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Calcium in PDB 5npf: Crystal Structure of TXGH116 (Beta-Glucosidase From Thermoanaerobacterium Xylolyticum) in Complex with Beta Cyclophellitol Cyclosulfate Probe ME594

Enzymatic activity of Crystal Structure of TXGH116 (Beta-Glucosidase From Thermoanaerobacterium Xylolyticum) in Complex with Beta Cyclophellitol Cyclosulfate Probe ME594

All present enzymatic activity of Crystal Structure of TXGH116 (Beta-Glucosidase From Thermoanaerobacterium Xylolyticum) in Complex with Beta Cyclophellitol Cyclosulfate Probe ME594:
3.2.1.45;

Protein crystallography data

The structure of Crystal Structure of TXGH116 (Beta-Glucosidase From Thermoanaerobacterium Xylolyticum) in Complex with Beta Cyclophellitol Cyclosulfate Probe ME594, PDB code: 5npf was solved by L.Wu, W.A.Offen, I.Z.Breen, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.57 / 1.38
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 178.180, 53.810, 83.300, 90.00, 90.00, 90.00
R / Rfree (%) 12.5 / 16.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of TXGH116 (Beta-Glucosidase From Thermoanaerobacterium Xylolyticum) in Complex with Beta Cyclophellitol Cyclosulfate Probe ME594 (pdb code 5npf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of TXGH116 (Beta-Glucosidase From Thermoanaerobacterium Xylolyticum) in Complex with Beta Cyclophellitol Cyclosulfate Probe ME594, PDB code: 5npf:

Calcium binding site 1 out of 1 in 5npf

Go back to Calcium Binding Sites List in 5npf
Calcium binding site 1 out of 1 in the Crystal Structure of TXGH116 (Beta-Glucosidase From Thermoanaerobacterium Xylolyticum) in Complex with Beta Cyclophellitol Cyclosulfate Probe ME594


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of TXGH116 (Beta-Glucosidase From Thermoanaerobacterium Xylolyticum) in Complex with Beta Cyclophellitol Cyclosulfate Probe ME594 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca914

b:25.6
occ:1.00
 OD1 A:ASP579 2.3 23.0 1.0
OD1 A:ASP583 2.4 20.5 0.3
O A:HOH1077 2.4 31.9 1.0
OD1 A:ASP583 2.4 34.8 0.7
O A:ILE581 2.4 20.2 1.0
OD1 A:ASP577 2.4 32.9 1.0
OD1 A:ASP575 2.4 23.8 1.0
O A:HOH1047 2.4 44.3 1.0
CG A:ASP579 3.2 24.6 1.0
CG A:ASP583 3.2 36.6 0.7
CG A:ASP575 3.5 23.8 1.0
CG A:ASP577 3.5 36.0 1.0
C A:ILE581 3.5 20.0 1.0
OD2 A:ASP583 3.6 36.5 0.7
CG A:ASP583 3.6 20.4 0.3
OD2 A:ASP579 3.6 25.5 1.0
OD2 A:ASP577 4.0 40.0 1.0
N A:ILE581 4.1 20.9 1.0
CA A:ASP575 4.1 21.9 1.0
N A:ASP583 4.1 20.8 0.3
CA A:ILE581 4.2 19.9 1.0
CB A:ASP575 4.2 22.1 1.0
N A:ASP583 4.2 20.1 0.7
C A:PRO582 4.2 20.9 1.0
N A:ASP577 4.3 28.8 1.0
N A:ASP579 4.3 25.4 1.0
CB A:ILE581 4.3 19.2 1.0
OD2 A:ASP583 4.3 23.6 0.3
OD2 A:ASP575 4.3 27.2 1.0
CB A:ASP583 4.4 30.1 0.7
CB A:ASP579 4.4 24.7 1.0
OG1 A:THR600 4.4 22.8 1.0
O A:PRO582 4.5 22.1 1.0
CA A:ASP583 4.5 26.2 0.7
CA A:ASP583 4.5 21.6 0.3
N A:LYS576 4.5 28.2 1.0
C A:ASP575 4.6 25.7 1.0
N A:PRO582 4.6 19.5 1.0
CB A:ASP583 4.6 21.6 0.3
CA A:PRO582 4.7 20.0 1.0
CB A:ASP577 4.7 30.0 1.0
CA A:ASP579 4.7 26.1 1.0
N A:ASN578 4.8 29.1 1.0
N A:GLY580 4.9 23.6 1.0
CA A:ASP577 4.9 23.6 1.0
C A:ASP577 4.9 26.9 1.0
C A:ASP579 5.0 27.8 1.0

Reference:

M.Artola, L.Wu, M.J.Ferraz, C.L.Kuo, L.Raich, I.Z.Breen, W.A.Offen, J.D.C.Codee, G.A.Van Der Marel, C.Rovira, J.M.F.G.Aerts, G.J.Davies, H.S.Overkleeft. 1,6-Cyclophellitol Cyclosulfates: A New Class of Irreversible Glycosidase Inhibitor. Acs Cent Sci V. 3 784 2017.
ISSN: ESSN 2374-7943
PubMed: 28776021
DOI: 10.1021/ACSCENTSCI.7B00214
Page generated: Wed Jul 9 09:08:33 2025

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