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Calcium in PDB 7dku: Crystal Structure of TXGH116 E441A Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Cellobiose

Enzymatic activity of Crystal Structure of TXGH116 E441A Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Cellobiose

All present enzymatic activity of Crystal Structure of TXGH116 E441A Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Cellobiose:
3.2.1.21;

Protein crystallography data

The structure of Crystal Structure of TXGH116 E441A Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Cellobiose, PDB code: 7dku 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) 88.63 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 177.259, 54.459, 83.154, 90, 90, 90
R / Rfree (%) 15.6 / 18

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of TXGH116 E441A Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Cellobiose (pdb code 7dku). 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 E441A Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Cellobiose, PDB code: 7dku:

Calcium binding site 1 out of 1 in 7dku

Go back to Calcium Binding Sites List in 7dku
Calcium binding site 1 out of 1 in the Crystal Structure of TXGH116 E441A Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Cellobiose


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 E441A Nucleophile Mutant From Thermoanaerobacterium Xylanolyticum with Cellobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1015

b:20.0
occ:1.00
 OD1 A:ASP583 2.2 19.7 1.0
OD1 A:ASP579 2.3 18.9 1.0
O A:ILE581 2.4 15.8 1.0
OD1 A:ASP575 2.4 18.6 1.0
OD1 A:ASP577 2.4 25.6 1.0
O A:HOH1134 2.4 18.6 1.0
O3 A:GOL1012 2.8 34.4 1.0
CG A:ASP583 3.2 20.5 1.0
CG A:ASP579 3.2 18.6 1.0
CG A:ASP575 3.4 19.1 1.0
C A:ILE581 3.5 15.9 1.0
OD2 A:ASP583 3.6 24.0 1.0
CG A:ASP577 3.6 27.0 1.0
OD2 A:ASP579 3.6 18.9 1.0
C3 A:GOL1012 4.0 32.2 1.0
OD2 A:ASP577 4.1 27.8 1.0
CA A:ASP575 4.1 20.1 1.0
N A:ILE581 4.1 16.0 1.0
N A:LYS576 4.2 23.4 1.0
CB A:ASP575 4.2 19.7 1.0
CA A:ILE581 4.2 15.8 1.0
C A:PRO582 4.2 16.0 1.0
N A:ASP583 4.2 16.7 1.0
N A:ASP577 4.3 26.4 1.0
OD2 A:ASP575 4.3 19.2 1.0
CB A:ASP579 4.3 19.3 1.0
N A:ASP579 4.3 21.3 1.0
CB A:ASP583 4.4 18.6 1.0
CB A:ILE581 4.4 15.8 1.0
O A:PRO582 4.4 16.9 1.0
OG1 A:THR600 4.5 15.6 1.0
C A:ASP575 4.5 21.4 1.0
CA A:ASP583 4.5 17.2 1.0
N A:PRO582 4.6 15.9 1.0
CA A:PRO582 4.7 16.2 1.0
CA A:ASP579 4.7 19.8 1.0
CB A:ASP577 4.8 26.6 1.0
N A:ASN578 4.9 25.9 1.0
CA A:ASP577 4.9 26.9 1.0
N A:GLY580 4.9 17.2 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 21:37:03 2025

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