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Magnesium in PDB 6gwg: Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile

Enzymatic activity of Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile

All present enzymatic activity of Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile:
3.2.1.22;

Protein crystallography data

The structure of Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile, PDB code: 6gwg 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) 24.36 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.730, 95.870, 97.440, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 21.5

Other elements in 6gwg:

The structure of Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile also contains other interesting chemical elements:

Fluorine (F) 1 atom

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 3 in 6gwg

Go back to Magnesium Binding Sites List in 6gwg
Magnesium binding site 1 out of 3 in the Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg610

b:47.8
occ:1.00
 N A:ASN341 3.6 30.4 1.0
CA A:LYS340 4.0 30.4 1.0
CB A:LYS340 4.3 30.6 1.0
O A:HOH1099 4.3 50.1 1.0
C A:LYS340 4.4 33.8 1.0
CB A:ASN341 4.5 45.6 1.0
CA A:ASN341 4.6 36.6 1.0
CG A:LYS340 4.7 34.1 1.0
O A:LYS339 4.9 30.2 1.0

Magnesium binding site 2 out of 3 in 6gwg

Go back to Magnesium Binding Sites List in 6gwg
Magnesium binding site 2 out of 3 in the Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg611

b:53.7
occ:1.00
 O A:HOH997 2.3 41.0 1.0
O A:HOH891 2.3 40.7 1.0
OE2 A:GLU2 2.7 54.8 1.0
CD A:GLU2 3.9 55.0 1.0
O A:HOH1018 4.3 39.8 1.0
O A:HOH786 4.3 39.9 1.0
O A:SER0 4.3 37.0 1.0
CG A:GLU2 4.4 44.1 1.0
OE2 A:GLU131 4.5 50.4 1.0
O A:HOH765 4.7 34.0 1.0
OE1 A:GLU2 4.9 52.6 1.0

Magnesium binding site 3 out of 3 in 6gwg

Go back to Magnesium Binding Sites List in 6gwg
Magnesium binding site 3 out of 3 in the Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose Covalently Linked to the Nucleophile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg612

b:24.6
occ:1.00
 OD2 A:ASP454 2.0 21.0 1.0
O A:HOH871 2.1 20.1 1.0
O A:HOH991 2.1 24.5 1.0
O A:HOH855 2.1 22.2 1.0
OD2 A:ASP419 2.1 20.3 1.0
O A:HOH781 2.2 20.8 1.0
CG A:ASP454 3.1 21.1 1.0
CG A:ASP419 3.1 21.9 1.0
OD1 A:ASP419 3.4 24.2 1.0
OD1 A:ASP454 3.5 22.2 1.0
O A:HOH828 3.8 24.8 1.0
NE2 A:HIS418 3.9 18.7 1.0
O A:HOH1041 4.3 45.8 1.0
O A:HOH771 4.3 26.9 1.0
CB A:ASP454 4.3 23.0 1.0
O A:GLY483 4.4 22.4 1.0
O A:HOH841 4.4 34.5 1.0
O A:HOH1047 4.5 38.6 1.0
CB A:ASP419 4.5 21.6 1.0
CD2 A:HIS418 4.8 17.9 1.0
O A:HOH915 4.8 30.3 1.0
O A:ASP454 4.8 20.5 1.0
CE1 A:HIS418 4.8 20.4 1.0
O A:HOH732 4.9 41.1 1.0
C A:GLY482 5.0 22.2 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 01:27:06 2024

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