:ASN65 4.9 26.9 1.0 OG1 A:THR69 5.0 26.3 1.0 C A:ASP66 5.0 21.3 1.0

A.S.Soares, Y.Yamada, J.Jakoncic, S.Mcsweeney, R.M.Sweet, J.Skinner, J.Foadi, M.R.Fuchs, D.K.Schneider, W.Shi, B.Andi, L.C.Andrews, H.J.Bernstein. Serial Crystallography with Multi-Stage Merging of Thousands of Images. Acta Crystallogr.,Sect.F V. 78 281 2022.
ISSN: ESSN 2053-230X
PubMed: 35787556
DOI: 10.1107/S2053230X22006422