Sodium in PDB 8dhl: Tannerella Forsythia Beta-Glucuronidase (L2)

The structure of Tannerella Forsythia Beta-Glucuronidase (L2), PDB code: 8dhl 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)	78.77 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.983, 119.209, 209.883, 90, 90, 90
R / Rfree (%)	17 / 21

The structure of Tannerella Forsythia Beta-Glucuronidase (L2) also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Tannerella Forsythia Beta-Glucuronidase (L2) (pdb code 8dhl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Tannerella Forsythia Beta-Glucuronidase (L2), PDB code: 8dhl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Tannerella Forsythia Beta-Glucuronidase (L2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Tannerella Forsythia Beta-Glucuronidase (L2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na905 b:18.0 occ:1.00 O A:THR774 2.3 16.2 1.0 OD1 A:ASN715 2.4 16.8 1.0 O A:LEU771 2.5 15.6 1.0 O A:SER876 2.5 15.4 1.0 O A:VAL716 2.5 14.3 1.0 OG1 A:THR774 2.5 18.2 1.0 C A:THR774 3.0 16.1 1.0 CB A:THR774 3.4 17.4 1.0 C A:SER876 3.4 17.4 1.0 CG A:ASN715 3.5 16.5 1.0 CA A:THR774 3.6 17.4 1.0 C A:VAL716 3.6 15.5 1.0 C A:LEU771 3.6 16.8 1.0 N A:VAL716 3.7 12.8 1.0 CA A:SER876 3.8 17.7 1.0 N A:THR774 3.8 16.6 1.0 N A:MET775 3.9 15.8 1.0 CB A:SER876 4.0 15.4 1.0 ND2 A:ASN715 4.2 18.0 1.0 CA A:LEU771 4.2 16.2 1.0 CA A:VAL716 4.2 14.3 1.0 C A:ASN715 4.2 15.7 1.0 O A:PRO770 4.4 21.8 1.0 CA A:MET775 4.4 17.6 1.0 CA A:ASN715 4.5 14.6 1.0 CB A:ASN715 4.6 14.7 1.0 N A:ALA877 4.6 13.9 1.0 N A:GLY717 4.7 17.5 1.0 N A:TYR772 4.7 15.4 1.0 OG A:SER876 4.7 16.6 1.0 C A:TYR772 4.8 15.9 1.0 CG2 A:THR774 4.8 13.4 1.0 O A:TYR772 4.8 14.3 1.0 CB A:VAL716 4.9 13.1 1.0 CA A:GLY717 4.9 18.5 1.0 CA A:TYR772 4.9 16.6 1.0 O A:ASN715 5.0 17.0 1.0

Sodium binding site 2 out of 2 in the Tannerella Forsythia Beta-Glucuronidase (L2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Tannerella Forsythia Beta-Glucuronidase (L2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na908 b:18.0 occ:1.00 OD1 B:ASN715 2.3 18.7 1.0 O B:THR774 2.4 17.6 1.0 O B:VAL716 2.4 19.5 1.0 O B:SER876 2.4 16.0 1.0 OG1 B:THR774 2.5 20.9 1.0 O B:LEU771 2.6 17.0 1.0 C B:THR774 3.1 19.1 1.0 CB B:THR774 3.4 17.4 1.0 C B:SER876 3.4 20.2 1.0 CG B:ASN715 3.5 19.1 1.0 C B:VAL716 3.5 20.4 1.0 CA B:THR774 3.6 15.2 1.0 N B:VAL716 3.6 18.3 1.0 C B:LEU771 3.7 15.0 1.0 CA B:SER876 3.8 18.7 1.0 N B:THR774 3.9 17.8 1.0 CB B:SER876 3.9 14.5 1.0 N B:MET775 4.0 20.6 1.0 C B:ASN715 4.0 20.1 1.0 CA B:VAL716 4.1 19.1 1.0 CA B:ASN715 4.3 19.4 1.0 ND2 B:ASN715 4.3 17.2 1.0 CA B:LEU771 4.4 17.1 1.0 CA B:MET775 4.4 20.6 1.0 CB B:ASN715 4.5 17.4 1.0 CD1 B:LEU771 4.5 14.3 1.0 N B:ALA877 4.6 19.0 1.0 O B:ASN715 4.6 19.1 1.0 N B:GLY717 4.6 20.9 1.0 O B:PRO770 4.7 20.0 1.0 CG2 B:THR774 4.8 19.8 1.0 CB B:VAL716 4.8 18.9 1.0 O B:TYR772 4.8 15.7 1.0 C B:TYR772 4.8 16.2 1.0 N B:TYR772 4.8 18.1 1.0 OG B:SER876 4.9 16.3 1.0 CB B:ALA718 4.9 21.3 1.0 CA B:GLY717 4.9 19.0 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