Chlorine in PDB 8dcu: Lysozyme Cluster 0028 (Benzamidine Ligand)

All present enzymatic activity of Lysozyme Cluster 0028 (Benzamidine Ligand):
3.2.1.17;

The structure of Lysozyme Cluster 0028 (Benzamidine Ligand), PDB code: 8dcu 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)	39.83 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.59, 79.59, 37.76, 90, 90, 90
R / Rfree (%)	20.8 / 26.2

The structure of Lysozyme Cluster 0028 (Benzamidine Ligand) also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Lysozyme Cluster 0028 (Benzamidine Ligand) (pdb code 8dcu). 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 0028 (Benzamidine Ligand), PDB code: 8dcu:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Lysozyme Cluster 0028 (Benzamidine 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 0028 (Benzamidine Ligand) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:71.3 occ:1.00 OD1 A:ASP87 3.3 58.7 1.0 NE2 A:HIS15 3.5 42.2 1.0 N A:ILE88 3.5 34.5 1.0 O A:HOH447 3.6 70.5 1.0 CG1 A:ILE88 3.7 32.8 1.0 CA A:ASP87 3.9 45.2 1.0 O A:HOH343 4.2 64.4 1.0 C A:ASP87 4.2 39.0 1.0 O A:SER86 4.2 39.7 1.0 CB A:ALA11 4.3 35.0 1.0 CD2 A:HIS15 4.3 43.6 1.0 CG A:ASP87 4.3 56.0 1.0 CB A:ILE88 4.4 32.8 1.0 CG2 A:ILE88 4.5 31.0 1.0 CE1 A:HIS15 4.5 45.9 1.0 CA A:ILE88 4.5 33.5 1.0 O A:HOH364 4.5 51.4 1.0 CD1 A:ILE88 4.6 33.2 1.0 CB A:ASP87 4.6 50.3 1.0 CZ A:PHE3 4.7 27.4 1.0 O A:HOH500 4.8 31.3 0.5 N A:ASP87 4.9 43.0 1.0 N A:THR89 4.9 31.8 1.0 C A:SER86 5.0 39.8 1.0

Chlorine binding site 2 out of 5 in the Lysozyme Cluster 0028 (Benzamidine 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 0028 (Benzamidine Ligand) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:34.2 occ:1.00 OH A:TYR23 3.0 20.3 1.0 O A:HOH328 3.5 28.3 1.0 CE2 A:TYR23 3.7 19.5 1.0 CZ A:TYR23 3.7 21.0 1.0 CA A:GLY104 4.0 21.5 1.0 N A:GLY104 4.4 21.3 1.0 O A:HOH359 4.7 37.2 1.0 O A:ARG21 4.8 28.6 1.0 CD2 A:TYR23 4.9 20.2 1.0

Chlorine binding site 3 out of 5 in the Lysozyme Cluster 0028 (Benzamidine 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 0028 (Benzamidine Ligand) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:38.9 occ:1.00 N A:GLY26 3.0 19.6 1.0 OG A:SER24 3.1 23.6 1.0 O A:HOH449 3.2 55.5 1.0 CA A:GLY26 3.4 19.7 1.0 CB A:SER24 3.5 20.8 1.0 CA A:GLN121 3.6 36.9 1.0 N A:GLN121 3.8 35.0 1.0 CD1 A:ILE124 4.0 38.8 1.0 N A:LEU25 4.1 19.8 1.0 CB A:GLN121 4.1 44.9 1.0 C A:SER24 4.2 20.2 1.0 C A:LEU25 4.2 20.5 1.0 C A:VAL120 4.2 32.0 1.0 CG1 A:ILE124 4.3 37.8 1.0 O A:VAL120 4.3 30.8 1.0 O A:HOH308 4.4 51.0 1.0 CG2 A:VAL120 4.4 27.4 1.0 CA A:SER24 4.4 20.3 1.0 CG A:GLN121 4.4 52.8 1.0 C A:GLY26 4.5 19.4 1.0 CA A:LEU25 4.6 21.0 1.0 O A:SER24 4.7 19.9 1.0 N A:ASN27 4.8 19.8 1.0 C A:GLN121 4.8 32.4 1.0 CB A:LEU25 4.8 21.6 1.0 CB A:VAL120 4.9 27.1 1.0

Chlorine binding site 4 out of 5 in the Lysozyme Cluster 0028 (Benzamidine 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 0028 (Benzamidine Ligand) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl205 b:64.2 occ:1.00 O A:HOH351 3.5 51.3 1.0 NZ A:LYS33 3.6 31.2 1.0 CE2 A:PHE38 3.9 25.9 1.0 CE A:LYS33 3.9 28.6 1.0 CZ3 A:TRP123 4.1 27.8 1.0 CD A:LYS33 4.1 26.7 1.0 CD A:ARG5 4.3 33.7 1.0 CB A:ARG5 4.3 30.3 1.0 CZ A:PHE38 4.6 25.3 1.0 CD2 A:PHE38 4.7 26.1 1.0 CG A:ARG5 4.8 32.0 1.0 CH2 A:TRP123 4.8 27.3 1.0 CE3 A:TRP123 4.9 25.9 1.0 NE A:ARG5 4.9 34.4 1.0 O A:HOH435 4.9 46.7 1.0

Chlorine binding site 5 out of 5 in the Lysozyme Cluster 0028 (Benzamidine 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 0028 (Benzamidine Ligand) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl206 b:34.8 occ:1.00 O A:HOH481 2.9 91.0 1.0 O A:HOH363 2.9 23.2 1.0 O A:HOH437 3.0 53.4 1.0 O A:THR69 3.0 35.9 1.0 O A:HOH379 3.1 45.4 1.0 N A:THR69 3.2 26.5 1.0 C A:THR69 3.5 33.0 1.0 N A:ARG68 3.6 26.5 1.0 C A:GLY67 3.7 26.2 1.0 CA A:GLY67 3.7 25.6 1.0 OD1 A:ASN65 3.8 27.4 1.0 OG A:SER72 3.8 34.0 1.0 CA A:THR69 3.8 29.6 1.0 N A:GLY67 3.9 25.3 1.0 O A:HOH372 4.0 26.4 1.0 C A:ARG68 4.2 27.4 1.0 CB A:THR69 4.3 27.7 1.0 O A:GLY67 4.3 25.2 1.0 N A:PRO70 4.3 34.9 1.0 CA A:ARG68 4.4 27.0 1.0 OD1 A:ASP66 4.4 25.2 1.0 NA A:NA201 4.5 28.2 1.0 O A:HOH346 4.6 57.6 1.0 CA A:PRO70 4.7 32.9 1.0 O A:HOH463 4.7 48.5 1.0 OG1 A:THR69 4.8 27.0 1.0 O A:HOH458 4.8 47.7 1.0 CG A:ASN65 4.9 26.6 1.0 CB A:SER72 4.9 34.4 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