Calcium in PDB 8i5s: Crystal Structure of TXGH116 D593N Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with 2-Deoxy-2-Fluoroglucoside

Enzymatic activity of Crystal Structure of TXGH116 D593N Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with 2-Deoxy-2-Fluoroglucoside

All present enzymatic activity of Crystal Structure of TXGH116 D593N Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with 2-Deoxy-2-Fluoroglucoside:
3.2.1.21;

Protein crystallography data

The structure of Crystal Structure of TXGH116 D593N Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with 2-Deoxy-2-Fluoroglucoside, PDB code: 8i5s 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) 35.00 / 1.45
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 177.192, 54.458, 83.094, 90, 90, 90
R / Rfree (%) 15.6 / 17.6

Other elements in 8i5s:

The structure of Crystal Structure of TXGH116 D593N Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with 2-Deoxy-2-Fluoroglucoside also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of TXGH116 D593N Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with 2-Deoxy-2-Fluoroglucoside (pdb code 8i5s). 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 TXGH116 D593N Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with 2-Deoxy-2-Fluoroglucoside, PDB code: 8i5s:

Calcium binding site 1 out of 1 in 8i5s

Go back to Calcium Binding Sites List in 8i5s
Calcium binding site 1 out of 1 in the Crystal Structure of TXGH116 D593N Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with 2-Deoxy-2-Fluoroglucoside


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 D593N Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with 2-Deoxy-2-Fluoroglucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1014

b:24.4
occ:1.00
 OD1 A:ASP579 2.3 21.8 1.0
OD1 A:ASP583 2.3 24.6 1.0
O A:ILE581 2.3 19.8 1.0
O A:HOH1217 2.4 22.7 1.0
OD1 A:ASP575 2.4 22.0 1.0
OD1 A:ASP577 2.4 32.8 1.0
CG A:ASP579 3.1 22.9 1.0
CG A:ASP583 3.2 25.7 1.0
O A:HOH1416 3.4 42.2 1.0
CG A:ASP575 3.4 21.6 1.0
C A:ILE581 3.5 19.9 1.0
CG A:ASP577 3.5 34.0 1.0
OD2 A:ASP583 3.6 29.0 1.0
OD2 A:ASP579 3.6 24.3 1.0
N A:ILE581 4.0 19.3 1.0
CA A:ASP575 4.1 22.9 1.0
OD2 A:ASP577 4.1 35.8 1.0
N A:LYS576 4.2 27.9 1.0
CB A:ASP575 4.2 22.4 1.0
CA A:ILE581 4.2 19.3 1.0
N A:ASP583 4.2 20.8 1.0
OD2 A:ASP575 4.2 22.6 1.0
N A:ASP577 4.2 32.5 1.0
CB A:ASP579 4.3 23.2 1.0
C A:PRO582 4.3 20.0 1.0
N A:ASP579 4.3 25.6 1.0
CB A:ILE581 4.3 19.2 1.0
CB A:ASP583 4.4 23.3 1.0
OG1 A:THR600 4.5 20.8 1.0
C A:ASP575 4.5 24.7 1.0
O A:PRO582 4.5 20.3 1.0
CA A:ASP583 4.5 21.4 1.0
N A:PRO582 4.6 19.6 1.0
CA A:PRO582 4.7 19.7 1.0
CA A:ASP579 4.7 23.9 1.0
CB A:ASP577 4.7 33.0 1.0
N A:ASN578 4.8 31.3 1.0
N A:GLY580 4.8 21.0 1.0
CA A:ASP577 4.8 32.8 1.0
C A:ASP579 4.9 23.1 1.0
C A:ASP577 5.0 32.5 1.0

Reference:

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
Page generated: Wed Jul 26 13:39:05 2023

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