Calcium 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:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the Tannerella Forsythia Beta-Glucuronidase (L2) (pdb code 8dhl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Tannerella Forsythia Beta-Glucuronidase (L2), PDB code: 8dhl:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tannerella Forsythia Beta-Glucuronidase (L2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tannerella Forsythia Beta-Glucuronidase (L2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca904 b:39.8 occ:1.00 O A:ILE762 2.3 23.5 1.0 O A:VAL765 2.5 28.1 1.0 OD2 A:ASP769 2.6 29.7 1.0 OD1 A:ASP769 2.9 31.4 1.0 CG A:ASP769 3.1 28.2 1.0 C A:ILE762 3.4 26.3 1.0 N A:ILE762 3.7 22.1 1.0 C A:VAL765 3.7 26.4 1.0 CA A:ILE762 3.9 24.2 1.0 CB A:ILE762 4.2 24.9 1.0 CA A:ASP766 4.3 29.2 1.0 C A:ASP761 4.4 28.4 1.0 N A:ASP766 4.4 24.4 1.0 O A:ASP766 4.5 32.7 1.0 N A:LEU763 4.5 25.1 1.0 N A:VAL765 4.6 26.9 1.0 CB A:ASP769 4.6 20.7 1.0 CB A:ASP761 4.7 25.5 1.0 CG2 A:VAL765 4.8 23.9 1.0 CA A:ASP761 4.8 27.9 1.0 CA A:VAL765 4.8 25.7 1.0 CA A:LEU763 4.8 25.6 1.0 C A:ASP766 4.8 28.0 1.0 C A:LEU763 4.9 26.1 1.0

Calcium binding site 2 out of 4 in the Tannerella Forsythia Beta-Glucuronidase (L2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tannerella Forsythia Beta-Glucuronidase (L2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca906 b:30.4 occ:1.00 OE2 B:GLU692 2.3 30.0 1.0 O B:HOH1265 2.5 30.2 1.0 OE1 B:GLU692 2.6 28.8 1.0 O B:HOH1042 2.6 28.2 1.0 O A:HOH1136 2.6 28.3 1.0 OE2 A:GLU692 2.6 32.7 1.0 O A:HOH1089 2.7 27.3 1.0 OE1 A:GLU692 2.7 28.1 1.0 CD B:GLU692 2.7 29.1 1.0 CD A:GLU692 3.0 31.1 1.0 CG B:GLU692 4.2 28.2 1.0 O A:HOH1017 4.4 29.5 1.0 O B:SER687 4.4 38.7 1.0 O A:SER687 4.5 37.0 1.0 CG A:GLU692 4.5 22.9 1.0 ND2 A:ASN655 4.7 28.5 1.0 ND2 B:ASN655 4.8 34.3 1.0 CA A:ASN686 4.8 31.7 1.0 CA B:ASN686 4.9 35.6 1.0 N A:SER687 4.9 33.1 1.0 N B:GLU692 4.9 23.7 1.0 N B:SER687 4.9 39.5 1.0 OD1 B:ASN686 5.0 36.6 1.0 O B:THR690 5.0 29.8 1.0

Calcium binding site 3 out of 4 in the Tannerella Forsythia Beta-Glucuronidase (L2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tannerella Forsythia Beta-Glucuronidase (L2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca907 b:20.4 occ:1.00 O B:ILE762 2.3 20.8 1.0 O B:VAL765 2.4 19.2 1.0 O B:HOH1383 2.4 21.1 1.0 OD1 B:ASP761 2.4 21.0 1.0 OD2 B:ASP769 2.5 23.9 1.0 O B:HOH1325 2.6 23.8 1.0 OD1 B:ASP769 2.6 22.4 1.0 CG B:ASP769 2.9 21.7 1.0 C B:ILE762 3.4 18.5 1.0 C B:VAL765 3.6 20.5 1.0 CG B:ASP761 3.6 22.1 1.0 N B:ILE762 3.8 19.5 1.0 O B:HOH1232 4.1 23.0 1.0 CA B:ILE762 4.1 17.6 1.0 O B:HOH1146 4.1 27.7 1.0 CA B:ASP766 4.2 21.3 1.0 OD2 B:ASP761 4.2 24.4 1.0 C B:ASP761 4.3 21.9 1.0 N B:ASP766 4.3 22.4 1.0 CB B:ASP769 4.4 17.3 1.0 O B:HOH1074 4.5 25.2 1.0 CB B:ILE762 4.5 17.6 1.0 N B:LEU763 4.5 18.8 1.0 N B:VAL765 4.5 17.4 1.0 CA B:LEU763 4.6 21.2 1.0 CA B:VAL765 4.6 18.1 1.0 CG2 B:VAL765 4.6 20.3 1.0 CA B:ASP761 4.6 19.9 1.0 O B:ASP766 4.7 22.6 1.0 CB B:ASP761 4.7 18.7 1.0 C B:LEU763 4.7 17.6 1.0 O B:LEU763 5.0 16.3 1.0 C B:ASP766 5.0 23.1 1.0 O B:HOH1367 5.0 21.9 1.0

Calcium binding site 4 out of 4 in the Tannerella Forsythia Beta-Glucuronidase (L2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tannerella Forsythia Beta-Glucuronidase (L2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca909 b:22.9 occ:1.00 O B:HOH1307 2.2 18.1 1.0 O B:GLY79 2.3 20.8 1.0 O B:ARG77 2.3 21.9 1.0 O B:ASP71 2.4 22.6 1.0 O B:HOH1096 2.5 20.0 1.0 OD2 B:ASP75 2.6 21.7 1.0 OD1 B:ASP75 2.6 21.5 1.0 CG B:ASP75 2.9 23.4 1.0 C B:ASP71 3.5 20.4 1.0 C B:GLY79 3.5 20.7 1.0 C B:ARG77 3.5 25.4 1.0 N B:GLY79 4.1 21.1 1.0 CA B:ASP71 4.1 20.5 1.0 O B:HOH1348 4.2 24.7 1.0 C B:ARG78 4.2 23.2 1.0 O B:LEU73 4.3 22.7 1.0 CB B:ARG77 4.3 22.4 1.0 CB B:ASP71 4.3 19.6 1.0 OE2 B:GLU576 4.4 24.1 1.0 CA B:ARG77 4.4 24.7 1.0 CA B:GLY79 4.4 21.0 1.0 CB B:ASP75 4.4 18.9 1.0 N B:TYR80 4.5 15.8 1.0 N B:ARG78 4.5 20.7 1.0 N B:VAL72 4.6 19.2 1.0 CA B:TYR80 4.6 15.1 1.0 N B:ARG77 4.6 22.9 1.0 CA B:ARG78 4.6 24.7 1.0 O B:ARG78 4.7 28.7 1.0 O B:HOH1040 4.7 20.5 1.0 CA B:VAL72 4.8 18.8 1.0 CG B:ARG77 4.9 24.7 1.0 CB B:TYR80 4.9 17.0 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