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Chlorine in PDB 6d7f: Bacteroides Uniformis Beta-Glucuronidase 1 Bound to Thiophenyl-Beta-D- Glucuronide

Enzymatic activity of Bacteroides Uniformis Beta-Glucuronidase 1 Bound to Thiophenyl-Beta-D- Glucuronide

All present enzymatic activity of Bacteroides Uniformis Beta-Glucuronidase 1 Bound to Thiophenyl-Beta-D- Glucuronide:
3.2.1.31;

Protein crystallography data

The structure of Bacteroides Uniformis Beta-Glucuronidase 1 Bound to Thiophenyl-Beta-D- Glucuronide, PDB code: 6d7f was solved by W.G.Walton, S.J.Pellock, M.R.Redinbo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.30 / 2.40
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 252.177, 252.177, 107.289, 90.00, 90.00, 120.00
R / Rfree (%) 17.4 / 24.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Bacteroides Uniformis Beta-Glucuronidase 1 Bound to Thiophenyl-Beta-D- Glucuronide (pdb code 6d7f). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Bacteroides Uniformis Beta-Glucuronidase 1 Bound to Thiophenyl-Beta-D- Glucuronide, PDB code: 6d7f:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 6d7f

Go back to Chlorine Binding Sites List in 6d7f
Chlorine binding site 1 out of 5 in the Bacteroides Uniformis Beta-Glucuronidase 1 Bound to Thiophenyl-Beta-D- Glucuronide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Bacteroides Uniformis Beta-Glucuronidase 1 Bound to Thiophenyl-Beta-D- Glucuronide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl702

b:18.2
occ:1.00
 NE2 A:GLN569 3.3 10.0 1.0
NZ A:LYS575 3.4 16.9 1.0
O D:HOH910 3.4 15.5 1.0
N A:ARG574 3.4 18.2 1.0
CG A:LYS575 3.9 16.5 1.0
OD1 A:ASN573 3.9 15.3 1.0
CE1 A:PHE525 4.0 12.3 1.0
CE A:LYS575 4.1 19.3 1.0
NH1 A:ARG563 4.1 16.2 1.0
CA A:ARG574 4.2 15.5 1.0
CB A:ARG574 4.2 15.6 1.0
CD A:ARG563 4.2 15.6 1.0
CA A:GLY512 4.2 19.0 1.0
CG A:ASN573 4.2 15.2 1.0
CA A:ASN573 4.2 15.8 1.0
C A:ASN573 4.3 14.8 1.0
N A:LYS575 4.4 16.5 1.0
C A:ARG574 4.4 17.5 1.0
CD A:GLN569 4.4 15.8 1.0
CZ A:PHE525 4.5 16.2 1.0
CD A:LYS575 4.6 20.8 1.0
ND2 A:ASN573 4.6 16.2 1.0
CZ A:ARG563 4.7 17.8 1.0
NE A:ARG563 4.7 18.2 1.0
CG A:GLN569 4.7 15.5 1.0
CZ2 A:TRP483 4.7 17.7 1.0
N A:GLY512 4.8 19.6 1.0
CB A:ASN573 4.9 14.4 1.0
OE2 D:GLU80 4.9 21.7 1.0
NE1 A:TRP483 4.9 18.5 1.0
O A:PHE572 4.9 15.0 1.0
CG A:ARG574 4.9 13.9 1.0
CG A:ARG563 4.9 18.6 1.0

Chlorine binding site 2 out of 5 in 6d7f

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Chlorine binding site 2 out of 5 in the Bacteroides Uniformis Beta-Glucuronidase 1 Bound to Thiophenyl-Beta-D- Glucuronide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Bacteroides Uniformis Beta-Glucuronidase 1 Bound to Thiophenyl-Beta-D- Glucuronide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl702

b:27.4
occ:1.00
 O B:HOH1533 3.2 31.5 1.0
NE2 B:GLN569 3.3 26.7 1.0
N B:ARG574 3.4 30.8 1.0
NZ B:LYS575 3.4 38.6 1.0
CG B:LYS575 3.8 33.5 1.0
CE B:LYS575 3.9 34.1 1.0
OD1 B:ASN573 3.9 27.0 1.0
CE1 B:PHE525 4.0 25.3 1.0
CD B:ARG563 4.1 30.4 1.0
CA B:ARG574 4.1 27.2 1.0
CB B:ARG574 4.1 29.8 1.0
CA B:GLY512 4.2 28.9 1.0
CA B:ASN573 4.2 28.1 1.0
CG B:ASN573 4.2 29.6 1.0
NH1 B:ARG563 4.2 34.9 1.0
N B:LYS575 4.3 32.3 1.0
C B:ASN573 4.3 29.0 1.0
CD B:GLN569 4.3 30.3 1.0
C B:ARG574 4.4 29.5 1.0
CD B:LYS575 4.5 33.9 1.0
CZ B:PHE525 4.6 26.1 1.0
CG B:GLN569 4.6 27.2 1.0
ND2 B:ASN573 4.6 26.3 1.0
NE B:ARG563 4.7 32.5 1.0
N B:GLY512 4.7 32.6 1.0
CZ B:ARG563 4.8 33.7 1.0
NE1 B:TRP483 4.8 39.0 1.0
CB B:ASN573 4.8 27.2 1.0
CG B:ARG563 4.8 31.2 1.0
O B:PHE572 4.9 29.9 1.0
CZ2 B:TRP483 4.9 32.9 1.0
CG B:ARG574 5.0 31.7 1.0

Chlorine binding site 3 out of 5 in 6d7f

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Chlorine binding site 3 out of 5 in the Bacteroides Uniformis Beta-Glucuronidase 1 Bound to Thiophenyl-Beta-D- Glucuronide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Bacteroides Uniformis Beta-Glucuronidase 1 Bound to Thiophenyl-Beta-D- Glucuronide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl702

b:28.6
occ:1.00
 N C:ARG574 3.2 27.1 1.0
NZ C:LYS575 3.3 26.6 1.0
O C:HOH941 3.4 23.4 1.0
NE2 C:GLN569 3.4 24.4 1.0
OD1 C:ASN573 3.8 26.8 1.0
CA C:ARG574 4.0 21.1 1.0
CE1 C:PHE525 4.0 26.4 1.0
CG C:LYS575 4.0 25.6 1.0
CB C:ARG574 4.0 21.1 1.0
CG C:ASN573 4.1 27.1 1.0
C C:ASN573 4.1 26.0 1.0
CA C:ASN573 4.1 21.1 1.0
N C:LYS575 4.2 22.3 1.0
CD C:ARG563 4.3 26.8 1.0
NH1 C:ARG563 4.3 27.8 1.0
C C:ARG574 4.3 24.0 1.0
CE C:LYS575 4.4 28.0 1.0
CA C:GLY512 4.4 26.0 1.0
CD C:GLN569 4.4 27.5 1.0
ND2 C:ASN573 4.5 26.9 1.0
CG C:GLN569 4.6 22.7 1.0
CZ C:PHE525 4.7 24.0 1.0
CB C:ASN573 4.7 21.3 1.0
NE C:ARG563 4.7 27.7 1.0
CZ C:ARG563 4.7 27.6 1.0
CD C:LYS575 4.8 26.1 1.0
CG C:ARG574 4.9 23.2 1.0
CZ2 C:TRP483 4.9 26.1 1.0
O C:PHE572 4.9 24.4 1.0
N C:GLY512 4.9 30.4 1.0

Chlorine binding site 4 out of 5 in 6d7f

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Chlorine binding site 4 out of 5 in the Bacteroides Uniformis Beta-Glucuronidase 1 Bound to Thiophenyl-Beta-D- Glucuronide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Bacteroides Uniformis Beta-Glucuronidase 1 Bound to Thiophenyl-Beta-D- Glucuronide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl702

b:30.1
occ:1.00
 O D:HOH1001 3.0 32.2 1.0
N D:ARG574 3.2 22.4 1.0
NZ D:LYS575 3.4 26.1 1.0
NE2 D:GLN569 3.4 19.7 1.0
OD1 D:ASN573 3.7 24.7 1.0
CG D:LYS575 3.9 28.4 1.0
CA D:ARG574 4.0 22.9 1.0
CB D:ARG574 4.0 23.3 1.0
CE1 D:PHE525 4.1 31.0 1.0
CA D:ASN573 4.1 25.0 1.0
C D:ASN573 4.1 24.9 1.0
CG D:ASN573 4.2 25.9 1.0
N D:LYS575 4.3 29.9 1.0
CD D:ARG563 4.3 24.0 1.0
CA D:GLY512 4.3 29.8 1.0
C D:ARG574 4.3 24.1 1.0
CE D:LYS575 4.4 33.5 1.0
CD D:GLN569 4.4 27.6 1.0
CG D:GLN569 4.5 28.1 1.0
NH1 D:ARG563 4.7 28.9 1.0
CB D:ASN573 4.7 18.9 1.0
NE D:ARG563 4.7 28.6 1.0
CD D:LYS575 4.7 27.5 1.0
ND2 D:ASN573 4.7 22.1 1.0
OE2 A:GLU80 4.8 40.4 1.0
CZ D:PHE525 4.8 25.4 1.0
O D:PHE572 4.9 26.2 1.0
CZ2 D:TRP483 4.9 28.7 1.0
CZ D:ARG563 4.9 29.5 1.0
CG D:ARG574 4.9 26.7 1.0
NE1 D:TRP483 5.0 29.0 1.0
CD1 D:PHE525 5.0 31.3 1.0

Chlorine binding site 5 out of 5 in 6d7f

Go back to Chlorine Binding Sites List in 6d7f
Chlorine binding site 5 out of 5 in the Bacteroides Uniformis Beta-Glucuronidase 1 Bound to Thiophenyl-Beta-D- Glucuronide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Bacteroides Uniformis Beta-Glucuronidase 1 Bound to Thiophenyl-Beta-D- Glucuronide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl702

b:22.2
occ:1.00
 O F:HOH919 3.1 16.8 1.0
NZ F:LYS575 3.1 19.6 1.0
N F:ARG574 3.4 17.7 1.0
NE2 F:GLN569 3.5 15.0 1.0
CG F:LYS575 3.7 19.0 1.0
CE F:LYS575 3.8 15.8 1.0
CE1 F:PHE525 3.9 17.1 1.0
OD1 F:ASN573 4.1 19.5 1.0
CA F:ARG574 4.2 20.4 1.0
CB F:ARG574 4.2 22.6 1.0
N F:LYS575 4.3 18.3 1.0
NH1 F:ARG563 4.3 24.4 1.0
CG F:ASN573 4.3 17.8 1.0
C F:ASN573 4.3 18.3 1.0
CA F:ASN573 4.3 15.5 1.0
C F:ARG574 4.4 20.5 1.0
CD F:LYS575 4.4 20.4 1.0
CA F:GLY512 4.4 20.4 1.0
CD F:ARG563 4.4 17.9 1.0
CD F:GLN569 4.5 18.5 1.0
CZ F:PHE525 4.5 17.6 1.0
CZ2 F:TRP483 4.5 18.4 1.0
CG F:GLN569 4.6 20.4 1.0
ND2 F:ASN573 4.6 16.8 1.0
CZ F:ARG563 4.8 23.6 1.0
NE F:ARG563 4.8 17.7 1.0
NE1 F:TRP483 4.9 18.7 1.0
N F:GLY512 4.9 20.4 1.0
CB F:ASN573 4.9 17.4 1.0
CE2 F:TRP483 5.0 17.3 1.0
CD1 F:PHE525 5.0 19.6 1.0
CB F:LYS575 5.0 19.4 1.0

Reference:

S.J.Pellock, W.G.Walton, K.A.Biernat, D.Torres-Rivera, B.C.Creekmore, Y.Xu, J.Liu, A.Tripathy, L.J.Stewart, M.R.Redinbo. Three Structurally and Functionally Distinct Beta-Glucuronidases From the Human Gut Microbebacteroides Uniformis. J. Biol. Chem. V. 293 18559 2018.
ISSN: ESSN 1083-351X
PubMed: 30301767
DOI: 10.1074/JBC.RA118.005414
Page generated: Sat Jul 27 21:26:23 2024

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