Magnesium in PDB 7msk: Thus Glycosin S-Glycosyltransferase

The structure of Thus Glycosin S-Glycosyltransferase, PDB code: 7msk was solved by N.Garg, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.06
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.833, 112.654, 90.31, 90, 90.11, 90
R / Rfree (%)	20.1 / 23.9

The structure of Thus Glycosin S-Glycosyltransferase also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Magnesium atom in the Thus Glycosin S-Glycosyltransferase (pdb code 7msk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Thus Glycosin S-Glycosyltransferase, PDB code: 7msk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Thus Glycosin S-Glycosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thus Glycosin S-Glycosyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:25.5 occ:1.00 O1A A:U2F501 2.0 33.5 1.0 O2B A:U2F501 2.1 24.2 1.0 OD2 A:ASP144 2.2 21.8 1.0 NE2 A:HIS224 2.3 28.9 1.0 OD1 A:ASP144 2.4 24.2 1.0 CG A:ASP144 2.6 25.1 1.0 CD2 A:HIS224 3.2 32.5 1.0 PB A:U2F501 3.2 28.3 1.0 PA A:U2F501 3.2 31.2 1.0 CE1 A:HIS224 3.2 31.2 1.0 O3A A:U2F501 3.5 32.3 1.0 O1 A:U2F501 3.6 30.7 1.0 O2A A:U2F501 4.1 29.2 1.0 CB A:ASP144 4.1 25.8 1.0 O A:HOH639 4.3 44.7 1.0 OD2 A:ASP142 4.3 28.1 1.0 ND1 A:HIS224 4.3 30.6 1.0 CG A:HIS224 4.4 31.0 1.0 CA A:GLY226 4.4 40.2 1.0 O5' A:U2F501 4.4 28.2 1.0 CB A:ASP142 4.4 24.2 1.0 O A:HOH743 4.4 27.6 1.0 C5' A:U2F501 4.5 26.4 1.0 O1B A:U2F501 4.6 27.4 1.0 CE A:LYS237 4.6 44.2 1.0 NZ A:LYS237 4.6 47.4 1.0 F1 A:U2F501 4.7 37.3 1.0 CG A:ASP142 4.8 25.5 1.0 C1 A:U2F501 4.9 28.1 1.0 N A:GLY226 5.0 37.8 1.0

Magnesium binding site 2 out of 2 in the Thus Glycosin S-Glycosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thus Glycosin S-Glycosyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:30.6 occ:1.00 O1A B:U2F502 2.0 44.5 1.0 O B:HOH642 2.1 34.0 1.0 O2B B:U2F502 2.1 30.2 1.0 NE2 B:HIS224 2.1 28.2 1.0 OD2 B:ASP144 2.3 28.2 1.0 OD1 B:ASP144 2.5 32.2 1.0 CG B:ASP144 2.7 32.5 1.0 CE1 B:HIS224 3.0 28.4 1.0 PA B:U2F502 3.1 38.2 1.0 CD2 B:HIS224 3.2 30.4 1.0 PB B:U2F502 3.2 30.8 1.0 O5' B:U2F502 3.4 41.7 1.0 O1 B:U2F502 3.5 30.9 1.0 O3A B:U2F502 3.6 37.0 1.0 NZ B:LYS237 4.0 63.9 1.0 ND1 B:HIS224 4.1 29.0 1.0 CB B:ASP144 4.2 31.6 1.0 OD2 B:ASP142 4.2 27.5 1.0 CG B:HIS224 4.2 27.8 1.0 O B:HOH731 4.3 28.0 1.0 CB B:ASP142 4.4 27.0 1.0 CA B:GLY226 4.4 36.9 1.0 O2A B:U2F502 4.5 42.2 1.0 O1B B:U2F502 4.5 32.7 1.0 F1 B:U2F502 4.6 36.2 1.0 CG B:ASP142 4.8 27.5 1.0 C1 B:U2F502 4.8 28.6 1.0 C5' B:U2F502 4.8 36.6 1.0 N B:GLY226 5.0 36.5 1.0

D.Fujinami, C.V.Garcia De Gonzalo, S.Biswas, Y.Hao, H.Wang, N.Garg, T.Lukk, S.K.Nair, W.A.Van Der Donk. Structural and Mechanistic Investigations of Protein S-Glycosyltransferases. Cell Chem Biol V. 28 1740 2021.
ISSN: ESSN 2451-9456
PubMed: 34283964
DOI: 10.1016/J.CHEMBIOL.2021.06.009