Chlorine in PDB 8dhe: Tannerella Forsythia Beta-Glucuronidase (ML1)

Protein crystallography data

The structure of Tannerella Forsythia Beta-Glucuronidase (ML1), PDB code: 8dhe 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) 51.71 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 100.442, 139.647, 109.821, 90, 94.5, 90
R / Rfree (%) 20.5 / 24.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Tannerella Forsythia Beta-Glucuronidase (ML1) (pdb code 8dhe). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Tannerella Forsythia Beta-Glucuronidase (ML1), PDB code: 8dhe:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8dhe

Go back to Chlorine Binding Sites List in 8dhe
Chlorine binding site 1 out of 4 in the Tannerella Forsythia Beta-Glucuronidase (ML1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Tannerella Forsythia Beta-Glucuronidase (ML1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl805

b:41.7
occ:1.00
 N A:GLY384 3.2 28.4 1.0
NZ A:LYS383 3.3 33.0 1.0
N A:THR422 3.3 30.4 1.0
OG1 A:THR422 3.4 33.6 1.0
CE A:LYS383 3.5 33.4 1.0
N A:PHE385 3.7 23.0 1.0
CD A:LYS383 3.8 30.3 1.0
O A:THR422 3.8 37.4 1.0
CA A:LEU421 3.8 27.9 1.0
CA A:GLY384 3.9 30.2 1.0
CB A:LEU421 4.1 29.2 1.0
C A:LEU421 4.1 33.5 1.0
CB A:LYS383 4.1 29.2 1.0
CD2 A:LEU421 4.1 25.9 1.0
CD A:PRO377 4.1 32.6 1.0
C A:LYS383 4.1 27.3 1.0
CA A:LYS383 4.2 30.5 1.0
C A:GLY384 4.2 28.1 1.0
CA A:THR422 4.2 28.9 1.0
CB A:PHE385 4.3 27.3 1.0
CB A:THR422 4.4 29.2 1.0
C A:THR422 4.5 36.1 1.0
CG A:LYS383 4.6 27.8 1.0
CA A:GLY376 4.6 32.8 1.0
CA A:PHE385 4.6 28.0 1.0
CG A:LEU421 4.7 28.7 1.0
O A:PHE385 4.9 30.4 1.0
CG A:PRO428 5.0 32.7 1.0

Chlorine binding site 2 out of 4 in 8dhe

Go back to Chlorine Binding Sites List in 8dhe
Chlorine binding site 2 out of 4 in the Tannerella Forsythia Beta-Glucuronidase (ML1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Tannerella Forsythia Beta-Glucuronidase (ML1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl703

b:34.5
occ:1.00
 N B:THR422 3.2 32.9 1.0
NZ B:LYS383 3.3 32.5 1.0
N B:GLY384 3.3 35.0 1.0
N B:PHE385 3.5 30.2 1.0
CE B:LYS383 3.6 31.1 1.0
CA B:GLY384 3.7 37.6 1.0
O B:THR422 3.7 38.3 1.0
CA B:LEU421 3.7 35.3 1.0
CG2 B:THR422 3.8 28.6 1.0
CD B:LYS383 3.8 31.2 1.0
CD2 B:LEU421 3.8 33.0 1.0
CB B:LEU421 3.9 37.6 1.0
C B:GLY384 4.0 31.5 1.0
C B:LEU421 4.0 33.2 1.0
CB B:PHE385 4.1 33.9 1.0
CA B:THR422 4.2 34.8 1.0
C B:LYS383 4.3 32.3 1.0
CD B:PRO377 4.3 32.9 1.0
CA B:PHE385 4.4 30.7 1.0
C B:THR422 4.4 34.8 1.0
CG B:LEU421 4.4 39.4 1.0
CB B:LYS383 4.5 28.1 1.0
CA B:LYS383 4.5 31.2 1.0
CB B:THR422 4.5 39.4 1.0
CA B:GLY376 4.7 30.2 1.0
CG B:LYS383 4.8 24.4 1.0
O B:PHE385 4.9 36.0 1.0
CG B:PRO428 5.0 32.3 1.0

Chlorine binding site 3 out of 4 in 8dhe

Go back to Chlorine Binding Sites List in 8dhe
Chlorine binding site 3 out of 4 in the Tannerella Forsythia Beta-Glucuronidase (ML1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Tannerella Forsythia Beta-Glucuronidase (ML1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl702

b:41.5
occ:1.00
 N C:GLY384 3.1 23.4 1.0
CG2 C:THR422 3.2 36.1 1.0
N C:THR422 3.3 37.7 1.0
NZ C:LYS383 3.3 30.7 1.0
N C:PHE385 3.6 24.8 1.0
CA C:GLY384 3.6 32.4 1.0
CE C:LYS383 3.8 25.6 1.0
CA C:LEU421 3.8 37.3 1.0
CD2 C:LEU421 3.8 32.2 1.0
O C:THR422 3.9 31.0 1.0
CD C:PRO377 3.9 31.2 1.0
C C:LEU421 4.0 34.9 1.0
C C:GLY384 4.0 29.2 1.0
CD C:LYS383 4.1 27.1 1.0
C C:LYS383 4.1 28.0 1.0
CB C:LEU421 4.1 34.5 1.0
CA C:LYS383 4.1 32.1 1.0
CA C:THR422 4.2 37.4 1.0
CB C:LYS383 4.3 24.1 1.0
CB C:THR422 4.3 40.8 1.0
CB C:PHE385 4.4 31.2 1.0
CA C:GLY376 4.5 27.8 1.0
C C:THR422 4.5 36.4 1.0
CG C:LEU421 4.5 34.5 1.0
CA C:PHE385 4.6 32.5 1.0
O C:GLU420 4.8 35.5 1.0
CG C:PRO377 4.8 31.5 1.0
CG C:LYS383 4.8 23.4 1.0
O C:PHE385 5.0 30.7 1.0

Chlorine binding site 4 out of 4 in 8dhe

Go back to Chlorine Binding Sites List in 8dhe
Chlorine binding site 4 out of 4 in the Tannerella Forsythia Beta-Glucuronidase (ML1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Tannerella Forsythia Beta-Glucuronidase (ML1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl704

b:40.5
occ:1.00
 N D:GLY384 3.1 32.2 1.0
N D:THR422 3.3 31.2 1.0
NZ D:LYS383 3.5 32.5 1.0
CG2 D:THR422 3.6 28.5 1.0
N D:PHE385 3.6 30.2 1.0
CE D:LYS383 3.8 30.5 1.0
CD D:PRO377 3.8 33.5 1.0
CA D:GLY384 3.8 38.5 1.0
CD D:LYS383 3.8 26.2 1.0
CD2 D:LEU421 3.8 30.4 1.0
CA D:LEU421 3.9 31.7 1.0
O D:THR422 4.0 35.1 1.0
C D:LYS383 4.1 31.6 1.0
C D:LEU421 4.1 31.1 1.0
CB D:LEU421 4.1 29.1 1.0
CA D:LYS383 4.1 33.8 1.0
C D:GLY384 4.1 29.1 1.0
CB D:LYS383 4.2 30.0 1.0
CA D:THR422 4.3 35.7 1.0
CB D:PHE385 4.4 34.0 1.0
CB D:THR422 4.5 32.5 1.0
CA D:GLY376 4.5 28.6 1.0
C D:THR422 4.6 33.1 1.0
CG D:LEU421 4.6 33.6 1.0
CG D:LYS383 4.6 25.6 1.0
CA D:PHE385 4.6 29.9 1.0
CG D:PRO377 4.7 30.3 1.0
O D:GLU420 4.9 32.6 1.0
N D:PRO377 5.0 34.8 1.0

Reference:

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
Page generated: Wed Jul 26 16:30:09 2023

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