Calcium in PDB 8i5p: Crystal Structure of TXGH116 D593A Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with Cellobiose

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

The structure of Crystal Structure of TXGH116 D593A Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with Cellobiose, PDB code: 8i5p 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 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.072, 100.504, 173.783, 90, 90, 90
R / Rfree (%)	19 / 24.1

The binding sites of Calcium atom in the Crystal Structure of TXGH116 D593A Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with Cellobiose (pdb code 8i5p). 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 Cellobiose, PDB code: 8i5p:
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 Cellobiose


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 Cellobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:50.3 occ:1.00 OD1 A:ASP579 2.2 43.9 1.0 O A:ILE581 2.3 44.6 1.0 OD1 A:ASP575 2.5 41.5 1.0 OD1 A:ASP583 2.6 47.4 1.0 OD1 A:ASP577 2.7 61.4 1.0 CG A:ASP579 3.1 46.5 1.0 CG A:ASP583 3.2 50.2 1.0 C A:ILE581 3.4 43.8 1.0 OD2 A:ASP583 3.4 54.2 1.0 OD2 A:ASP579 3.5 48.4 1.0 CG A:ASP577 3.5 61.9 1.0 CG A:ASP575 3.5 44.2 1.0 OD2 A:ASP577 3.8 66.3 1.0 N A:ILE581 4.0 43.1 1.0 N A:ASP583 4.0 46.7 1.0 C A:PRO582 4.1 46.8 1.0 CA A:ILE581 4.1 42.3 1.0 CA A:ASP575 4.1 47.1 1.0 CB A:ILE581 4.2 41.9 1.0 CB A:ASP575 4.3 44.3 1.0 N A:ASP579 4.3 48.4 1.0 O A:PRO582 4.3 45.6 1.0 CB A:ASP583 4.3 49.2 1.0 OG1 A:THR600 4.4 38.1 1.0 CA A:ASP583 4.4 46.7 1.0 OD2 A:ASP575 4.4 44.4 1.0 CB A:ASP579 4.4 46.1 1.0 N A:LYS576 4.4 54.1 1.0 N A:PRO582 4.4 45.6 1.0 N A:ASP577 4.4 59.6 1.0 CA A:PRO582 4.6 46.4 1.0 C A:ASP575 4.6 48.6 1.0 CA A:ASP579 4.7 46.1 1.0 N A:ASN578 4.8 56.0 1.0 CB A:ASP577 4.8 61.5 1.0 N A:GLY580 4.9 42.6 1.0 CA A:ASP577 5.0 59.3 1.0 CG2 A:ILE581 5.0 41.7 1.0 C A:ASP579 5.0 44.5 1.0

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


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 Cellobiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:75.7 occ:1.00 OD1 B:ASP583 2.3 70.3 1.0 O B:ILE581 2.3 67.9 1.0 OD1 B:ASP579 2.4 82.8 1.0 OD1 B:ASP575 2.5 75.0 1.0 OD1 B:ASP577 2.8 101.1 1.0 CG B:ASP583 3.1 68.6 1.0 CG B:ASP579 3.2 82.8 1.0 OD2 B:ASP579 3.5 83.0 1.0 C B:ILE581 3.5 69.8 1.0 OD2 B:ASP583 3.5 71.3 1.0 CG B:ASP575 3.6 78.8 1.0 CG B:ASP577 3.6 98.7 1.0 OD2 B:ASP577 3.9 98.3 1.0 N B:ASP583 4.0 63.2 1.0 N B:ILE581 4.1 68.7 1.0 CA B:ASP575 4.2 81.0 1.0 C B:PRO582 4.2 64.4 1.0 CA B:ILE581 4.2 70.6 1.0 CB B:ASP583 4.2 66.5 1.0 N B:ASP579 4.3 88.0 1.0 N B:LYS576 4.3 88.4 1.0 CA B:ASP583 4.3 63.6 1.0 CB B:ILE581 4.3 71.1 1.0 CB B:ASP575 4.3 79.3 1.0 OG1 B:THR600 4.3 56.9 1.0 N B:ASP577 4.3 96.4 1.0 CB B:ASP579 4.4 83.5 1.0 OD2 B:ASP575 4.5 81.5 1.0 N B:PRO582 4.5 68.2 1.0 C B:ASP575 4.5 82.6 1.0 O B:PRO582 4.6 68.3 1.0 N B:ASN578 4.6 91.0 1.0 CA B:PRO582 4.6 66.3 1.0 CA B:ASP579 4.8 85.3 1.0 CB B:ASP577 4.8 97.7 1.0 CA B:ASP577 4.9 95.7 1.0 N B:GLY580 5.0 78.4 1.0 C B:ASP577 5.0 93.5 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