Sodium in PDB 2y4j: Mannosylglycerate Synthase in Complex with Lactate

All present enzymatic activity of Mannosylglycerate Synthase in Complex with Lactate:
2.4.1.217;

The structure of Mannosylglycerate Synthase in Complex with Lactate, PDB code: 2y4j 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)	129.02 / 2.30
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.975, 148.975, 154.973, 90.00, 90.00, 120.00
R / Rfree (%)	19.816 / 22.163

The binding sites of Sodium atom in the Mannosylglycerate Synthase in Complex with Lactate (pdb code 2y4j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Mannosylglycerate Synthase in Complex with Lactate, PDB code: 2y4j:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Mannosylglycerate Synthase in Complex with Lactate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mannosylglycerate Synthase in Complex with Lactate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:26.7 occ:1.00 OG1 A:THR59 2.6 51.8 1.0 O A:ALA24 2.7 41.2 1.0 O A:VAL29 2.7 40.2 1.0 O A:HIS26 2.8 43.5 1.0 C A:HIS26 3.8 42.7 1.0 CB A:THR59 3.8 50.2 1.0 C A:VAL29 3.9 40.3 1.0 C A:ALA24 3.9 41.6 1.0 CG2 A:THR59 4.1 50.5 1.0 N A:HIS26 4.3 42.5 1.0 C A:ALA25 4.3 42.4 1.0 O A:ALA25 4.4 43.5 1.0 O A:PRO27 4.4 41.7 1.0 N A:VAL29 4.5 39.8 1.0 O A:THR57 4.5 53.7 1.0 CA A:VAL29 4.5 39.6 1.0 C A:PRO27 4.6 41.9 1.0 CB A:VAL29 4.6 39.1 1.0 CA A:PRO27 4.6 42.3 1.0 N A:PRO27 4.6 42.8 1.0 CA A:HIS26 4.6 42.1 1.0 CA A:ALA25 4.8 42.1 1.0 N A:ALA25 4.8 41.5 1.0 CA A:ALA24 4.8 41.4 1.0 O A:ALA23 4.9 41.1 1.0 N A:HIS30 5.0 41.2 1.0

Sodium binding site 2 out of 2 in the Mannosylglycerate Synthase in Complex with Lactate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mannosylglycerate Synthase in Complex with Lactate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:34.9 occ:1.00 O B:VAL29 2.5 42.7 1.0 O B:HIS26 2.6 44.1 1.0 O B:ALA24 2.7 44.4 1.0 OG1 B:THR59 2.8 52.7 1.0 C B:VAL29 3.7 42.7 1.0 C B:HIS26 3.7 43.7 1.0 C B:ALA24 3.8 44.5 1.0 CB B:THR59 4.0 52.2 1.0 CG2 B:THR59 4.0 53.0 1.0 N B:VAL29 4.2 42.0 1.0 CA B:VAL29 4.3 41.9 1.0 CB B:VAL29 4.4 41.4 1.0 C B:ALA25 4.4 45.0 1.0 N B:HIS26 4.4 44.6 1.0 C B:PRO27 4.5 43.2 1.0 O B:PRO27 4.5 43.3 1.0 CA B:PRO27 4.5 43.3 1.0 N B:PRO27 4.6 43.7 1.0 O B:ALA25 4.6 45.8 1.0 CA B:ALA24 4.6 44.3 1.0 CA B:HIS26 4.7 43.8 1.0 N B:HIS30 4.8 43.3 1.0 N B:ALA25 4.8 44.4 1.0 O B:ALA23 4.8 43.5 1.0 CA B:ALA25 4.9 44.7 1.0 CA B:HIS30 5.0 44.8 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