Manganese in PDB 2y4l: Mannosylglycerate Synthase in Complex with Manganese and Gdp

All present enzymatic activity of Mannosylglycerate Synthase in Complex with Manganese and Gdp:
2.4.1.217;

The structure of Mannosylglycerate Synthase in Complex with Manganese and Gdp, PDB code: 2y4l 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)	129.69 / 2.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	149.756, 149.756, 154.710, 90.00, 90.00, 120.00
R / Rfree (%)	18.762 / 22.041

The binding sites of Manganese atom in the Mannosylglycerate Synthase in Complex with Manganese and Gdp (pdb code 2y4l). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Mannosylglycerate Synthase in Complex with Manganese and Gdp, PDB code: 2y4l:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Mannosylglycerate Synthase in Complex with Manganese and Gdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Mannosylglycerate Synthase in Complex with Manganese and Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn400 b:68.4 occ:1.00 OD2 A:ASP102 2.1 57.2 1.0 O3B A:GDP401 2.2 64.1 1.0 O2A A:GDP401 2.3 57.0 1.0 O A:HOH2057 2.4 59.9 1.0 O A:HOH2056 2.5 51.1 1.0 ND1 A:HIS217 2.7 86.6 1.0 CG A:ASP102 3.0 54.8 1.0 OD1 A:ASP102 3.2 55.6 1.0 PB A:GDP401 3.4 62.2 1.0 PA A:GDP401 3.4 54.4 1.0 CB A:HIS217 3.5 84.0 1.0 CG A:HIS217 3.5 85.4 1.0 O3A A:GDP401 3.5 57.4 1.0 CE1 A:HIS217 3.8 87.9 1.0 NZ A:LYS215 4.1 77.4 1.0 O1B A:GDP401 4.2 63.6 1.0 N A:ARG218 4.2 85.8 1.0 O5' A:GDP401 4.4 51.4 1.0 CB A:ASP102 4.4 53.0 1.0 O1A A:GDP401 4.4 52.3 1.0 O2B A:GDP401 4.4 60.4 1.0 C5' A:GDP401 4.5 49.0 1.0 OD2 A:ASP100 4.6 49.6 1.0 O A:ARG218 4.7 87.2 1.0 CD2 A:HIS217 4.7 87.5 1.0 CA A:HIS217 4.7 84.1 1.0 CB A:ARG218 4.8 86.8 1.0 NH1 A:ARG218 4.8 90.1 1.0 NE2 A:HIS217 4.8 88.6 1.0 C A:HIS217 4.9 84.8 1.0 CA A:ARG218 4.9 86.9 1.0

Manganese binding site 2 out of 2 in the Mannosylglycerate Synthase in Complex with Manganese and Gdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Mannosylglycerate Synthase in Complex with Manganese and Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn400 b:0.8 occ:1.00 O3B B:GDP401 2.2 80.4 1.0 O2A B:GDP401 2.3 66.7 1.0 OD2 B:ASP102 2.8 70.5 1.0 OD1 B:ASP102 2.8 69.0 1.0 CG B:ASP102 3.1 68.4 1.0 PB B:GDP401 3.6 80.9 1.0 PA B:GDP401 3.6 68.5 1.0 O3A B:GDP401 3.9 75.2 1.0 OD2 B:ASP100 4.4 61.4 1.0 CB B:ASP102 4.5 66.5 1.0 O2B B:GDP401 4.5 80.4 1.0 O1B B:GDP401 4.6 79.7 1.0 O5' B:GDP401 4.6 65.8 1.0 O1A B:GDP401 4.7 68.6 1.0 C5' B:GDP401 4.7 59.2 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