Chlorine in PDB 8oi4: Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154

Enzymatic activity of Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154

All present enzymatic activity of Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154:
3.2.1.23;

Protein crystallography data

The structure of Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154, PDB code: 8oi4 was solved by T.Pijning, L.Hameleers, E.Jurak, A.Guskov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.40 / 1.76
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 96.316, 94.581, 108.264, 90, 105.45, 90
R / Rfree (%) 15.2 / 17.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154 (pdb code 8oi4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154, PDB code: 8oi4:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 8oi4

Go back to Chlorine Binding Sites List in 8oi4
Chlorine binding site 1 out of 6 in the Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:29.2
occ:1.00
 O A:HOH698 3.1 30.5 1.0
O A:HOH710 3.1 25.3 1.0
NH2 A:ARG292 3.2 27.4 1.0
NE1 A:TRP177 3.2 27.4 1.0
NH1 A:ARG292 3.4 24.4 1.0
ND2 A:ASN176 3.6 23.7 1.0
C3 A:GOL501 3.7 37.6 1.0
CD1 A:TRP177 3.7 25.0 1.0
CZ A:ARG292 3.7 30.2 1.0
CE2 A:TYR228 4.0 23.2 1.0
C1 A:GOL501 4.0 36.7 1.0
OH A:TYR228 4.2 24.8 1.0
CZ A:TYR228 4.3 22.8 1.0
OD1 A:ASN176 4.3 26.1 1.0
C2 A:GOL501 4.4 34.3 1.0
CG A:ASN176 4.4 27.7 1.0
O A:HOH720 4.5 37.6 1.0
CE2 A:TRP177 4.5 26.1 1.0
O3 A:GOL501 4.6 40.1 1.0
CD2 A:TYR228 4.7 22.9 1.0

Chlorine binding site 2 out of 6 in 8oi4

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Chlorine binding site 2 out of 6 in the Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:30.2
occ:1.00
 NH2 B:ARG292 3.1 26.4 1.0
O B:HOH655 3.1 31.1 1.0
O B:HOH686 3.2 27.4 1.0
NE1 B:TRP177 3.2 26.6 1.0
NH1 B:ARG292 3.4 25.6 1.0
ND2 B:ASN176 3.6 25.5 1.0
CZ B:ARG292 3.7 29.1 1.0
CD1 B:TRP177 3.7 26.4 1.0
C3 B:GOL501 3.8 37.7 1.0
C1 B:GOL501 3.9 34.4 1.0
CE2 B:TYR228 4.0 25.6 1.0
OH B:TYR228 4.2 25.4 1.0
CZ B:TYR228 4.3 24.1 1.0
OD1 B:ASN176 4.3 26.4 1.0
C2 B:GOL501 4.3 35.8 1.0
CG B:ASN176 4.4 24.2 1.0
CE2 B:TRP177 4.5 24.9 1.0
O B:HOH724 4.5 36.4 1.0
O3 B:GOL501 4.6 36.5 1.0
CD2 B:TYR228 4.7 26.7 1.0
NE B:ARG292 5.0 28.2 1.0

Chlorine binding site 3 out of 6 in 8oi4

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Chlorine binding site 3 out of 6 in the Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:41.5
occ:1.00
 O B:ARG292 2.7 23.0 1.0
O B:PHE290 2.8 23.3 1.0
N B:TYR227 2.9 21.0 1.0
CB B:ASP226 3.4 24.4 1.0
C B:GLY291 3.5 25.2 1.0
CD2 B:TYR227 3.5 21.6 1.0
CB B:TYR227 3.6 24.0 1.0
CA B:GLY291 3.6 23.6 1.0
CA B:ASP226 3.7 22.2 1.0
C B:ASP226 3.7 24.2 1.0
O B:GLY291 3.8 25.2 1.0
N B:ARG292 3.8 24.6 1.0
CA B:TYR227 3.8 21.7 1.0
C B:ARG292 3.8 23.2 1.0
C B:PHE290 3.8 21.4 1.0
OH B:TYR231 3.9 23.6 1.0
CG B:TYR227 4.0 20.8 1.0
CE2 B:TYR231 4.2 22.8 1.0
N B:GLY291 4.2 24.4 1.0
SD B:MET294 4.3 28.4 1.0
CG B:ASP226 4.4 25.8 1.0
CA B:ARG292 4.4 25.2 1.0
CZ B:TYR231 4.4 21.9 1.0
CE2 B:TYR227 4.6 20.1 1.0
C B:TYR227 4.6 24.7 1.0
C B:SER293 4.7 23.4 1.0
OD1 B:ASP226 4.8 27.3 1.0
O B:SER293 4.8 24.8 1.0
N B:TYR228 4.9 23.1 1.0
N B:MET294 4.9 23.0 1.0
N B:SER293 4.9 24.1 1.0
O B:ASP226 4.9 27.8 1.0

Chlorine binding site 4 out of 6 in 8oi4

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Chlorine binding site 4 out of 6 in the Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl502

b:31.1
occ:1.00
 NH2 C:ARG292 3.1 30.2 1.0
O C:HOH617 3.2 30.7 1.0
O C:HOH690 3.2 33.3 1.0
NE1 C:TRP177 3.2 28.4 1.0
NH1 C:ARG292 3.4 27.1 1.0
ND2 C:ASN176 3.6 25.6 1.0
C1 C:GOL501 3.6 34.9 1.0
CZ C:ARG292 3.7 32.2 1.0
CD1 C:TRP177 3.7 27.1 1.0
C3 C:GOL501 3.9 39.1 1.0
CE1 C:TYR228 4.1 25.4 1.0
OD1 C:ASN176 4.3 27.2 1.0
CZ C:TYR228 4.3 26.2 1.0
OH C:TYR228 4.3 28.2 1.0
C2 C:GOL501 4.3 46.9 1.0
CG C:ASN176 4.4 28.9 1.0
O C:HOH659 4.4 36.2 1.0
CE2 C:TRP177 4.5 26.6 1.0
CD1 C:TYR228 4.8 25.1 1.0
O1 C:GOL501 4.8 39.6 1.0
NE C:ARG292 5.0 30.8 1.0

Chlorine binding site 5 out of 6 in 8oi4

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Chlorine binding site 5 out of 6 in the Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl503

b:53.0
occ:1.00
 O D:GLY285 2.8 31.6 1.0
O D:ALA329 2.8 29.6 1.0
NE1 C:TRP399 2.9 27.5 1.0
CZ2 C:TRP399 3.4 26.7 1.0
CE2 C:TRP399 3.5 27.2 1.0
CG D:ARG332 3.5 45.9 0.5
N D:LEU333 3.5 31.9 1.0
CB D:LEU333 3.6 31.3 1.0
C D:ALA329 3.7 30.5 1.0
CB D:ARG332 3.7 32.6 0.5
CG D:ARG332 3.7 34.1 0.5
CB D:ARG332 3.8 38.4 0.5
CA D:ALA329 3.8 30.0 1.0
CA D:LEU333 3.9 31.3 1.0
C D:GLY285 4.0 29.5 1.0
CE1 D:PHE287 4.0 28.7 1.0
CD1 C:TRP399 4.1 27.9 1.0
C D:ARG332 4.2 34.9 1.0
CD1 D:LEU333 4.2 33.6 1.0
CB D:ALA329 4.2 29.8 1.0
CA D:THR286 4.3 26.4 1.0
CG D:LEU333 4.4 31.1 1.0
CA D:ARG332 4.4 34.5 0.5
CA D:ARG332 4.5 37.0 0.5
CD1 D:PHE287 4.6 28.6 1.0
N D:THR286 4.6 25.7 1.0
CH2 C:TRP399 4.7 26.1 1.0
CD2 C:TRP399 4.8 26.8 1.0
CD2 D:LEU333 4.8 31.8 1.0
CD D:ARG332 4.9 46.2 0.5
N D:ARG332 4.9 33.6 1.0
CG2 D:THR286 4.9 29.5 1.0
CZ D:PHE287 4.9 28.8 1.0
N D:MET330 4.9 30.0 1.0
O D:ALA328 5.0 33.3 1.0
O D:ARG332 5.0 37.0 1.0

Chlorine binding site 6 out of 6 in 8oi4

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Chlorine binding site 6 out of 6 in the Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Metagenomic Beta-Galactosidase From Glycoside Hydrolase Family GH154 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl503

b:30.5
occ:1.00
 O D:HOH648 3.0 30.8 1.0
NH2 D:ARG292 3.1 29.5 1.0
NE1 D:TRP177 3.2 26.2 1.0
O D:HOH656 3.2 27.9 1.0
NH1 D:ARG292 3.4 25.6 1.0
ND2 D:ASN176 3.6 26.8 1.0
CD1 D:TRP177 3.7 25.7 1.0
C3 D:GOL501 3.7 40.5 1.0
CZ D:ARG292 3.7 32.4 1.0
C1 D:GOL501 3.9 33.9 1.0
CE2 D:TYR228 4.0 27.9 1.0
OH D:TYR228 4.2 26.3 1.0
OD1 D:ASN176 4.2 27.2 1.0
CZ D:TYR228 4.2 28.8 1.0
C2 D:GOL501 4.3 43.3 1.0
O D:HOH772 4.3 55.0 1.0
CG D:ASN176 4.4 25.5 1.0
CE2 D:TRP177 4.5 26.2 1.0
O D:HOH679 4.6 33.0 1.0
O3 D:GOL501 4.7 37.0 1.0
CD2 D:TYR228 4.7 25.7 1.0
O D:HOH773 4.9 53.1 1.0

Reference:

L.Hameleers, T.Pijning, B.B.Gray, R.Faure, E.Jurak. Novel Beta-Galactosidase Activity and First Crystal Structure of Glycoside Hydrolase Family 154. N Biotechnol V. 80 1 2023.
ISSN: ESSN 1876-4347
PubMed: 38163476
DOI: 10.1016/J.NBT.2023.12.011
Page generated: Tue Jul 30 11:07:04 2024

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