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

Go back to Chlorine Binding Sites List in 6d7f
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

Go back to Chlorine Binding Sites List in 6d7f
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

Go back to Chlorine Binding Sites List in 6d7f
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 Dec 12 12:52:35 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy