Calcium in PDB 8i5q: Crystal Structure of TXGH116 D593A Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with Laminaribiose

All present enzymatic activity of Crystal Structure of TXGH116 D593A Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with Laminaribiose:
3.2.1.21;

The structure of Crystal Structure of TXGH116 D593A Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with Laminaribiose, PDB code: 8i5q 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)	40.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.898, 100.625, 173.556, 90, 90, 90
R / Rfree (%)	19.1 / 24.1

The binding sites of Calcium atom in the Crystal Structure of TXGH116 D593A Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with Laminaribiose (pdb code 8i5q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of TXGH116 D593A Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with Laminaribiose, PDB code: 8i5q:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of TXGH116 D593A Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with Laminaribiose


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 D593A Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with Laminaribiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:43.6 occ:1.00 O A:ILE581 2.3 35.9 1.0 OD1 A:ASP579 2.3 37.2 1.0 O A:HOH1150 2.4 39.0 1.0 OD1 A:ASP575 2.5 39.8 1.0 OD1 A:ASP577 2.6 51.9 1.0 OD1 A:ASP583 2.6 42.0 1.0 CG A:ASP583 3.2 43.8 1.0 CG A:ASP579 3.3 40.2 1.0 CG A:ASP577 3.4 54.1 1.0 OD2 A:ASP583 3.4 50.6 1.0 C A:ILE581 3.5 35.8 1.0 CG A:ASP575 3.5 41.5 1.0 OD2 A:ASP577 3.6 57.5 1.0 OD2 A:ASP579 3.7 40.4 1.0 N A:ASP583 4.0 39.2 1.0 CA A:ASP575 4.0 42.7 1.0 N A:ILE581 4.1 35.3 1.0 C A:PRO582 4.1 39.5 1.0 CB A:ASP575 4.2 41.3 1.0 CA A:ILE581 4.2 35.0 1.0 N A:ASP577 4.3 54.7 1.0 N A:LYS576 4.3 49.4 1.0 N A:ASP579 4.3 41.1 1.0 CB A:ASP583 4.4 41.7 1.0 CB A:ILE581 4.4 35.3 1.0 CA A:ASP583 4.4 39.1 1.0 OD2 A:ASP575 4.4 41.6 1.0 O A:PRO582 4.5 36.3 1.0 N A:PRO582 4.5 38.0 1.0 C A:ASP575 4.5 45.4 1.0 OG1 A:THR600 4.5 33.4 1.0 CB A:ASP579 4.5 39.9 1.0 CA A:PRO582 4.5 38.4 1.0 CB A:ASP577 4.7 54.1 1.0 N A:ASN578 4.7 49.6 1.0 CA A:ASP579 4.8 39.2 1.0 CA A:ASP577 4.8 53.5 1.0 N A:GLY580 4.9 34.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of TXGH116 D593A Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with Laminaribiose


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 D593A Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with Laminaribiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:75.7 occ:1.00 O B:ILE581 2.4 64.8 1.0 OD1 B:ASP579 2.4 74.0 1.0 OD1 B:ASP575 2.5 64.7 1.0 OD1 B:ASP583 2.5 60.0 1.0 CG B:ASP583 3.0 60.0 1.0 OD1 B:ASP577 3.0 86.2 1.0 OD2 B:ASP583 3.0 61.9 1.0 CG B:ASP579 3.2 75.5 1.0 OD2 B:ASP579 3.5 74.7 1.0 C B:ILE581 3.6 64.7 1.0 CG B:ASP575 3.6 70.9 1.0 CG B:ASP577 3.9 88.8 1.0 N B:ASP583 3.9 56.0 1.0 OG1 B:THR600 4.0 65.0 1.0 CB B:ASP583 4.1 58.5 1.0 C B:PRO582 4.1 57.0 1.0 OD2 B:ASP577 4.2 83.5 1.0 CA B:ASP583 4.2 56.6 1.0 CA B:ILE581 4.3 66.3 1.0 CB B:ILE581 4.3 67.6 1.0 N B:ILE581 4.3 63.5 1.0 N B:ASP579 4.4 82.9 1.0 CA B:ASP575 4.4 74.4 1.0 OD2 B:ASP575 4.4 69.6 1.0 CB B:ASP575 4.4 71.2 1.0 CB B:ASP579 4.5 75.6 1.0 N B:PRO582 4.5 62.3 1.0 O B:PRO582 4.6 58.3 1.0 CA B:PRO582 4.6 60.0 1.0 N B:LYS576 4.7 81.9 1.0 N B:ASN578 4.8 84.8 1.0 C B:ASP575 4.9 76.1 1.0 N B:ASP577 4.9 90.7 1.0 CA B:ASP579 4.9 79.8 1.0

S.Pengthaisong, B.Piniello, G.J.Davies, C.Rovira, J.R.K.Cairns. Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation Acs Catalysis 5850 2023.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.3C00620