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Magnesium in PDB 6gta: Alpha-Galactosidase Mutant D378A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 3,5 Difluorophenyl Leaving Group

Enzymatic activity of Alpha-Galactosidase Mutant D378A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 3,5 Difluorophenyl Leaving Group

All present enzymatic activity of Alpha-Galactosidase Mutant D378A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 3,5 Difluorophenyl Leaving Group:
3.2.1.22;

Protein crystallography data

The structure of Alpha-Galactosidase Mutant D378A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 3,5 Difluorophenyl Leaving Group, PDB code: 6gta was solved by T.M.Gloster, R.J.Pengelly, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.50 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.890, 97.940, 98.650, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 23.7

Other elements in 6gta:

The structure of Alpha-Galactosidase Mutant D378A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 3,5 Difluorophenyl Leaving Group also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Alpha-Galactosidase Mutant D378A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 3,5 Difluorophenyl Leaving Group (pdb code 6gta). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Alpha-Galactosidase Mutant D378A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 3,5 Difluorophenyl Leaving Group, PDB code: 6gta:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6gta

Go back to Magnesium Binding Sites List in 6gta
Magnesium binding site 1 out of 2 in the Alpha-Galactosidase Mutant D378A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 3,5 Difluorophenyl 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 D378A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 3,5 Difluorophenyl Leaving Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:37.5
occ:1.00
 OD2 A:ASP454 2.0 30.9 1.0
O A:HOH839 2.0 28.5 1.0
O A:HOH756 2.2 33.8 1.0
OD2 A:ASP419 2.2 33.8 1.0
O A:HOH781 2.2 26.8 1.0
O A:HOH819 2.2 29.8 1.0
CG A:ASP454 3.1 32.0 1.0
CG A:ASP419 3.1 36.4 1.0
OD1 A:ASP419 3.3 37.8 1.0
O A:HOH701 3.5 32.7 1.0
OD1 A:ASP454 3.6 34.1 1.0
NE2 A:HIS418 3.6 29.5 1.0
CB A:ASP454 4.3 31.0 1.0
O A:GLY483 4.3 42.4 1.0
CD2 A:HIS418 4.4 27.5 1.0
O A:HOH750 4.5 34.5 1.0
CB A:ASP419 4.5 34.3 1.0
CE1 A:HIS418 4.5 31.6 1.0
O A:ASP454 4.7 27.8 1.0

Magnesium binding site 2 out of 2 in 6gta

Go back to Magnesium Binding Sites List in 6gta
Magnesium binding site 2 out of 2 in the Alpha-Galactosidase Mutant D378A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 3,5 Difluorophenyl Leaving Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Alpha-Galactosidase Mutant D378A From Thermotoga Maritima in Complex with Intact Cyclohexene-Based Carbasugar Mimic of Galactose with 3,5 Difluorophenyl Leaving Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:59.3
occ:1.00
 O A:HOH725 2.2 43.5 1.0
OE2 A:GLU2 2.4 67.3 1.0
O A:HOH719 2.4 38.3 1.0
CD A:GLU2 3.6 58.1 1.0
O A:HOH890 3.9 51.1 1.0
OE1 A:GLU131 4.0 48.5 1.0
CG A:GLU2 4.2 51.2 1.0
O A:SER0 4.4 35.8 1.0
OE1 A:GLU2 4.5 57.0 1.0
CD A:ARG50 4.8 44.4 1.0
O A:HOH736 5.0 33.8 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: Tue Oct 1 01:24:16 2024

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