Atomistry » Calcium » PDB 7d4p-7dkx » 7dkw
Atomistry »
  Calcium »
    PDB 7d4p-7dkx »
      7dkw »

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: Fri Jul 19 00:06:33 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