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Calcium in PDB 7dkw: Crystal Structure of TXGH116 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside.

Enzymatic activity of Crystal Structure of TXGH116 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside.

All present enzymatic activity of Crystal Structure of TXGH116 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside.:
3.2.1.21;

Protein crystallography data

The structure of Crystal Structure of TXGH116 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside., PDB code: 7dkw 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 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 179.214, 54.602, 164.55, 90, 90, 90
R / Rfree (%) 15.8 / 18.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of TXGH116 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside. (pdb code 7dkw). 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 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside., PDB code: 7dkw:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7dkw

Go back to Calcium Binding Sites List in 7dkw
Calcium binding site 1 out of 2 in the Crystal Structure of TXGH116 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-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 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:36.6
occ:1.00
OD1 A:ASP583 2.3 32.9 1.0
OD1 A:ASP579 2.3 41.1 1.0
O A:ILE581 2.4 33.0 1.0
OD1 A:ASP577 2.4 46.1 1.0
O A:HOH1132 2.5 34.3 1.0
OD1 A:ASP575 2.5 35.3 1.0
O A:HOH1414 2.8 50.7 1.0
CG A:ASP579 3.1 40.5 1.0
CG A:ASP583 3.3 34.4 1.0
CG A:ASP575 3.5 34.9 1.0
OD2 A:ASP579 3.6 38.3 1.0
C A:ILE581 3.6 33.6 1.0
CG A:ASP577 3.6 48.8 1.0
OD2 A:ASP583 3.8 39.6 1.0
CA A:ASP575 4.2 38.2 1.0
N A:LYS576 4.2 45.3 1.0
N A:ILE581 4.2 33.6 1.0
OD2 A:ASP577 4.2 52.5 1.0
CB A:ASP575 4.2 37.0 1.0
OD2 A:ASP575 4.2 33.5 1.0
N A:ASP577 4.3 46.9 1.0
CB A:ASP579 4.3 41.7 1.0
CA A:ILE581 4.3 33.6 1.0
N A:ASP579 4.3 45.2 1.0
C A:PRO582 4.3 31.9 1.0
N A:ASP583 4.3 30.8 1.0
OG1 A:THR600 4.4 31.4 1.0
CB A:ILE581 4.4 32.9 1.0
O A:PRO582 4.5 33.1 1.0
CB A:ASP583 4.5 33.0 1.0
C A:ASP575 4.6 41.9 1.0
CA A:ASP583 4.6 31.6 1.0
N A:PRO582 4.6 32.4 1.0
CA A:ASP579 4.7 41.8 1.0
N A:ASN578 4.8 44.9 1.0
CB A:ASP577 4.8 48.0 1.0
CA A:PRO582 4.8 32.1 1.0
CA A:ASP577 4.9 46.7 1.0
C A:ASP577 4.9 46.3 1.0
N A:GLY580 4.9 35.9 1.0

Calcium binding site 2 out of 2 in 7dkw

Go back to Calcium Binding Sites List in 7dkw
Calcium binding site 2 out of 2 in the Crystal Structure of TXGH116 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside.


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 E441G Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Autocondensation Products From Alpha-Fluoroglucoside. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca905

b:27.6
occ:1.00
OD1 B:ASP579 2.2 24.1 1.0
OD1 B:ASP583 2.3 26.4 1.0
O B:ILE581 2.3 25.1 1.0
OD1 B:ASP575 2.4 27.2 1.0
OD1 B:ASP577 2.4 34.3 1.0
O B:HOH1032 2.5 23.0 1.0
CG B:ASP579 3.2 25.9 1.0
CG B:ASP583 3.2 27.6 1.0
O B:HOH1225 3.3 42.2 1.0
CG B:ASP575 3.4 26.2 1.0
C B:ILE581 3.5 23.1 1.0
CG B:ASP577 3.6 38.7 1.0
OD2 B:ASP579 3.6 27.1 1.0
OD2 B:ASP583 3.7 31.9 1.0
N B:ILE581 4.1 23.4 1.0
CA B:ASP575 4.1 27.8 1.0
OD2 B:ASP577 4.1 41.4 1.0
CA B:ILE581 4.2 23.1 1.0
CB B:ASP575 4.2 26.9 1.0
N B:LYS576 4.2 33.0 1.0
N B:ASP577 4.2 35.6 1.0
OD2 B:ASP575 4.3 25.9 1.0
C B:PRO582 4.3 22.7 1.0
N B:ASP579 4.3 28.5 1.0
N B:ASP583 4.3 22.7 1.0
CB B:ASP579 4.3 26.8 1.0
CB B:ILE581 4.3 22.1 1.0
CB B:ASP583 4.4 26.1 1.0
O B:PRO582 4.5 24.5 1.0
OG1 B:THR600 4.5 22.9 1.0
N B:PRO582 4.5 23.1 1.0
CA B:ASP583 4.5 24.0 1.0
C B:ASP575 4.5 30.6 1.0
CA B:PRO582 4.7 22.8 1.0
CA B:ASP579 4.7 27.2 1.0
CB B:ASP577 4.8 36.2 1.0
N B:ASN578 4.8 32.8 1.0
N B:GLY580 4.8 24.7 1.0
CA B:ASP577 4.9 35.7 1.0
C B:ASP579 4.9 26.0 1.0
C B:ASP577 5.0 35.3 1.0

Reference:

S.Pengthaisong, Y.Hua, J.R.Ketudat Cairns. Structural Basis For Transglycosylation in Glycoside Hydrolase Family GH116 Glycosynthases. Arch.Biochem.Biophys. V. 706 08924 2021.
ISSN: ESSN 1096-0384
PubMed: 34019851
DOI: 10.1016/J.ABB.2021.108924
Page generated: Wed Jul 9 21:37:20 2025

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