Magnesium in PDB 7shg: Polysaccharide Ribofuranosyl Transferase From Thermobacillus Composti

The structure of Polysaccharide Ribofuranosyl Transferase From Thermobacillus Composti, PDB code: 7shg was solved by M.S.Kimber, S.D.Kelly, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.16 / 2.50
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.74, 82.5, 234.92, 90, 90, 90
R / Rfree (%)	25.1 / 29.5

The structure of Polysaccharide Ribofuranosyl Transferase From Thermobacillus Composti also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Polysaccharide Ribofuranosyl Transferase From Thermobacillus Composti (pdb code 7shg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Polysaccharide Ribofuranosyl Transferase From Thermobacillus Composti, PDB code: 7shg:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Polysaccharide Ribofuranosyl Transferase From Thermobacillus Composti


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Polysaccharide Ribofuranosyl Transferase From Thermobacillus Composti within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:51.9 occ:1.00 O A:PHE18 2.1 57.9 1.0 O A:HOH829 2.1 35.3 1.0 OD2 A:ASP16 2.2 53.6 1.0 O A:HOH836 2.4 64.8 1.0 OD1 A:ASP205 2.7 51.2 1.0 CG A:ASP16 3.0 54.1 1.0 OD1 A:ASP16 3.2 58.6 1.0 C A:PHE18 3.3 54.6 1.0 OD2 A:ASP205 3.4 67.8 1.0 CG A:ASP205 3.5 60.4 1.0 CL A:CL701 3.6 54.5 1.0 O A:HOH814 3.7 61.2 1.0 N A:PHE18 3.9 49.5 1.0 CA A:PHE18 4.0 50.5 1.0 OG1 A:THR20 4.2 54.9 1.0 CB A:PHE18 4.2 56.7 1.0 N A:ASP19 4.3 50.5 1.0 CB A:ASP19 4.4 53.6 1.0 CB A:ASP16 4.4 55.0 1.0 OD2 A:ASP210 4.5 53.2 1.0 CA A:ASP19 4.7 55.9 1.0 C A:ILE17 4.8 51.4 1.0 C A:ASP19 4.9 58.4 1.0 OD2 A:ASP19 4.9 54.8 1.0 N A:THR20 4.9 56.5 1.0 CB A:ASP205 4.9 52.1 1.0 N A:ILE17 5.0 53.6 1.0

Magnesium binding site 2 out of 3 in the Polysaccharide Ribofuranosyl Transferase From Thermobacillus Composti


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Polysaccharide Ribofuranosyl Transferase From Thermobacillus Composti within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:52.4 occ:1.00 O A:HOH858 2.4 54.5 1.0 O A:HOH854 2.5 58.9 1.0 O A:HOH888 2.9 57.1 1.0 O A:HOH879 3.0 54.4 1.0 OD1 A:ASN25 3.2 77.0 1.0 O A:GLN119 3.7 49.9 1.0 O A:GLY117 3.9 60.2 1.0 CG A:ASN25 4.5 77.3 1.0 O A:HOH818 4.6 53.3 1.0 O A:VAL118 4.7 51.1 1.0 C A:VAL118 4.7 51.7 1.0 C A:GLN119 4.7 49.5 1.0 C A:GLY117 4.8 51.7 1.0 CB A:TYR120 4.8 52.2 1.0 CA A:VAL118 4.9 56.5 1.0 O A:HOH875 5.0 70.8 1.0

Magnesium binding site 3 out of 3 in the Polysaccharide Ribofuranosyl Transferase From Thermobacillus Composti


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Polysaccharide Ribofuranosyl Transferase From Thermobacillus Composti within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:49.8 occ:1.00 O B:PHE18 2.0 45.0 1.0 OD1 B:ASP205 2.1 47.2 1.0 OD2 B:ASP16 2.3 45.6 1.0 O B:HOH834 2.5 47.2 1.0 O B:HOH867 2.6 39.0 1.0 OD2 B:ASP205 2.6 49.2 1.0 CG B:ASP205 2.7 48.2 1.0 C B:PHE18 3.2 50.9 1.0 CG B:ASP16 3.5 43.8 1.0 CB B:ASP19 3.6 43.5 1.0 OG1 B:THR20 3.8 50.4 1.0 C B:ASP19 4.0 49.0 1.0 N B:ASP19 4.0 48.2 1.0 O B:ASP19 4.0 44.7 1.0 CA B:ASP19 4.1 46.9 1.0 OD1 B:ASP16 4.1 45.1 1.0 CB B:ASP205 4.1 54.2 1.0 CA B:PHE18 4.3 44.9 1.0 N B:THR20 4.4 48.5 1.0 N B:PHE18 4.4 40.6 1.0 O B:HOH819 4.5 44.2 1.0 OD2 B:ASP19 4.5 39.0 1.0 O B:HOH864 4.6 31.1 1.0 CG B:ASP19 4.6 49.0 1.0 OD2 B:ASP210 4.6 49.6 1.0 CB B:ASP16 4.6 37.5 1.0 N B:ASP205 4.6 50.8 1.0 CB B:PHE18 4.7 46.4 1.0 CB B:THR20 4.8 50.4 1.0 CA B:ASP205 4.9 50.0 1.0 N B:ASN206 5.0 50.5 1.0

S.D.Kelly, D.M.Williams, J.T.Nothof, T.Kim, T.L.Lowary, M.S.Kimber, C.Whitfield. The Biosynthetic Origin of Ribofuranose in Bacterial Polysaccharides. Nat.Chem.Biol. V. 18 530 2022.
ISSN: ESSN 1552-4469
PubMed: 35393575
DOI: 10.1038/S41589-022-01006-6