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Magnesium in PDB 6gvd: Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose

Enzymatic activity of Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose

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

Protein crystallography data

The structure of Alpha-Galactosidase From Thermotoga Maritima in Complex with Cyclohexene-Based Carbasugar Mimic of Galactose, PDB code: 6gvd 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) 68.59 / 1.22
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.957, 96.135, 97.900, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 18.8

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 (pdb code 6gvd). 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, PDB code: 6gvd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6gvd

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:10.5
occ:1.00
 OD2 A:ASP454 2.0 9.7 1.0
O A:HOH960 2.1 11.5 1.0
O A:HOH1059 2.1 15.7 1.0
O A:HOH1096 2.1 15.4 1.0
O A:HOH743 2.1 11.1 1.0
OD2 A:ASP419 2.1 9.9 1.0
CG A:ASP454 3.1 8.5 1.0
CG A:ASP419 3.1 9.1 1.0
OD1 A:ASP419 3.4 10.5 1.0
OD1 A:ASP454 3.6 9.8 1.0
O A:HOH911 3.9 13.8 1.0
NE2 A:HIS418 4.0 7.4 1.0
O A:HOH829 4.1 40.6 1.0
O A:HOH1206 4.2 39.2 1.0
O A:HOH1175 4.2 36.1 1.0
O A:HOH736 4.2 14.3 1.0
O A:HOH1383 4.3 44.7 1.0
O A:HOH1240 4.3 33.0 1.0
O A:HOH918 4.3 16.1 1.0
CB A:ASP454 4.4 8.1 1.0
O A:GLY483 4.4 11.6 1.0
CB A:ASP419 4.5 8.2 1.0
O A:HOH954 4.7 33.7 1.0
CD2 A:HIS418 4.8 7.3 1.0
O A:HOH803 4.8 36.2 1.0
O A:HOH1265 4.9 52.4 1.0
O A:ASP454 4.9 9.0 1.0
CE1 A:HIS418 4.9 7.9 1.0
C A:GLY482 4.9 12.9 1.0

Magnesium binding site 2 out of 3 in 6gvd

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:16.6
occ:1.00
 O A:HOH1347 2.0 16.6 1.0
O A:HOH843 2.0 15.4 1.0
O A:HOH1041 2.1 16.3 1.0
O A:HOH1152 2.1 18.9 1.0
OE1 A:GLU242 3.8 13.6 1.0
O A:HOH1027 4.1 19.3 1.0
O A:HOH1423 4.1 25.7 0.5
N A:SER239 4.2 10.9 1.0
O A:HOH1225 4.3 17.1 1.0
CA A:PRO238 4.5 10.5 1.0
C A:PRO238 4.5 9.9 1.0
O A:HOH850 4.6 28.8 1.0
CD A:GLU242 4.8 12.1 1.0
CB A:SER239 4.8 12.6 1.0
OE2 A:GLU242 4.9 14.1 1.0
CA A:SER239 4.9 10.0 1.0

Magnesium binding site 3 out of 3 in 6gvd

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:13.8
occ:1.00
 O A:HOH900 2.6 22.4 0.5
O A:ASP425 2.8 7.8 1.0
NE A:ARG383 2.9 7.2 1.0
N A:GLY385 2.9 7.6 1.0
O A:HOH900 2.9 9.1 0.5
N A:ILE384 3.3 7.2 1.0
O A:GLY385 3.4 6.6 1.0
CD A:ARG383 3.4 8.5 1.0
C A:PRO426 3.4 8.3 1.0
CA A:GLY385 3.5 7.4 1.0
N A:ASP427 3.5 7.0 1.0
CA A:PRO426 3.8 7.4 1.0
C A:ASP425 3.8 7.1 1.0
C A:GLY385 3.8 6.4 1.0
C A:ILE384 3.8 6.6 1.0
O A:PRO426 3.9 8.7 1.0
CA A:ARG383 3.9 7.0 1.0
CZ A:ARG383 3.9 6.0 1.0
CB A:ASP427 3.9 7.5 1.0
C A:ARG383 4.0 7.3 1.0
CB A:ARG383 4.0 8.4 1.0
CD1 A:ILE384 4.0 6.7 1.0
CA A:ILE384 4.1 6.2 1.0
NH2 A:ARG383 4.1 6.5 1.0
N A:PRO426 4.2 7.8 1.0
CA A:ASP427 4.2 7.0 1.0
CG A:ARG383 4.3 8.7 1.0
O A:PRO386 4.6 8.0 1.0
CG1 A:ILE384 4.7 7.7 1.0
CG A:ASP427 4.7 6.4 1.0
O A:ILE384 4.9 6.8 1.0
N A:PRO386 4.9 7.2 1.0
O A:ARG383 5.0 8.0 1.0
OD1 A:ASP425 5.0 10.6 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 06:46:12 2025

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