Fluorine 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:

Calcium (Ca) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of TXGH116 D593N Acid/Base Mutant From Thermoanaerobacterium Xylanolyticum with 2-Deoxy-2-Fluoroglucoside, PDB code: 8i5s:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8i5s

Go back to Fluorine Binding Sites List in 8i5s
Fluorine binding site 1 out of 3 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 Fluorine with other atoms in the F 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:F1000

b:12.9
occ:1.00
 F2 A:G2F1000 0.0 12.9 1.0
C2 A:G2F1000 1.4 12.3 1.0
C3 A:G2F1000 2.4 12.2 1.0
C1 A:G2F1000 2.4 12.6 1.0
O3 A:G2F1000 2.7 12.7 1.0
OE1 A:GLU441 2.8 13.1 1.0
OE2 A:GLU441 2.8 12.4 1.0
CE1 A:HIS507 2.9 11.7 1.0
NE2 A:HIS507 3.0 12.1 1.0
CD A:GLU441 3.0 11.9 1.0
O5 A:G2F1000 3.6 12.6 1.0
CG2 A:THR450 3.6 11.3 1.0
C4 A:G2F1000 3.7 11.8 1.0
CD1 A:TYR523 4.0 17.4 1.0
CE1 A:TYR523 4.1 18.3 1.0
C5 A:G2F1000 4.2 12.2 1.0
CG A:GLU441 4.2 11.3 1.0
CB A:THR450 4.2 11.4 1.0
ND1 A:HIS507 4.2 12.2 1.0
CD2 A:TYR447 4.3 15.2 1.0
CD2 A:HIS507 4.3 12.4 1.0
O3 A:GOL1002 4.7 42.0 1.0
CG A:TYR523 4.8 16.2 1.0
O4 A:G2F1000 4.8 11.8 1.0
OG1 A:THR450 4.8 12.0 1.0
CE2 A:TYR447 4.9 16.9 1.0
OD1 A:ASP452 4.9 12.9 1.0
CZ A:TYR523 4.9 18.3 1.0
OD2 A:ASP452 4.9 12.5 1.0
CB A:GLU441 4.9 11.1 1.0
O1 A:GOL1003 4.9 37.0 1.0
CG A:HIS507 5.0 12.1 1.0

Fluorine binding site 2 out of 3 in 8i5s

Go back to Fluorine Binding Sites List in 8i5s
Fluorine binding site 2 out of 3 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 Fluorine with other atoms in the F binding site number 2 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:F1016

b:33.3
occ:0.80
 F A:NFG1016 0.0 33.3 0.8
C2 A:NFG1016 1.4 32.6 0.8
C1 A:NFG1016 2.4 31.1 0.8
C3 A:NFG1016 2.4 33.8 0.8
O1 A:NFG1016 2.9 28.4 0.8
O3 A:NFG1016 2.9 36.5 0.8
O11 A:NFG1016 3.1 35.3 0.8
O5 A:NFG1016 3.6 31.6 0.8
C4 A:NFG1016 3.7 33.6 0.8
O A:HOH1318 3.8 28.2 1.0
C11 A:NFG1016 3.9 26.0 0.8
C5 A:NFG1016 4.1 32.2 0.8
N1 A:NFG1016 4.2 29.6 0.8
C12 A:NFG1016 4.5 26.5 0.8
O4 A:NFG1016 4.8 35.9 0.8
CG2 A:VAL482 4.8 20.9 1.0
C16 A:NFG1016 4.9 25.6 0.8

Fluorine binding site 3 out of 3 in 8i5s

Go back to Fluorine Binding Sites List in 8i5s
Fluorine binding site 3 out of 3 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 Fluorine with other atoms in the F binding site number 3 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:F1017

b:26.4
occ:0.80
 F A:NFG1017 0.0 26.4 0.8
C2 A:NFG1017 1.4 24.9 0.8
C1 A:NFG1017 2.3 26.1 0.8
C3 A:NFG1017 2.3 23.3 0.8
O1 A:NFG1017 2.8 29.4 0.8
O3 A:NFG1017 2.9 22.2 0.8
CG A:ASP291 2.9 14.5 1.0
CB A:ASP291 3.0 14.2 1.0
OD1 A:ASP291 3.2 14.4 1.0
O A:HOH1142 3.3 15.2 1.0
N A:ASP291 3.3 13.6 1.0
OD2 A:ASP291 3.4 14.4 1.0
O5 A:NFG1017 3.5 24.2 0.8
CA A:ASP291 3.7 14.1 1.0
C4 A:NFG1017 3.7 22.3 0.8
C11 A:NFG1017 3.7 36.9 0.8
C5 A:NFG1017 4.0 23.0 0.8
OD1 A:ASP288 4.2 14.7 1.0
O A:HOH1151 4.2 25.6 1.0
OG A:SER290 4.3 15.2 1.0
O A:HOH1116 4.3 31.6 1.0
N A:SER290 4.4 13.2 1.0
C12 A:NFG1017 4.4 40.9 0.8
N1 A:NFG1017 4.4 42.6 0.8
C A:SER290 4.4 13.4 1.0
C16 A:NFG1017 4.5 39.0 0.8
O4 A:NFG1017 4.7 19.7 0.8
O11 A:NFG1017 4.7 42.5 0.8
O12 A:NFG1017 4.7 44.9 0.8
N A:GLY289 4.8 12.8 1.0
CA A:SER290 4.9 13.8 1.0
C A:GLY289 4.9 12.4 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: Thu Jul 27 14:41:51 2023

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