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Calcium in PDB 5fjs: Bacterial Beta-Glucosidase Reveals the Structural and Functional Basis of Genetic Defects in Human Glucocerebrosidase 2 (GBA2) Disorders

Enzymatic activity of Bacterial Beta-Glucosidase Reveals the Structural and Functional Basis of Genetic Defects in Human Glucocerebrosidase 2 (GBA2) Disorders

All present enzymatic activity of Bacterial Beta-Glucosidase Reveals the Structural and Functional Basis of Genetic Defects in Human Glucocerebrosidase 2 (GBA2) Disorders:
3.2.1.21;

Protein crystallography data

The structure of Bacterial Beta-Glucosidase Reveals the Structural and Functional Basis of Genetic Defects in Human Glucocerebrosidase 2 (GBA2) Disorders, PDB code: 5fjs was solved by R.Charoenwattanasatien, S.Pengthaisong, I.Breen, R.Mutoha, S.Sansenya, Y.Hua, A.Tankrathok, L.Wu, C.Songsiriritthigul, H.Tanaka, S.J.Williams, G.J.Davies, 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) 162.61 / 2.60
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 187.974, 187.974, 99.075, 90.00, 90.00, 120.00
R / Rfree (%) 20.559 / 26.649

Calcium Binding Sites:

The binding sites of Calcium atom in the Bacterial Beta-Glucosidase Reveals the Structural and Functional Basis of Genetic Defects in Human Glucocerebrosidase 2 (GBA2) Disorders (pdb code 5fjs). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Bacterial Beta-Glucosidase Reveals the Structural and Functional Basis of Genetic Defects in Human Glucocerebrosidase 2 (GBA2) Disorders, PDB code: 5fjs:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5fjs

Go back to Calcium Binding Sites List in 5fjs
Calcium binding site 1 out of 2 in the Bacterial Beta-Glucosidase Reveals the Structural and Functional Basis of Genetic Defects in Human Glucocerebrosidase 2 (GBA2) Disorders


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bacterial Beta-Glucosidase Reveals the Structural and Functional Basis of Genetic Defects in Human Glucocerebrosidase 2 (GBA2) Disorders within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1804

b:62.9
occ:1.00
 OD1 A:ASP583 2.1 58.0 1.0
OD1 A:ASP577 2.1 69.9 1.0
O A:ILE581 2.3 38.0 1.0
OD1 A:ASP579 2.5 44.0 1.0
OD1 A:ASP575 2.6 52.5 1.0
CG A:ASP577 3.1 68.6 1.0
CG A:ASP579 3.2 46.1 1.0
CG A:ASP583 3.3 57.0 1.0
OD2 A:ASP577 3.4 81.2 1.0
C A:ILE581 3.4 38.8 1.0
OD2 A:ASP579 3.5 44.3 1.0
CG A:ASP575 3.6 52.2 1.0
N A:ILE581 4.0 45.5 1.0
C A:PRO582 4.0 46.3 1.0
OD2 A:ASP583 4.0 65.9 1.0
N A:ASP583 4.1 46.7 1.0
CA A:ASP575 4.1 48.4 1.0
CA A:ILE581 4.1 40.0 1.0
O A:PRO582 4.2 46.6 1.0
CA A:ASP583 4.2 46.7 1.0
CB A:ASP575 4.3 48.3 1.0
CB A:ILE581 4.3 39.2 1.0
CB A:ASP583 4.3 51.7 1.0
OG1 A:THR600 4.4 44.7 1.0
N A:PRO582 4.4 40.0 1.0
N A:ASP577 4.4 54.5 1.0
CB A:ASP579 4.4 41.6 1.0
N A:ASP579 4.4 50.0 1.0
CB A:ASP577 4.4 62.0 1.0
CA A:PRO582 4.5 43.1 1.0
OD2 A:ASP575 4.5 56.5 1.0
C A:ASP575 4.6 52.4 1.0
CA A:ASP577 4.8 54.9 1.0
N A:LYS576 4.8 57.4 1.0
CA A:ASP579 4.8 43.1 1.0
N A:ASN578 4.9 56.1 1.0
C A:ASP577 4.9 56.0 1.0
N A:GLY580 4.9 36.4 1.0
C A:ASP579 4.9 39.9 1.0

Calcium binding site 2 out of 2 in 5fjs

Go back to Calcium Binding Sites List in 5fjs
Calcium binding site 2 out of 2 in the Bacterial Beta-Glucosidase Reveals the Structural and Functional Basis of Genetic Defects in Human Glucocerebrosidase 2 (GBA2) Disorders


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bacterial Beta-Glucosidase Reveals the Structural and Functional Basis of Genetic Defects in Human Glucocerebrosidase 2 (GBA2) Disorders within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1804

b:74.6
occ:1.00
 O B:ILE581 2.3 62.4 1.0
OD1 B:ASP583 2.4 63.1 1.0
OD1 B:ASP577 2.4 66.8 1.0
OD1 B:ASP579 2.4 56.6 1.0
OD1 B:ASP575 2.7 70.6 1.0
CG B:ASP583 3.1 66.7 1.0
CG B:ASP579 3.3 61.3 1.0
CG B:ASP577 3.3 72.4 1.0
C B:ILE581 3.4 66.8 1.0
OD2 B:ASP577 3.5 75.1 1.0
OD2 B:ASP583 3.5 67.5 1.0
OD2 B:ASP579 3.6 50.4 1.0
CG B:ASP575 3.7 69.3 1.0
N B:ASP583 3.9 54.5 1.0
C B:PRO582 4.0 51.7 1.0
OG1 B:THR600 4.1 57.4 1.0
CA B:ASP583 4.1 57.6 1.0
CA B:ILE581 4.2 72.0 1.0
N B:ILE581 4.2 71.4 1.0
CB B:ILE581 4.2 69.1 1.0
CB B:ASP583 4.2 66.3 1.0
O B:PRO582 4.2 55.1 1.0
CA B:ASP575 4.3 69.1 1.0
N B:PRO582 4.4 60.8 1.0
CB B:ASP575 4.4 66.2 1.0
N B:ASP577 4.5 69.9 1.0
CA B:PRO582 4.5 57.6 1.0
CB B:ASP579 4.5 65.5 1.0
N B:LYS576 4.5 72.6 1.0
CB B:ASP577 4.6 72.7 1.0
OD2 B:ASP575 4.6 76.6 1.0
N B:ASP579 4.7 70.1 1.0
C B:ASP575 4.7 72.5 1.0
CG2 B:ILE581 4.8 67.4 1.0
CA B:ASP577 5.0 69.1 1.0
CA B:ASP579 5.0 63.0 1.0

Reference:

R.Charoenwattanasatien, S.Pengthaisong, I.Breen, R.Mutoha, 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: ISSN 1554-8929
PubMed: 27115290
DOI: 10.1021/ACSCHEMBIO.6B00192
Page generated: Sun Jul 14 19:14:13 2024

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