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Calcium in PDB 5bx3: Crystal Structure of Thermoanaerobacterium Xylanolyticum GH116 Beta- Glucosidase with Deoxynojirimycin

Enzymatic activity of Crystal Structure of Thermoanaerobacterium Xylanolyticum GH116 Beta- Glucosidase with Deoxynojirimycin

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

Protein crystallography data

The structure of Crystal Structure of Thermoanaerobacterium Xylanolyticum GH116 Beta- Glucosidase with Deoxynojirimycin, PDB code: 5bx3 was solved by R.Charoenwattanasatien, S.Pengthaisong, S.Sansenya, R.Mutoh, A.Tankrathok, 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 / 1.96
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 177.309, 54.662, 83.078, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 17.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Thermoanaerobacterium Xylanolyticum GH116 Beta- Glucosidase with Deoxynojirimycin (pdb code 5bx3). 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 Deoxynojirimycin, PDB code: 5bx3:

Calcium binding site 1 out of 1 in 5bx3

Go back to Calcium Binding Sites List in 5bx3
Calcium binding site 1 out of 1 in the Crystal Structure of Thermoanaerobacterium Xylanolyticum GH116 Beta- Glucosidase with Deoxynojirimycin


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 Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca917

b:21.5
occ:1.00
 OD1 A:ASP579 2.2 21.6 1.0
OD1 A:ASP583 2.2 26.3 1.0
OD1 A:ASP575 2.2 23.2 1.0
O A:ILE581 2.3 20.1 1.0
OD1 A:ASP577 2.3 32.4 1.0
O A:HOH1123 2.4 25.7 1.0
CG A:ASP579 3.1 22.8 1.0
CG A:ASP583 3.2 27.0 1.0
CG A:ASP575 3.3 23.2 1.0
O3 A:GOL913 3.3 52.2 1.0
C A:ILE581 3.4 20.7 1.0
OD2 A:ASP579 3.5 24.0 1.0
CG A:ASP577 3.5 36.3 1.0
OD2 A:ASP583 3.7 31.7 1.0
N A:ILE581 3.9 19.7 1.0
CA A:ASP575 4.0 25.1 1.0
CB A:ASP575 4.0 23.6 1.0
OD2 A:ASP577 4.0 40.7 1.0
CA A:ILE581 4.1 20.5 1.0
N A:ASP579 4.1 26.9 1.0
OD2 A:ASP575 4.2 21.4 1.0
N A:ASP583 4.2 20.7 1.0
CB A:ILE581 4.2 20.7 1.0
N A:ASP577 4.2 33.7 1.0
C A:PRO582 4.3 20.8 1.0
CB A:ASP579 4.3 23.6 1.0
N A:LYS576 4.3 32.0 1.0
C A:ASP575 4.4 27.6 1.0
CB A:ASP583 4.4 23.5 1.0
OG1 A:THR600 4.5 20.3 1.0
N A:PRO582 4.5 21.5 1.0
O A:PRO582 4.5 22.1 1.0
CA A:ASP583 4.5 20.8 1.0
CA A:ASP579 4.6 24.1 1.0
N A:GLY580 4.6 20.5 1.0
CA A:PRO582 4.6 21.1 1.0
C3 A:GOL913 4.6 50.4 1.0
CB A:ASP577 4.7 33.8 1.0
N A:ASN578 4.7 32.0 1.0
C A:ASP579 4.8 22.6 1.0
CA A:ASP577 4.8 33.8 1.0
C A:ASP577 4.8 33.4 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: Sun Jul 14 16:59:02 2024

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