Calcium in PDB 8jbo: Crystal Structure of TXGH116 From Thermoanaerobacterium Xylanolyticum with Isofagomine

The structure of Crystal Structure of TXGH116 From Thermoanaerobacterium Xylanolyticum with Isofagomine, PDB code: 8jbo was solved by S.Pengthaisong, J.R.Ketudat Cairns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.791, 164.399, 179.614, 90, 90, 90
R / Rfree (%)	15.5 / 19.3

The binding sites of Calcium atom in the Crystal Structure of TXGH116 From Thermoanaerobacterium Xylanolyticum with Isofagomine (pdb code 8jbo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of TXGH116 From Thermoanaerobacterium Xylanolyticum with Isofagomine, PDB code: 8jbo:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of TXGH116 From Thermoanaerobacterium Xylanolyticum with Isofagomine


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 From Thermoanaerobacterium Xylanolyticum with Isofagomine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:26.1 occ:1.00 OD1 A:ASP579 2.1 24.0 1.0 OD1 A:ASP583 2.3 30.2 1.0 O A:ILE581 2.3 26.0 1.0 OD1 A:ASP575 2.4 31.2 1.0 O A:HOH1296 2.4 24.1 1.0 OD1 A:ASP577 2.5 37.9 1.0 CG A:ASP579 3.1 27.6 1.0 CG A:ASP583 3.2 31.9 1.0 CG A:ASP575 3.4 30.5 1.0 C A:ILE581 3.5 25.1 1.0 CG A:ASP577 3.5 42.4 1.0 OD2 A:ASP579 3.6 25.7 1.0 OD2 A:ASP583 3.7 34.5 1.0 OD2 A:ASP577 4.0 43.4 1.0 CA A:ASP575 4.1 31.7 1.0 N A:ILE581 4.1 22.5 1.0 CB A:ASP575 4.2 32.0 1.0 C A:PRO582 4.2 23.4 1.0 CA A:ILE581 4.2 24.2 1.0 N A:ASP579 4.2 30.6 1.0 N A:LYS576 4.2 37.2 1.0 N A:ASP583 4.2 25.1 1.0 OD2 A:ASP575 4.2 31.1 1.0 N A:ASP577 4.3 42.2 1.0 CB A:ASP579 4.3 27.8 1.0 CB A:ILE581 4.4 24.7 1.0 CB A:ASP583 4.4 28.2 1.0 O A:PRO582 4.4 22.4 1.0 CA A:ASP583 4.5 25.2 1.0 C A:ASP575 4.5 34.3 1.0 N A:PRO582 4.5 25.2 1.0 OG1 A:THR600 4.6 23.5 1.0 CA A:ASP579 4.6 27.2 1.0 CA A:PRO582 4.7 24.1 1.0 N A:ASN578 4.7 37.5 1.0 CB A:ASP577 4.7 40.0 1.0 N A:GLY580 4.8 24.5 1.0 CA A:ASP577 4.9 39.6 1.0 C A:ASP579 4.9 27.1 1.0 C A:ASP577 4.9 38.6 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of TXGH116 From Thermoanaerobacterium Xylanolyticum with Isofagomine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of TXGH116 From Thermoanaerobacterium Xylanolyticum with Isofagomine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca914 b:25.8 occ:1.00 O A:HOH1393 3.0 17.5 1.0 O B:HOH1364 3.1 15.7 1.0 N A:ASP401 3.3 14.4 1.0 N B:ASP401 3.3 14.1 1.0 CB A:ASP401 3.8 16.7 1.0 CA B:PRO400 3.9 14.7 1.0 CA A:PRO400 3.9 15.8 1.0 CG A:ASP401 3.9 18.8 1.0 CB B:ASP401 3.9 15.4 1.0 CG B:ASP401 3.9 17.5 1.0 CB B:PRO400 4.1 14.9 1.0 CB A:PRO400 4.1 15.3 1.0 C A:PRO400 4.1 14.7 1.0 C B:PRO400 4.1 13.7 1.0 OD2 A:ASP401 4.1 20.2 1.0 CA A:ASP401 4.2 15.5 1.0 OD2 B:ASP401 4.2 20.3 1.0 CA B:ASP401 4.2 14.2 1.0 OD1 B:ASP401 4.3 19.1 1.0 OD1 A:ASP401 4.4 18.6 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of TXGH116 From Thermoanaerobacterium Xylanolyticum with Isofagomine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of TXGH116 From Thermoanaerobacterium Xylanolyticum with Isofagomine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca913 b:32.8 occ:1.00 OD1 B:ASP579 2.2 30.8 1.0 O B:ILE581 2.3 30.7 1.0 OD1 B:ASP583 2.3 36.1 1.0 OD1 B:ASP575 2.4 32.3 1.0 O B:HOH1211 2.4 32.0 1.0 OD1 B:ASP577 2.5 44.5 1.0 CG B:ASP579 3.1 32.1 1.0 CG B:ASP583 3.3 40.7 1.0 CG B:ASP575 3.4 33.1 1.0 C B:ILE581 3.5 30.8 1.0 CG B:ASP577 3.5 46.1 1.0 OD2 B:ASP579 3.6 30.5 1.0 OD2 B:ASP583 3.7 48.8 1.0 OD2 B:ASP577 3.9 49.1 1.0 N B:ILE581 4.0 29.8 1.0 CA B:ASP575 4.0 36.1 1.0 CB B:ASP575 4.1 33.8 1.0 N B:ASP579 4.1 40.1 1.0 CA B:ILE581 4.2 31.1 1.0 N B:LYS576 4.2 45.7 1.0 C B:PRO582 4.2 30.7 1.0 CB B:ASP579 4.3 35.4 1.0 OD2 B:ASP575 4.3 32.2 1.0 N B:ASP577 4.3 47.7 1.0 N B:ASP583 4.3 31.3 1.0 CB B:ILE581 4.3 30.7 1.0 O B:PRO582 4.4 31.3 1.0 C B:ASP575 4.4 39.3 1.0 CB B:ASP583 4.5 36.2 1.0 N B:PRO582 4.5 30.6 1.0 OG1 B:THR600 4.6 32.0 1.0 CA B:ASP579 4.6 36.6 1.0 CA B:ASP583 4.6 32.6 1.0 CA B:PRO582 4.7 30.4 1.0 N B:ASN578 4.7 44.7 1.0 N B:GLY580 4.8 30.9 1.0 CB B:ASP577 4.8 45.1 1.0 C B:ASP579 4.8 33.6 1.0 CA B:ASP577 4.9 44.4 1.0 C B:ASP577 4.9 46.2 1.0

W.Meelua, N.Thinkumrob, P.Saparpakorn, S.Pengthaisong, S.Hannongbua, J.R.Ketudat Cairns, J.Jitonnom. Structural Basis For Inhibition of A GH116 Beta-Glucosidase and Its Missense Mutants By GBA2 Inhibitors: Crystallographic and Quantum Chemical Study. Chem.Biol.Interact. V. 384 10717 2023.
ISSN: ISSN 0009-2797
PubMed: 37726065
DOI: 10.1016/J.CBI.2023.110717