Magnesium in PDB 2y4k: Mannosylglycerate Synthase in Complex with Mg-Gdp

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

The structure of Mannosylglycerate Synthase in Complex with Mg-Gdp, PDB code: 2y4k 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)	47.76 / 2.45
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	149.646, 149.646, 154.112, 90.00, 90.00, 120.00
R / Rfree (%)	20.087 / 22.479

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

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Mannosylglycerate Synthase in Complex with Mg-Gdp (pdb code 2y4k). 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 Mg-Gdp, PDB code: 2y4k:
Jump to Magnesium binding site number: 1; 2;

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


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 Mg-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg400 b:73.0 occ:1.00 O2B A:GDP401 2.1 85.3 1.0 OD2 A:ASP102 2.4 64.2 1.0 O2A A:GDP401 2.7 73.9 1.0 CG A:ASP102 3.2 62.8 1.0 OD1 A:ASP102 3.2 64.0 1.0 PB A:GDP401 3.3 85.6 1.0 O1B A:GDP401 3.7 85.4 1.0 PA A:GDP401 3.9 73.4 1.0 O3A A:GDP401 4.1 79.8 1.0 O A:ALA216 4.1 86.9 1.0 CE A:LYS215 4.4 81.7 1.0 O3B A:GDP401 4.5 83.1 1.0 OD2 A:ASP100 4.6 56.6 1.0 CB A:ASP102 4.6 62.4 1.0 O A:HOH2070 4.7 49.8 1.0 O5' A:GDP401 4.9 70.5 1.0 C5' A:GDP401 4.9 64.2 1.0 O1A A:GDP401 5.0 73.5 1.0 CA A:HIS217 5.0 86.7 1.0

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


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 Mg-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg400 b:63.2 occ:1.00 O2A B:GDP401 2.1 52.7 0.5 O2B B:GDP401 2.3 45.6 0.5 O2A B:GDP401 2.7 56.3 0.5 OD1 B:ASP102 2.8 56.3 1.0 OD2 B:ASP102 2.8 55.8 1.0 CG B:ASP102 3.2 54.0 1.0 O1A B:GDP401 3.2 55.1 0.5 OD2 B:ASP100 3.3 45.3 1.0 PA B:GDP401 3.4 51.4 0.5 PA B:GDP401 3.5 53.9 0.5 PB B:GDP401 3.5 50.0 0.5 O3A B:GDP401 3.7 51.5 0.5 CE B:LYS215 3.9 63.5 1.0 C5' B:GDP401 4.0 50.1 0.5 C5' B:GDP401 4.0 51.4 0.5 O5' B:GDP401 4.1 51.3 0.5 CG B:ASP100 4.1 45.3 1.0 O3B B:GDP401 4.2 47.7 0.5 CB B:ASP100 4.2 43.6 1.0 O5' B:GDP401 4.3 53.2 0.5 O1A B:GDP401 4.5 52.0 0.5 C3' B:GDP401 4.6 49.9 0.5 C3' B:GDP401 4.6 49.3 0.5 C4' B:GDP401 4.7 49.6 0.5 CB B:ASP102 4.7 51.9 1.0 C4' B:GDP401 4.7 50.5 0.5 O1B B:GDP401 4.7 47.2 0.5 O3A B:GDP401 4.9 53.9 0.5

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