Magnesium in PDB 2yfn: Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask

All present enzymatic activity of Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask:
3.2.1.22;

The structure of Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, PDB code: 2yfn was solved by G.Sulzenbacher, L.Bruel, M.Tison-Cervera, A.Pujol, C.Nicoletti, J.Perrier, A.Galinier, D.Ropartz, M.Fons, F.Pompeo, T.Giardina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.19 / 1.45
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	105.058, 111.650, 154.886, 90.00, 90.00, 90.00
R / Rfree (%)	13.007 / 14.957

The binding sites of Magnesium atom in the Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask (pdb code 2yfn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, PDB code: 2yfn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1725 b:11.9 occ:1.00 O A:PHE280 2.2 8.8 1.0 O A:GLU277 2.4 10.0 1.0 O A:GLU176 2.4 8.8 1.0 O A:HOH2513 2.5 11.1 0.6 O A:HOH2516 2.6 29.4 1.0 OE1 A:GLU176 2.9 12.9 1.0 C A:GLU176 3.3 8.4 1.0 O A:HOH2531 3.4 17.6 1.0 C A:PHE280 3.4 9.0 1.0 C A:GLU277 3.5 10.2 1.0 CA A:GLU176 3.5 9.1 1.0 CG A:GLU277 3.5 12.9 0.4 CB A:GLU176 3.8 9.1 1.0 CA A:GLU277 3.9 10.0 0.6 CA A:GLU277 3.9 10.2 0.4 OG A:SER281 4.0 9.8 0.6 CD A:GLU176 4.0 13.0 1.0 CB A:GLU277 4.1 11.5 0.6 CA A:PHE280 4.2 8.9 1.0 N A:PHE280 4.2 8.8 1.0 CB A:PHE280 4.3 8.7 1.0 CB A:GLU277 4.3 11.1 0.4 O A:HOH2518 4.3 8.5 0.6 N A:SER281 4.4 9.2 1.0 OE2 A:GLU277 4.5 18.9 0.4 CG A:GLU176 4.5 11.3 1.0 CD A:GLU277 4.6 15.0 0.4 CD2 A:PHE280 4.6 10.5 1.0 N A:LYS177 4.6 7.8 1.0 CA A:SER281 4.6 9.7 0.4 CA A:SER281 4.6 9.4 0.6 N A:GLU278 4.6 10.0 1.0 O A:HOH2207 4.7 25.7 1.0 CG A:GLU277 4.8 12.1 0.6 N A:GLU176 4.8 8.4 1.0 CB A:SER281 4.9 10.0 0.4 O A:ILE175 4.9 9.1 1.0 CG A:PHE280 4.9 9.6 1.0 CB A:SER281 4.9 9.7 0.6

Magnesium binding site 2 out of 2 in the Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1726 b:15.2 occ:0.50 O A:HOH2511 2.0 10.7 0.6 OE2 A:GLU277 2.1 19.1 0.6 O A:HOH2177 2.1 29.5 1.0 O A:HOH2527 2.1 21.2 1.0 O A:HOH2519 2.1 27.4 1.0 O A:HOH2521 2.4 21.4 0.5 CD A:GLU277 3.0 17.1 0.6 OE1 A:GLU277 3.2 18.3 0.6 O A:HOH2522 3.3 12.1 0.4 O A:HOH2176 3.9 37.6 1.0 OE2 A:GLU278 3.9 20.6 0.4 O A:HOH2514 4.0 37.2 1.0 O A:HOH2491 4.0 30.2 1.0 O A:HOH2520 4.1 22.8 1.0 OE2 A:GLU278 4.2 18.9 0.6 OG A:SER258 4.3 10.8 0.6 OD1 A:ASN276 4.4 11.6 1.0 CG A:GLU277 4.4 12.1 0.6 O A:HOH2492 4.4 26.4 1.0 OE2 A:GLU260 4.5 18.5 1.0 O A:HOH2427 4.6 45.5 1.0 CG A:GLU278 4.7 11.5 0.6 CD A:GLU278 4.7 15.5 0.6 CG A:GLU278 4.7 12.2 0.4 CD A:GLU278 4.8 15.7 0.4 CB A:SER258 4.9 8.2 0.4

L.Bruel, G.Sulzenbacher, M.Tison-Cervera, A.Pujol, C.Nicoletti, J.Perrier, A.Galinier, D.Ropartz, M.Fons, F.Pompeo, T.Giardina. Agask, A Bifunctional Enzyme From the Human Microbiome Coupling Galactosidase and Kinase Activities J.Biol.Chem. V. 286 40814 2011.
ISSN: ISSN 0021-9258
PubMed: 21931163
DOI: 10.1074/JBC.M111.286039