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: Fri Aug 2 20:33:48 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy