Magnesium in PDB 6npx: Xanthomonas Citri Dephospho-Pgm in Complex with Mannose-6-Phosphate

The structure of Xanthomonas Citri Dephospho-Pgm in Complex with Mannose-6-Phosphate, PDB code: 6npx was solved by K.M.Stiers, L.J.Beamer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.29 / 1.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.693, 54.334, 170.625, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23.2

The binding sites of Magnesium atom in the Xanthomonas Citri Dephospho-Pgm in Complex with Mannose-6-Phosphate (pdb code 6npx). 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 Xanthomonas Citri Dephospho-Pgm in Complex with Mannose-6-Phosphate, PDB code: 6npx:

Magnesium binding site 1 out of 1 in the Xanthomonas Citri Dephospho-Pgm in Complex with Mannose-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Xanthomonas Citri Dephospho-Pgm in Complex with Mannose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:9.4 occ:1.00 OD2 A:ASP237 2.0 15.4 1.0 O A:HOH623 2.1 18.1 1.0 OD1 A:ASP241 2.1 12.2 1.0 OD1 A:ASP239 2.1 12.8 1.0 OG A:SER97 2.1 21.9 1.0 O A:HOH840 2.2 28.8 1.0 CG A:ASP237 3.0 11.8 1.0 CG A:ASP239 3.0 13.3 1.0 CG A:ASP241 3.1 10.2 1.0 OD2 A:ASP239 3.1 18.3 1.0 OD1 A:ASP237 3.3 9.8 1.0 OD2 A:ASP241 3.4 16.0 1.0 CB A:SER97 3.4 38.3 1.0 O A:HOH621 3.5 42.3 1.0 O A:HOH670 4.1 37.3 1.0 CA A:SER97 4.1 70.0 1.0 O A:HOH638 4.1 32.2 1.0 NE A:ARG242 4.2 16.0 1.0 CB A:ASP237 4.2 9.9 1.0 N A:ASP241 4.3 11.8 1.0 CB A:ASP239 4.4 10.4 1.0 CB A:ASP241 4.4 9.6 1.0 O A:HOH630 4.4 47.4 1.0 CG A:ARG242 4.6 12.1 1.0 N A:ARG242 4.7 9.2 1.0 N A:ASP239 4.7 10.2 1.0 CA A:ASP241 4.7 9.7 1.0 C A:SER97 4.8 82.1 1.0 NH2 A:ARG242 4.8 17.9 1.0 N A:PHE240 4.8 9.7 1.0 C A:ASP239 4.9 9.9 1.0 CA A:ASP239 4.9 10.2 1.0 C A:ASP241 4.9 9.2 1.0 CD A:ARG242 4.9 16.7 1.0 CZ A:ARG242 5.0 23.5 1.0

K.M.Stiers, A.C.Graham, J.S.Zhu, D.L.Jakeman, J.C.Nix, L.J.Beamer. Structural and Dynamical Description of the Enzymatic Reaction of A Phosphohexomutase. Struct Dyn. V. 6 24703 2019.
ISSN: ESSN 2329-7778
PubMed: 31041362
DOI: 10.1063/1.5092803