Magnesium in PDB 5cuy: Crystal Structure of Trypanosoma Brucei Vacuolar Soluble Pyrophosphatases in Apo Form

The structure of Crystal Structure of Trypanosoma Brucei Vacuolar Soluble Pyrophosphatases in Apo Form, PDB code: 5cuy was solved by Y.Y.Yang, T.P.Ko, W.D.Liu, Y.Y.Zheng, C.C.Chen, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	199.917, 70.137, 141.759, 90.00, 106.38, 90.00
R / Rfree (%)	19.4 / 25.2

The binding sites of Magnesium atom in the Crystal Structure of Trypanosoma Brucei Vacuolar Soluble Pyrophosphatases in Apo Form (pdb code 5cuy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Trypanosoma Brucei Vacuolar Soluble Pyrophosphatases in Apo Form, PDB code: 5cuy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Trypanosoma Brucei Vacuolar Soluble Pyrophosphatases in Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Trypanosoma Brucei Vacuolar Soluble Pyrophosphatases in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:49.8 occ:1.00 OD2 A:ASP296 2.5 57.7 1.0 CG A:ASP296 3.0 52.8 1.0 O A:PRO294 3.0 49.2 1.0 OD1 A:ASP296 3.2 55.9 1.0 CG A:ASP291 3.3 80.1 1.0 OD1 A:ASP291 3.4 81.1 1.0 OD2 A:ASP291 3.5 80.8 1.0 OD1 A:ASP328 3.7 52.1 1.0 CB A:ASP293 3.7 62.8 1.0 CB A:ASP291 3.9 78.0 1.0 N A:ASP296 3.9 47.8 1.0 C A:PRO294 4.2 48.3 1.0 CB A:ASP296 4.2 50.3 1.0 O A:HOH1003 4.3 51.7 1.0 CA A:VAL295 4.5 47.0 1.0 C A:VAL295 4.6 48.0 1.0 CG A:ASP293 4.6 66.0 1.0 C A:ASP293 4.6 57.4 1.0 CG A:ASP328 4.6 54.9 1.0 CA A:ASP296 4.7 47.0 1.0 OD2 A:ASP293 4.7 68.1 1.0 CA A:ASP293 4.8 60.1 1.0 N A:VAL295 4.8 47.0 1.0 O A:ASP293 4.8 57.8 1.0 O A:TRP329 4.8 43.9 1.0 N A:PRO294 4.8 52.5 1.0 NZ A:LYS330 4.9 36.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Trypanosoma Brucei Vacuolar Soluble Pyrophosphatases in Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Trypanosoma Brucei Vacuolar Soluble Pyrophosphatases in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:59.0 occ:1.00 O B:HOH1025 2.5 30.5 1.0 O B:HOH1094 2.5 59.3 1.0 OD1 B:ASP328 2.6 47.9 1.0 O B:HOH1036 2.6 34.1 1.0 OD2 B:ASP296 2.8 44.2 1.0 O B:HOH1050 2.9 27.3 1.0 CG B:ASP328 3.6 46.0 1.0 CG B:ASP296 3.7 42.5 1.0 O B:TRP329 3.9 38.2 1.0 CA B:ASP328 3.9 40.6 1.0 N B:TRP329 4.1 37.5 1.0 C B:ASP328 4.3 38.8 1.0 CB B:ASP328 4.3 41.7 1.0 CB B:ASP296 4.4 42.3 1.0 OD2 B:ASP328 4.4 47.2 1.0 CG B:GLU278 4.5 60.4 1.0 NZ B:LYS330 4.6 24.6 1.0 N B:ASP296 4.6 40.5 1.0 OD1 B:ASP296 4.6 46.2 1.0 CB B:GLU278 4.7 58.7 1.0 O B:MET327 4.8 45.4 1.0 C B:TRP329 4.8 37.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Trypanosoma Brucei Vacuolar Soluble Pyrophosphatases in Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Trypanosoma Brucei Vacuolar Soluble Pyrophosphatases in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg902 b:49.2 occ:1.00 OD2 C:ASP296 2.7 49.4 1.0 OD1 C:ASP328 2.8 51.2 1.0 O C:HOH1080 3.0 43.2 1.0 OD2 C:ASP291 3.1 55.0 1.0 O C:HOH1018 3.2 40.9 1.0 CG C:ASP296 3.3 46.4 1.0 OD1 C:ASP296 3.6 50.2 1.0 O C:PRO294 3.7 41.4 1.0 O C:HOH1008 3.8 47.4 1.0 CG C:ASP328 3.9 51.1 1.0 CB C:ASP293 3.9 51.5 1.0 CG C:ASP291 4.0 56.1 1.0 OD1 C:ASP291 4.0 55.0 1.0 O C:HOH1046 4.3 57.3 1.0 CB C:ASP296 4.3 43.2 1.0 N C:ASP296 4.5 38.6 1.0 OD2 C:ASP328 4.6 53.6 1.0 OD2 C:ASP293 4.7 57.4 1.0 CG C:ASP293 4.8 55.8 1.0 CA C:ASP328 4.9 47.6 1.0 C C:PRO294 4.9 40.2 1.0 CB C:ASP328 4.9 50.1 1.0 O C:TRP329 4.9 43.5 1.0 CA C:ASP296 5.0 39.0 1.0 C C:ASP293 5.0 44.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Trypanosoma Brucei Vacuolar Soluble Pyrophosphatases in Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Trypanosoma Brucei Vacuolar Soluble Pyrophosphatases in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg902 b:49.8 occ:1.00 OD2 D:ASP296 2.6 47.1 1.0 OD2 D:ASP291 2.6 52.0 1.0 OD1 D:ASP328 2.6 46.5 1.0 CG D:ASP291 3.6 50.5 1.0 CG D:ASP328 3.7 46.8 1.0 CG D:ASP296 3.8 46.0 1.0 OD2 D:ASP293 3.8 58.1 1.0 OD1 D:ASP291 3.9 50.4 1.0 O D:PRO294 4.1 39.3 1.0 CB D:ASP293 4.1 49.9 1.0 CG D:ASP293 4.5 53.9 1.0 OD2 D:ASP328 4.5 47.9 1.0 OD1 D:ASP296 4.5 50.9 1.0 O D:HOH1010 4.6 48.6 1.0 CB D:ASP328 4.7 43.7 1.0 CB D:ASP291 4.7 52.2 1.0 CB D:ASP296 4.8 42.0 1.0 CA D:ASP328 4.9 43.8 1.0 N D:ASP296 4.9 34.8 1.0

Y.Y.Yang, T.P.Ko, Y.Y.Zheng, W.D.Liu, C.C.Chen, R.T.Guo. Crystal Structure of Trypanosoma Cruzi Protein in Complex with Ligand Acs Chem.Biol. 2016.
ISSN: ESSN 1554-8937