Calcium in PDB 6np8: Xanthomonas Citri Phospho-Pgm in Complex with Mannose-6-Phosphate

The structure of Xanthomonas Citri Phospho-Pgm in Complex with Mannose-6-Phosphate, PDB code: 6np8 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)	45.85 / 1.41
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.930, 54.300, 171.140, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.3

The binding sites of Calcium atom in the Xanthomonas Citri Phospho-Pgm in Complex with Mannose-6-Phosphate (pdb code 6np8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Xanthomonas Citri Phospho-Pgm in Complex with Mannose-6-Phosphate, PDB code: 6np8:

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Xanthomonas Citri Phospho-Pgm in Complex with Mannose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:12.2 occ:0.80 OD2 A:ASP237 2.0 14.2 1.0 O2P A:SEP97 2.0 21.3 0.6 OD1 A:ASP239 2.0 15.7 1.0 OD1 A:ASP241 2.0 15.0 1.0 O A:HOH750 2.2 20.0 0.4 O A:HOH686 2.3 23.8 1.0 CG A:ASP239 2.9 17.7 1.0 CG A:ASP237 3.0 12.6 1.0 CG A:ASP241 3.0 18.7 1.0 OD2 A:ASP239 3.1 15.5 1.0 P A:SEP97 3.3 24.9 0.6 OD1 A:ASP237 3.3 13.3 1.0 OD2 A:ASP241 3.4 16.6 1.0 O3P A:SEP97 3.6 23.1 0.6 NZ A:LYS107 3.8 22.0 0.6 O1P A:SEP97 3.9 33.5 0.6 O A:HOH761 4.1 30.9 1.0 O A:HOH751 4.1 29.4 1.0 O A:HOH706 4.2 51.0 1.0 O3P A:SEP97 4.2 20.9 0.4 CB A:ASP237 4.2 13.4 1.0 N A:ASP241 4.2 12.4 1.0 NE A:ARG242 4.2 20.8 1.0 CB A:SEP97 4.3 35.9 0.4 CB A:ASP239 4.3 12.1 1.0 CB A:ASP241 4.4 10.9 1.0 CG A:ARG242 4.5 15.0 1.0 OG A:SEP97 4.5 32.5 0.6 O2P A:SEP97 4.6 27.6 0.4 N A:ARG242 4.6 11.6 1.0 CA A:ASP241 4.7 10.8 1.0 N A:ASP239 4.7 13.2 1.0 N A:PHE240 4.7 11.4 1.0 C A:ASP239 4.8 11.6 1.0 CB A:SEP97 4.8 37.2 0.6 CA A:ASP239 4.8 12.6 1.0 CD A:ARG242 4.9 15.2 1.0 C A:ASP241 4.9 14.1 1.0 CB A:ARG242 4.9 14.1 1.0 P A:SEP97 4.9 23.4 0.4

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