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Chlorine in PDB 5ost: Beta-Glucosidase From Thermoanaerobacterium Xylolyticum GH116 in Complex with Gluco-1H-Imidazole

Enzymatic activity of Beta-Glucosidase From Thermoanaerobacterium Xylolyticum GH116 in Complex with Gluco-1H-Imidazole

All present enzymatic activity of Beta-Glucosidase From Thermoanaerobacterium Xylolyticum GH116 in Complex with Gluco-1H-Imidazole:
3.2.1.45;

Protein crystallography data

The structure of Beta-Glucosidase From Thermoanaerobacterium Xylolyticum GH116 in Complex with Gluco-1H-Imidazole, PDB code: 5ost was solved by G.J.Davies, W.A.Offen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 88.97 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 177.617, 54.090, 83.559, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 25.1

Other elements in 5ost:

The structure of Beta-Glucosidase From Thermoanaerobacterium Xylolyticum GH116 in Complex with Gluco-1H-Imidazole also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Beta-Glucosidase From Thermoanaerobacterium Xylolyticum GH116 in Complex with Gluco-1H-Imidazole (pdb code 5ost). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Beta-Glucosidase From Thermoanaerobacterium Xylolyticum GH116 in Complex with Gluco-1H-Imidazole, PDB code: 5ost:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5ost

Go back to Chlorine Binding Sites List in 5ost
Chlorine binding site 1 out of 5 in the Beta-Glucosidase From Thermoanaerobacterium Xylolyticum GH116 in Complex with Gluco-1H-Imidazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Beta-Glucosidase From Thermoanaerobacterium Xylolyticum GH116 in Complex with Gluco-1H-Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl910

b:38.4
occ:0.50
 O A:HOH1217 2.8 26.6 1.0
N A:ASP401 3.3 22.7 1.0
CB A:ASP401 3.7 24.7 1.0
CG A:ASP401 4.0 25.8 1.0
CA A:PRO400 4.0 24.3 1.0
OD2 A:ASP401 4.1 33.9 1.0
CA A:ASP401 4.1 25.4 1.0
C A:PRO400 4.1 23.4 1.0
CB A:PRO400 4.2 24.0 1.0
OD1 A:ASP401 4.7 26.6 1.0
O1 A:EDO909 4.8 20.8 0.5
N A:TRP402 4.9 23.4 1.0

Chlorine binding site 2 out of 5 in 5ost

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Chlorine binding site 2 out of 5 in the Beta-Glucosidase From Thermoanaerobacterium Xylolyticum GH116 in Complex with Gluco-1H-Imidazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Beta-Glucosidase From Thermoanaerobacterium Xylolyticum GH116 in Complex with Gluco-1H-Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl911

b:52.1
occ:1.00
 N A:ASN446 3.3 20.9 1.0
O A:HOH1238 3.5 38.8 1.0
O A:ASP444 3.5 18.4 1.0
CB A:ASN446 3.8 19.5 1.0
CA A:TYR445 4.1 19.9 1.0
CA A:ASN446 4.1 20.8 1.0
C A:TYR445 4.1 19.0 1.0
OH A:TYR447 4.1 32.6 1.0
CE2 A:TYR513 4.2 23.6 1.0
C A:ASP444 4.2 19.3 1.0
CZ A:TYR447 4.3 29.2 1.0
N A:TYR445 4.5 17.2 1.0
CE1 A:TYR447 4.5 25.8 1.0
CD2 A:TYR513 4.7 23.5 1.0
C A:ASN446 4.8 22.5 1.0
O A:PHE443 4.9 29.2 1.0
CE2 A:TYR447 4.9 29.4 1.0

Chlorine binding site 3 out of 5 in 5ost

Go back to Chlorine Binding Sites List in 5ost
Chlorine binding site 3 out of 5 in the Beta-Glucosidase From Thermoanaerobacterium Xylolyticum GH116 in Complex with Gluco-1H-Imidazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Beta-Glucosidase From Thermoanaerobacterium Xylolyticum GH116 in Complex with Gluco-1H-Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl912

b:72.5
occ:1.00
 N A:LYS61 3.2 34.3 1.0
CD1 A:TYR62 3.6 24.0 0.5
CB A:VAL60 3.7 30.7 1.0
CA A:VAL60 3.9 33.8 1.0
CE1 A:TYR62 3.9 22.2 0.5
CB A:LYS61 3.9 33.9 0.5
C A:VAL60 4.0 33.3 1.0
CA A:LYS61 4.1 35.2 1.0
CG1 A:VAL60 4.1 32.9 1.0
N A:TYR62 4.3 32.6 1.0
C A:LYS61 4.7 34.2 1.0
CG A:TYR62 4.8 25.0 0.5
O A:HOH1256 4.9 39.1 1.0
CG2 A:VAL60 4.9 32.0 1.0
O A:HOH1193 5.0 30.9 1.0

Chlorine binding site 4 out of 5 in 5ost

Go back to Chlorine Binding Sites List in 5ost
Chlorine binding site 4 out of 5 in the Beta-Glucosidase From Thermoanaerobacterium Xylolyticum GH116 in Complex with Gluco-1H-Imidazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Beta-Glucosidase From Thermoanaerobacterium Xylolyticum GH116 in Complex with Gluco-1H-Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl913

b:53.9
occ:1.00
 N A:LYS352 3.2 17.7 1.0
CE A:LYS425 3.7 24.0 0.5
O A:LYS352 3.8 18.9 1.0
CA A:ASP351 3.9 19.1 1.0
CB A:LYS352 3.9 19.5 1.0
CA A:LYS352 4.0 19.1 1.0
C A:ASP351 4.0 18.8 1.0
CG A:LYS425 4.1 25.0 1.0
O A:VAL426 4.2 33.9 1.0
O A:GLY350 4.3 18.3 1.0
NZ A:LYS425 4.3 24.6 0.5
C A:LYS352 4.3 17.5 1.0
CG A:LYS352 4.4 23.3 1.0
OD1 A:ASP351 4.4 20.9 1.0
CD A:LYS425 4.4 24.4 0.5
CB A:ASP351 4.6 20.4 1.0
N A:VAL426 4.6 29.1 1.0
CG A:ASP351 4.8 20.0 1.0
CB A:VAL426 4.9 28.1 1.0
N A:ASP351 4.9 19.3 1.0
C A:GLY350 5.0 19.8 1.0

Chlorine binding site 5 out of 5 in 5ost

Go back to Chlorine Binding Sites List in 5ost
Chlorine binding site 5 out of 5 in the Beta-Glucosidase From Thermoanaerobacterium Xylolyticum GH116 in Complex with Gluco-1H-Imidazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Beta-Glucosidase From Thermoanaerobacterium Xylolyticum GH116 in Complex with Gluco-1H-Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl914

b:52.3
occ:1.00
 N A:THR331 2.9 34.0 1.0
O A:THR331 3.3 35.4 1.0
CA A:GLN330 3.7 35.8 1.0
CG A:GLN330 3.7 36.7 1.0
C A:GLN330 3.8 33.9 1.0
CA A:THR331 3.8 36.2 1.0
C A:THR331 4.0 36.8 1.0
O A:HOH1033 4.0 38.8 1.0
CB A:THR331 4.2 36.8 1.0
CB A:GLN330 4.2 35.4 1.0
O A:GLY329 4.4 43.9 1.0
N A:GLN330 4.9 37.1 1.0
OG1 A:THR331 4.9 37.3 1.0
CD A:GLN330 4.9 36.8 1.0

Reference:

S.P.Schroder, L.Wu, M.Artola, T.Hansen, W.A.Offen, M.J.Ferraz, K.Y.Li, J.M.F.G.Aerts, G.A.Van Der Marel, J.D.C.Codee, G.J.Davies, H.S.Overkleeft. Gluco-1 H-Imidazole: A New Class of Azole-Type Beta-Glucosidase Inhibitor. J. Am. Chem. Soc. V. 140 5045 2018.
ISSN: ESSN 1520-5126
PubMed: 29601200
DOI: 10.1021/JACS.8B02399
Page generated: Fri Jul 26 14:46:51 2024

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