Magnesium in PDB 5mlz: Dolichyl Phosphate Mannose Synthase in Complex with Gdp and MG2+

The structure of Dolichyl Phosphate Mannose Synthase in Complex with Gdp and MG2+, PDB code: 5mlz was solved by R.Gandini, T.Reichenbach, T.C.Tan, C.Divne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.02 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	90.870, 146.210, 95.350, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 25.7

The structure of Dolichyl Phosphate Mannose Synthase in Complex with Gdp and MG2+ also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Dolichyl Phosphate Mannose Synthase in Complex with Gdp and MG2+ (pdb code 5mlz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Dolichyl Phosphate Mannose Synthase in Complex with Gdp and MG2+, PDB code: 5mlz:

Magnesium binding site 1 out of 1 in the Dolichyl Phosphate Mannose Synthase in Complex with Gdp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dolichyl Phosphate Mannose Synthase in Complex with Gdp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:59.7 occ:1.00 OE1 A:GLN93 1.9 56.7 1.0 O2A A:GDP401 2.0 48.9 1.0 O2B A:GDP401 2.0 56.1 1.0 OD2 A:ASP91 2.1 58.8 1.0 PB A:GDP401 2.9 65.5 1.0 CD A:GLN93 3.1 58.4 1.0 O3B A:GDP401 3.2 71.3 1.0 PA A:GDP401 3.2 64.7 1.0 CG A:ASP91 3.3 64.3 1.0 O3A A:GDP401 3.4 65.3 1.0 NH1 A:ARG202 3.5 73.5 1.0 CG A:GLN93 3.7 62.1 1.0 OD1 A:ASP91 3.8 63.2 1.0 O1A A:GDP401 4.2 70.0 1.0 NE2 A:GLN93 4.2 60.5 1.0 O1B A:GDP401 4.3 68.4 1.0 O5' A:GDP401 4.3 60.8 1.0 C5' A:GDP401 4.3 60.2 1.0 CB A:GLN93 4.4 60.2 1.0 CB A:ASP91 4.5 65.3 1.0 CD A:ARG202 4.5 70.3 1.0 OD2 A:ASP89 4.6 55.2 1.0 CZ A:ARG202 4.7 75.8 1.0 CZ A:PHE199 4.8 59.8 1.0 CB A:ARG202 4.9 63.5 1.0

R.Gandini, T.Reichenbach, T.C.Tan, C.Divne. Structural Basis For Dolichylphosphate Mannose Biosynthesis. Nat Commun V. 8 120 2017.
ISSN: ESSN 2041-1723
PubMed: 28743912
DOI: 10.1038/S41467-017-00187-2