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Magnesium in PDB 6gwf: Alpha-Galactosidase Mutant D387A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 2,4- Dinitro Leaving Group

Enzymatic activity of Alpha-Galactosidase Mutant D387A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 2,4- Dinitro Leaving Group

All present enzymatic activity of Alpha-Galactosidase Mutant D387A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 2,4- Dinitro Leaving Group:
3.2.1.22;

Protein crystallography data

The structure of Alpha-Galactosidase Mutant D387A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 2,4- Dinitro Leaving Group, PDB code: 6gwf was solved by T.M.Gloster, V.Oehler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.49 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.389, 95.789, 97.453, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20.3

Other elements in 6gwf:

The structure of Alpha-Galactosidase Mutant D387A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 2,4- Dinitro Leaving Group also contains other interesting chemical elements:

Fluorine (F) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Alpha-Galactosidase Mutant D387A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 2,4- Dinitro Leaving Group (pdb code 6gwf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Alpha-Galactosidase Mutant D387A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 2,4- Dinitro Leaving Group, PDB code: 6gwf:

Magnesium binding site 1 out of 1 in 6gwf

Go back to Magnesium Binding Sites List in 6gwf
Magnesium binding site 1 out of 1 in the Alpha-Galactosidase Mutant D387A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 2,4- Dinitro Leaving Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Alpha-Galactosidase Mutant D387A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 2,4- Dinitro Leaving Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:18.1
occ:1.00
 O A:HOH933 2.0 22.7 1.0
OD2 A:ASP454 2.1 14.4 1.0
O A:HOH960 2.1 17.6 1.0
O A:HOH971 2.1 19.9 1.0
O A:HOH736 2.1 15.2 1.0
OD2 A:ASP419 2.1 17.6 1.0
CG A:ASP419 3.1 17.3 1.0
CG A:ASP454 3.1 16.3 1.0
OD1 A:ASP419 3.4 16.6 1.0
OD1 A:ASP454 3.6 16.3 1.0
O A:HOH857 3.9 18.6 1.0
NE2 A:HIS418 3.9 14.1 1.0
O A:HOH936 4.2 45.5 1.0
O A:HOH930 4.2 45.3 1.0
O A:HOH739 4.3 23.8 1.0
O A:HOH914 4.3 21.8 1.0
CB A:ASP454 4.4 16.1 1.0
O A:GLY483 4.4 17.4 1.0
CB A:ASP419 4.5 16.2 1.0
O A:HOH1125 4.5 44.4 1.0
O A:HOH1086 4.5 31.1 1.0
O A:HOH859 4.7 39.5 1.0
CD2 A:HIS418 4.8 13.6 1.0
CE1 A:HIS418 4.8 14.8 1.0
O A:ASP454 4.9 16.3 1.0
O A:HOH1157 4.9 47.4 1.0
C A:GLY482 4.9 18.2 1.0
O A:GLY482 5.0 19.1 1.0
CA A:GLY482 5.0 19.5 1.0

Reference:

W.Ren, R.Pengelly, M.Farren-Dai, S.Shamsi Kazem Abadi, V.Oehler, O.Akintola, J.Draper, M.Meanwell, S.Chakladar, K.Swiderek, V.Moliner, R.Britton, T.M.Gloster, A.J.Bennet. Revealing the Mechanism For Covalent Inhibition of Glycoside Hydrolases By Carbasugars at An Atomic Level. Nat Commun V. 9 3243 2018.
ISSN: ESSN 2041-1723
PubMed: 30104598
DOI: 10.1038/S41467-018-05702-7
Page generated: Wed Aug 13 06:46:50 2025

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