Magnesium in PDB 2y4m: Mannosylglycerate Synthase in Complex with Gdp-Mannose

All present enzymatic activity of Mannosylglycerate Synthase in Complex with Gdp-Mannose:
2.4.1.217;

The structure of Mannosylglycerate Synthase in Complex with Gdp-Mannose, PDB code: 2y4m was solved by M.M.Nielsen, M.D.L.Suits, M.Yang, C.S.Barry, C.Martinez-Fleites, L.E.Tailford, J.E.Flint, B.G.Davis, G.J.Davies, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	129.47 / 2.70
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	149.500, 149.500, 154.321, 90.00, 90.00, 120.00
R / Rfree (%)	19.136 / 21.878

The structure of Mannosylglycerate Synthase in Complex with Gdp-Mannose also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Mannosylglycerate Synthase in Complex with Gdp-Mannose (pdb code 2y4m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Mannosylglycerate Synthase in Complex with Gdp-Mannose, PDB code: 2y4m:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Mannosylglycerate Synthase in Complex with Gdp-Mannose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mannosylglycerate Synthase in Complex with Gdp-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg400 b:40.5 occ:1.00 O3B A:GDX401 2.0 43.0 1.0 OD2 A:ASP102 2.1 39.2 1.0 O A:HOH2010 2.1 47.3 1.0 O1A A:GDX401 2.1 36.4 1.0 ND1 A:HIS217 2.3 68.0 1.0 O A:HOH2011 2.4 27.1 1.0 PB A:GDX401 3.0 38.2 1.0 CE1 A:HIS217 3.1 68.8 1.0 PA A:GDX401 3.2 36.0 1.0 CG A:ASP102 3.3 38.1 1.0 CG A:HIS217 3.4 66.7 1.0 O3A A:GDX401 3.4 37.2 1.0 O2B A:GDX401 3.7 38.3 1.0 OD1 A:ASP102 3.8 41.0 1.0 CB A:HIS217 3.9 65.4 1.0 O A:ARG218 4.1 70.7 1.0 O2A A:GDX401 4.2 34.1 1.0 NE2 A:HIS217 4.3 69.0 1.0 O1B A:GDX401 4.4 41.9 1.0 CB A:ASP102 4.5 36.0 1.0 CD2 A:HIS217 4.5 68.4 1.0 O5D A:GDX401 4.5 33.1 1.0 N A:ARG218 4.5 68.3 1.0 C5D A:GDX401 4.7 31.5 1.0 NH1 A:ARG218 4.8 72.0 1.0 OD2 A:ASP100 4.9 35.4 1.0 CB A:ARG218 4.9 70.1 1.0 C A:ARG218 5.0 70.5 1.0

Magnesium binding site 2 out of 2 in the Mannosylglycerate Synthase in Complex with Gdp-Mannose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mannosylglycerate Synthase in Complex with Gdp-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg400 b:54.7 occ:1.00 O1A B:GDX401 2.1 50.8 1.0 O3B B:GDX401 2.1 54.7 1.0 OD2 B:ASP102 2.2 53.5 1.0 ND1 B:HIS217 2.6 86.5 1.0 CG B:ASP102 3.1 52.0 1.0 PB B:GDX401 3.2 54.4 1.0 PA B:GDX401 3.2 48.2 1.0 OD1 B:ASP102 3.3 53.6 1.0 CG B:HIS217 3.4 84.2 1.0 CB B:HIS217 3.4 81.9 1.0 O3A B:GDX401 3.5 53.0 1.0 CE1 B:HIS217 3.6 87.4 1.0 O2B B:GDX401 3.9 53.9 1.0 N B:ARG218 4.2 81.3 1.0 O5D B:GDX401 4.3 47.9 1.0 O2A B:GDX401 4.3 49.6 1.0 O B:HOH2068 4.3 40.0 1.0 C5D B:GDX401 4.4 45.8 1.0 CB B:ASP102 4.5 51.8 1.0 CB B:ARG218 4.5 80.8 1.0 O1B B:GDX401 4.6 54.3 1.0 O B:ARG218 4.6 80.6 1.0 CD2 B:HIS217 4.6 86.6 1.0 CA B:HIS217 4.7 81.4 1.0 NE2 B:HIS217 4.7 87.6 1.0 C B:HIS217 4.7 81.5 1.0 OD2 B:ASP100 4.8 47.9 1.0 CA B:ARG218 4.8 81.0 1.0

M.M.Nielsen, M.D.L.Suits, M.Yang, C.S.Barry, C.Martinez-Fleites, L.E.Tailford, J.E.Flint, C.Dumon, B.G.Davis, H.J.Gilbert, G.J.Davies. Substrate and Metal Ion Promiscuity in Mannosylglycerate Synthase. J.Biol.Chem. V. 286 15155 2011.
ISSN: ISSN 0021-9258
PubMed: 21288903
DOI: 10.1074/JBC.M110.199844