Chlorine in PDB 8dhv: Treponema Lecithinolyticum Beta-Glucuronidase

All present enzymatic activity of Treponema Lecithinolyticum Beta-Glucuronidase:
3.2.1.31;

The structure of Treponema Lecithinolyticum Beta-Glucuronidase, PDB code: 8dhv was solved by A.D.Lietzan, M.R.Redinbo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.15 / 1.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.302, 94.302, 287.954, 90, 90, 90
R / Rfree (%)	16.7 / 19.6

The binding sites of Chlorine atom in the Treponema Lecithinolyticum Beta-Glucuronidase (pdb code 8dhv). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Treponema Lecithinolyticum Beta-Glucuronidase, PDB code: 8dhv:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Treponema Lecithinolyticum Beta-Glucuronidase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Treponema Lecithinolyticum Beta-Glucuronidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl709 b:25.1 occ:1.00 NZ A:LYS594 3.0 24.5 1.0 OH A:TYR499 3.1 24.2 1.0 O A:HOH825 3.2 33.6 1.0 ND2 A:ASN592 3.3 21.8 1.0 O A:HOH1002 3.6 23.7 1.0 CE A:LYS594 3.6 26.2 1.0 CD1 A:TRP575 3.6 19.1 1.0 CD A:LYS594 3.7 21.9 1.0 NH2 A:ARG588 3.7 21.6 1.0 NE1 A:TRP575 3.7 19.9 1.0 OH A:TYR495 3.9 21.9 1.0 CE2 A:TYR499 3.9 25.3 1.0 CZ A:TYR499 3.9 23.3 1.0 C1 A:MPD707 4.0 35.5 1.0 OD2 A:ASP188 4.2 23.0 1.0 CZ A:TYR495 4.2 21.5 1.0 CG A:ASN592 4.3 20.6 1.0 CE1 A:TYR495 4.4 21.0 1.0 OD1 A:ASN592 4.6 21.9 1.0 CG A:LYS594 4.6 20.2 1.0 O2 A:MPD707 4.6 35.6 1.0 CZ A:ARG588 4.7 20.6 1.0 C2 A:MPD707 4.8 43.1 1.0 CG A:TRP575 4.9 18.9 1.0 C3 A:MPD707 4.9 41.3 1.0 CE2 A:TYR495 4.9 22.0 1.0 CE2 A:TRP575 5.0 18.9 1.0

Chlorine binding site 2 out of 4 in the Treponema Lecithinolyticum Beta-Glucuronidase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Treponema Lecithinolyticum Beta-Glucuronidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl710 b:28.7 occ:1.00 O A:HOH1002 3.1 23.7 1.0 NE2 A:HIS320 3.2 20.8 1.0 O A:HOH1148 3.3 26.5 1.0 CD2 A:PHE189 3.4 20.4 1.0 CD2 A:HIS354 3.5 22.2 1.0 NE2 A:HIS354 3.5 21.5 1.0 CZ2 A:TRP575 3.6 17.1 1.0 CB A:ASP188 3.7 21.8 1.0 N A:PHE189 3.7 23.3 1.0 CE1 A:HIS320 3.9 21.4 1.0 CE2 A:PHE580 3.9 19.1 1.0 CB A:PHE189 3.9 20.1 1.0 CZ A:PHE580 3.9 19.4 1.0 CG A:PHE189 4.2 19.8 1.0 CH2 A:TRP575 4.2 18.4 1.0 CD2 A:HIS320 4.3 18.7 1.0 N A:ASP188 4.3 23.0 1.0 CA A:PHE189 4.3 19.7 1.0 CA A:ASP188 4.3 22.8 1.0 C A:ASP188 4.4 29.9 1.0 CE2 A:PHE189 4.4 22.8 1.0 CE2 A:TRP575 4.6 18.9 1.0 CG A:ASP188 4.6 24.5 1.0 OD2 A:ASP188 4.6 23.0 1.0 O A:HOH853 4.7 32.7 1.0 CE1 A:HIS354 4.8 18.7 1.0 CG A:HIS354 4.9 20.1 1.0 NE1 A:TRP575 4.9 19.9 1.0

Chlorine binding site 3 out of 4 in the Treponema Lecithinolyticum Beta-Glucuronidase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Treponema Lecithinolyticum Beta-Glucuronidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl707 b:28.3 occ:1.00 NZ B:LYS594 3.0 30.7 1.0 OH B:TYR499 3.0 26.3 1.0 O B:HOH982 3.1 33.4 1.0 ND2 B:ASN592 3.4 25.1 1.0 CE B:LYS594 3.6 27.6 1.0 O B:HOH951 3.6 26.5 1.0 CD1 B:TRP575 3.7 21.8 1.0 NH2 B:ARG588 3.7 27.0 1.0 CD B:LYS594 3.7 23.6 1.0 NE1 B:TRP575 3.8 21.1 1.0 OH B:TYR495 3.9 25.2 1.0 CM B:MPD702 3.9 49.2 1.0 CE2 B:TYR499 3.9 23.6 1.0 CZ B:TYR499 3.9 28.6 1.0 OD2 B:ASP188 4.2 28.1 1.0 CZ B:TYR495 4.2 23.3 1.0 CG B:ASN592 4.4 24.2 1.0 CE1 B:TYR495 4.4 24.0 1.0 O2 B:MPD702 4.5 49.0 1.0 OD1 B:ASN592 4.6 25.6 1.0 CG B:LYS594 4.6 23.1 1.0 CZ B:ARG588 4.7 28.1 1.0 C2 B:MPD702 4.7 48.6 1.0 CE2 B:TYR495 4.9 28.1 1.0 CG B:TRP575 4.9 23.8 1.0

Chlorine binding site 4 out of 4 in the Treponema Lecithinolyticum Beta-Glucuronidase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Treponema Lecithinolyticum Beta-Glucuronidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl708 b:29.1 occ:1.00 O B:HOH951 3.1 26.5 1.0 NE2 B:HIS320 3.1 22.0 1.0 O B:HOH1085 3.4 30.4 1.0 CD2 B:PHE189 3.5 22.6 1.0 CD2 B:HIS354 3.5 23.5 1.0 NE2 B:HIS354 3.5 24.3 1.0 CZ2 B:TRP575 3.6 22.9 1.0 CB B:ASP188 3.6 27.1 1.0 N B:PHE189 3.7 23.7 1.0 CE1 B:HIS320 3.8 22.3 1.0 CB B:PHE189 3.9 25.3 1.0 CZ B:PHE580 4.0 20.9 1.0 CE2 B:PHE580 4.0 19.9 1.0 CG B:PHE189 4.2 22.4 1.0 CH2 B:TRP575 4.3 23.9 1.0 CD2 B:HIS320 4.3 24.4 1.0 CA B:PHE189 4.3 22.8 1.0 CA B:ASP188 4.3 23.5 1.0 N B:ASP188 4.3 23.9 1.0 C B:ASP188 4.4 29.4 1.0 CE2 B:PHE189 4.4 25.5 1.0 O B:HOH829 4.5 34.2 1.0 CG B:ASP188 4.6 27.6 1.0 CE2 B:TRP575 4.6 22.2 1.0 OD2 B:ASP188 4.6 28.1 1.0 CG B:HIS354 4.8 24.3 1.0 CE1 B:HIS354 4.8 26.0 1.0 NE1 B:TRP575 4.9 21.1 1.0

A.D.Lietzan, J.B.Simpson, W.G.Walton, P.B.Jariwala, Y.Xu, M.H.Boynton, J.Liu, M.R.Redinbo. Microbial Beta-Glucuronidases Drive Human Periodontal Disease Etiology. Sci Adv V. 9 G3390 2023.
ISSN: ESSN 2375-2548
PubMed: 37146137
DOI: 10.1126/SCIADV.ADG3390