Chlorine in PDB 8dcv: Lysozyme Cluster 0043, Nag Ligand

All present enzymatic activity of Lysozyme Cluster 0043, Nag Ligand:
3.2.1.17;

The structure of Lysozyme Cluster 0043, Nag Ligand, PDB code: 8dcv 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)	39.26 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.46, 78.46, 37.69, 90, 90, 90
R / Rfree (%)	14.7 / 18.7

The structure of Lysozyme Cluster 0043, Nag Ligand also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Lysozyme Cluster 0043, Nag Ligand (pdb code 8dcv). 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 0043, Nag Ligand, PDB code: 8dcv:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Lysozyme Cluster 0043, Nag Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Lysozyme Cluster 0043, Nag Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:41.6 occ:1.00 O A:HOH332 2.7 51.8 1.0 N A:ILE88 3.3 17.1 1.0 O A:HOH336 3.4 32.3 1.0 O A:HOH436 3.4 45.2 1.0 O A:HOH488 3.6 28.3 0.5 CG1 A:ILE88 3.7 15.2 1.0 CA A:ASP87 3.8 21.9 1.0 C A:ASP87 4.0 19.7 1.0 NE2 A:HIS15 4.0 26.1 1.0 OD1 A:ASP87 4.1 33.6 1.0 O A:SER86 4.2 22.4 1.0 CG2 A:ILE88 4.3 16.2 1.0 CB A:ILE88 4.3 15.9 1.0 CZ A:PHE3 4.3 16.8 1.0 CA A:ILE88 4.4 16.8 1.0 CB A:ALA11 4.4 17.7 1.0 CD1 A:ILE88 4.6 16.0 1.0 CB A:ASP87 4.6 25.4 1.0 CD2 A:HIS15 4.7 24.7 1.0 CG A:ASP87 4.7 34.5 1.0 N A:ASP87 4.8 20.1 1.0 NH1 A:ARG14 4.9 54.8 1.0 CE2 A:PHE3 4.9 15.9 1.0 C A:SER86 4.9 20.7 1.0

Chlorine binding site 2 out of 5 in the Lysozyme Cluster 0043, Nag Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Lysozyme Cluster 0043, Nag Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:18.1 occ:1.00 OH A:TYR23 2.9 10.1 1.0 O A:HOH398 3.3 18.1 1.0 CZ A:TYR23 3.6 10.7 1.0 CE2 A:TYR23 3.6 11.1 1.0 CA A:GLY104 4.1 13.9 1.0 O A:ARG21 4.6 17.8 1.0 N A:GLY104 4.7 13.8 1.0 CE1 A:TYR23 4.8 11.3 1.0 CD2 A:TYR23 4.8 11.0 1.0 O A:HOH339 5.0 21.3 1.0

Chlorine binding site 3 out of 5 in the Lysozyme Cluster 0043, Nag Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Lysozyme Cluster 0043, Nag Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:20.3 occ:1.00 O A:HOH455 2.9 40.9 1.0 OG A:SER24 3.0 13.8 1.0 N A:GLY26 3.2 12.7 1.0 CB A:SER24 3.4 14.1 1.0 CA A:GLY26 3.5 12.4 1.0 CA A:GLN121 3.6 21.8 1.0 N A:GLN121 3.9 20.2 1.0 CD1 A:ILE124 4.0 27.8 1.0 CB A:GLN121 4.1 28.6 1.0 N A:LEU25 4.1 14.4 1.0 CG1 A:ILE124 4.2 22.1 1.0 C A:VAL120 4.3 19.0 1.0 C A:SER24 4.3 15.0 1.0 C A:LEU25 4.3 13.6 1.0 CG A:GLN121 4.3 32.2 1.0 O A:VAL120 4.4 16.1 1.0 CA A:SER24 4.5 13.2 1.0 CG2 A:VAL120 4.5 18.1 1.0 C A:GLY26 4.6 11.7 1.0 CA A:LEU25 4.7 14.6 1.0 O A:HOH305 4.7 43.3 1.0 N A:ASN27 4.7 11.2 1.0 C A:GLN121 4.9 19.6 1.0 O A:SER24 4.9 13.0 1.0 CB A:LEU25 5.0 15.7 1.0

Chlorine binding site 4 out of 5 in the Lysozyme Cluster 0043, Nag Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Lysozyme Cluster 0043, Nag Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl205 b:48.9 occ:1.00 O A:HOH371 3.5 53.7 1.0 O A:HOH418 3.6 35.4 1.0 CE2 A:PHE38 3.7 15.7 1.0 CZ3 A:TRP123 3.9 20.4 1.0 CD A:ARG5 4.0 21.7 1.0 CB A:ARG5 4.1 18.8 1.0 NZ A:LYS33 4.1 30.3 1.0 CE A:LYS33 4.4 26.2 1.0 CZ A:PHE38 4.5 16.4 1.0 CD A:LYS33 4.5 20.7 1.0 NE A:ARG5 4.6 21.4 1.0 CG A:ARG5 4.6 18.2 1.0 CD2 A:PHE38 4.7 17.3 1.0 CE3 A:TRP123 4.7 19.3 1.0 CH2 A:TRP123 4.8 22.8 1.0

Chlorine binding site 5 out of 5 in the Lysozyme Cluster 0043, Nag Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Lysozyme Cluster 0043, Nag Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl206 b:24.2 occ:1.00 O A:HOH469 3.0 36.1 1.0 O A:HOH451 3.1 31.8 1.0 O A:HOH382 3.1 10.6 1.0 N A:THR69 3.2 17.6 1.0 O A:THR69 3.3 17.0 1.0 N A:ARG68 3.6 18.6 1.0 C A:THR69 3.6 18.3 1.0 O A:HOH377 3.6 32.5 1.0 OD1 A:ASN65 3.6 16.1 1.0 C A:GLY67 3.7 18.5 1.0 OG A:SER72 3.7 19.7 1.0 CA A:THR69 3.8 18.0 1.0 CA A:GLY67 3.8 16.3 1.0 N A:GLY67 3.9 14.8 1.0 O A:HOH410 4.1 21.7 1.0 CB A:THR69 4.2 16.9 1.0 C A:ARG68 4.2 18.4 1.0 OD1 A:ASP66 4.3 14.0 1.0 N A:PRO70 4.3 21.4 1.0 O A:GLY67 4.4 19.4 1.0 CA A:ARG68 4.4 18.7 1.0 NA A:NA201 4.7 13.6 1.0 OG1 A:THR69 4.7 15.6 1.0 CG A:ASN65 4.8 18.1 1.0 CA A:PRO70 4.8 21.9 1.0 O A:HOH470 4.9 55.5 1.0 C A:ASP66 4.9 13.6 1.0 O A:HOH319 5.0 21.0 0.5 CB A:SER72 5.0 20.1 1.0 N A:ASP66 5.0 12.2 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