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Calcium in PDB 5bx2: Crystal Structure of Thermoanaerobacterium Xylanolyticum GH116 Beta- Glucosidase with 2-Deoxy-2-Fluoroglucoside

Enzymatic activity of Crystal Structure of Thermoanaerobacterium Xylanolyticum GH116 Beta- Glucosidase with 2-Deoxy-2-Fluoroglucoside

All present enzymatic activity of Crystal Structure of Thermoanaerobacterium Xylanolyticum GH116 Beta- Glucosidase with 2-Deoxy-2-Fluoroglucoside:
3.2.1.21;

Protein crystallography data

The structure of Crystal Structure of Thermoanaerobacterium Xylanolyticum GH116 Beta- Glucosidase with 2-Deoxy-2-Fluoroglucoside, PDB code: 5bx2 was solved by R.Charoenwattanasatien, S.Pengthaisong, S.Sansenya, R.Mutoh, H.Tanaka, G.Kurisu, J.R.Ketudat Cairns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.61
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 177.112, 54.688, 83.269, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 17.6

Other elements in 5bx2:

The structure of Crystal Structure of Thermoanaerobacterium Xylanolyticum GH116 Beta- Glucosidase with 2-Deoxy-2-Fluoroglucoside also contains other interesting chemical elements:

Fluorine (F) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Thermoanaerobacterium Xylanolyticum GH116 Beta- Glucosidase with 2-Deoxy-2-Fluoroglucoside (pdb code 5bx2). 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 Thermoanaerobacterium Xylanolyticum GH116 Beta- Glucosidase with 2-Deoxy-2-Fluoroglucoside, PDB code: 5bx2:

Calcium binding site 1 out of 1 in 5bx2

Go back to Calcium Binding Sites List in 5bx2
Calcium binding site 1 out of 1 in the Crystal Structure of Thermoanaerobacterium Xylanolyticum GH116 Beta- Glucosidase with 2-Deoxy-2-Fluoroglucoside


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 Thermoanaerobacterium Xylanolyticum GH116 Beta- Glucosidase with 2-Deoxy-2-Fluoroglucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1019

b:20.7
occ:1.00
 OD1 A:ASP583 2.2 20.6 1.0
OD1 A:ASP579 2.4 20.7 1.0
O A:HOH1161 2.4 17.9 1.0
O A:ILE581 2.4 16.5 1.0
OD1 A:ASP575 2.4 19.6 1.0
OD1 A:ASP577 2.4 25.2 1.0
O3 A:GOL1015 2.6 32.7 1.0
CG A:ASP579 3.2 20.7 1.0
CG A:ASP583 3.2 20.4 1.0
CG A:ASP575 3.5 20.0 1.0
C A:ILE581 3.5 16.7 1.0
CG A:ASP577 3.6 27.6 1.0
OD2 A:ASP579 3.6 21.2 1.0
OD2 A:ASP583 3.6 23.6 1.0
C3 A:GOL1015 3.9 32.1 1.0
OD2 A:ASP577 4.1 28.2 1.0
N A:ILE581 4.1 16.5 1.0
CA A:ASP575 4.1 21.1 1.0
CB A:ASP575 4.2 20.8 1.0
CA A:ILE581 4.2 16.7 1.0
N A:ASP583 4.2 17.2 1.0
N A:LYS576 4.2 24.0 1.0
C A:PRO582 4.2 17.0 1.0
N A:ASP577 4.3 26.8 1.0
CB A:ASP579 4.3 20.8 1.0
OD2 A:ASP575 4.3 20.6 1.0
N A:ASP579 4.3 22.6 1.0
CB A:ILE581 4.4 16.7 1.0
CB A:ASP583 4.4 19.0 1.0
OG1 A:THR600 4.4 15.7 1.0
O A:PRO582 4.4 17.3 1.0
CA A:ASP583 4.5 17.7 1.0
C A:ASP575 4.5 22.8 1.0
N A:PRO582 4.6 16.8 1.0
CA A:PRO582 4.7 16.9 1.0
CA A:ASP579 4.7 21.0 1.0
CB A:ASP577 4.7 27.4 1.0
N A:GLY580 4.9 17.7 1.0
N A:ASN578 4.9 27.3 1.0
CA A:ASP577 4.9 27.6 1.0
C A:ASP577 5.0 27.7 1.0
C A:ASP579 5.0 19.4 1.0

Reference:

R.Charoenwattanasatien, S.Pengthaisong, I.Breen, R.Mutoh, S.Sansenya, Y.Hua, A.Tankrathok, L.Wu, C.Songsiriritthigul, H.Tanaka, S.J.Williams, G.J.Davies, G.Kurisu, J.R.Ketudat Cairns. Bacterial Beta-Glucosidase Reveals the Structural and Functional Basis of Genetic Defects in Human Glucocerebrosidase 2 (GBA2) Acs Chem.Biol. V. 11 1891 2016.
ISSN: ESSN 1554-8937
PubMed: 27115290
DOI: 10.1021/ACSCHEMBIO.6B00192
Page generated: Wed Jul 9 04:28:47 2025

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