Magnesium in PDB 6upd: Structure of Trehalose-6-Phosphate Phosphatase From Salmonella Typhimurium in Complex with Trehalose

All present enzymatic activity of Structure of Trehalose-6-Phosphate Phosphatase From Salmonella Typhimurium in Complex with Trehalose:
3.1.3.12;

The structure of Structure of Trehalose-6-Phosphate Phosphatase From Salmonella Typhimurium in Complex with Trehalose, PDB code: 6upd was solved by C.M.Harvey, K.H.O'toole, K.N.Allen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.45 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.767, 52.955, 108.762, 90.00, 100.61, 90.00
R / Rfree (%)	21.8 / 26.2

The structure of Structure of Trehalose-6-Phosphate Phosphatase From Salmonella Typhimurium in Complex with Trehalose also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Structure of Trehalose-6-Phosphate Phosphatase From Salmonella Typhimurium in Complex with Trehalose (pdb code 6upd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Trehalose-6-Phosphate Phosphatase From Salmonella Typhimurium in Complex with Trehalose, PDB code: 6upd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Trehalose-6-Phosphate Phosphatase From Salmonella Typhimurium in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Trehalose-6-Phosphate Phosphatase From Salmonella Typhimurium in Complex with Trehalose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:29.2 occ:1.00 O A:ASP22 2.0 32.7 1.0 OD2 A:ASP20 2.1 32.2 1.0 O A:HOH426 2.1 24.9 1.0 O A:HOH460 2.1 26.0 1.0 OD1 A:ASP198 2.1 34.3 1.0 O A:HOH453 2.1 27.0 1.0 CG A:ASP198 3.1 24.6 1.0 CG A:ASP20 3.2 26.3 1.0 C A:ASP22 3.2 30.9 1.0 OD2 A:ASP198 3.4 29.5 1.0 OD1 A:ASP20 3.7 31.4 1.0 CA A:ASP22 4.1 25.5 1.0 N A:GLY23 4.2 30.6 1.0 OD2 A:ASP202 4.2 30.7 1.0 N A:ASP22 4.2 29.5 1.0 CB A:ASP22 4.3 24.6 1.0 CB A:ASP199 4.3 27.4 1.0 CA A:GLY23 4.3 32.8 1.0 OG1 A:THR24 4.3 33.6 1.0 CL A:CL303 4.4 33.6 1.0 CB A:ASP20 4.4 24.5 1.0 O A:HOH410 4.4 31.9 1.0 CB A:ASP198 4.4 25.3 1.0 N A:ASP199 4.6 29.9 1.0 C A:GLY23 4.6 31.4 1.0 N A:ASP198 4.7 25.0 1.0 N A:THR24 4.8 26.3 1.0 C A:LEU21 4.9 28.4 1.0 CA A:ASP198 4.9 26.0 1.0 C A:ASP198 4.9 28.9 1.0

Magnesium binding site 2 out of 2 in the Structure of Trehalose-6-Phosphate Phosphatase From Salmonella Typhimurium in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Trehalose-6-Phosphate Phosphatase From Salmonella Typhimurium in Complex with Trehalose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:44.9 occ:1.00 O B:ASP22 2.0 43.0 1.0 O B:HOH411 2.1 34.6 1.0 OD1 B:ASP198 2.1 40.5 1.0 O B:HOH418 2.1 45.2 1.0 O B:HOH417 2.2 41.3 1.0 OD2 B:ASP20 2.4 45.5 1.0 CG B:ASP198 3.0 42.8 1.0 C B:ASP22 3.2 41.1 1.0 OD2 B:ASP198 3.3 44.5 1.0 CG B:ASP20 3.5 47.1 1.0 OD1 B:ASP20 3.9 41.6 1.0 N B:GLY23 4.1 40.7 1.0 CA B:ASP22 4.2 43.2 1.0 CA B:GLY23 4.2 42.7 1.0 OD2 B:ASP202 4.2 37.5 1.0 CB B:ASP199 4.2 42.1 1.0 CL B:CL302 4.2 45.6 1.0 CB B:ASP22 4.3 53.2 1.0 O B:HOH423 4.3 41.3 1.0 N B:ASP22 4.4 44.3 1.0 CB B:ASP198 4.4 38.2 1.0 N B:ASP199 4.6 37.6 1.0 OG1 B:THR24 4.6 42.5 1.0 C B:GLY23 4.6 41.6 1.0 CB B:ASP20 4.7 45.1 1.0 N B:ASP198 4.7 39.3 1.0 C B:ASP198 4.9 42.0 1.0 CA B:ASP198 4.9 38.9 1.0 N B:THR24 4.9 40.7 1.0 C B:LEU21 5.0 46.9 1.0

C.M.Harvey, K.H.O'toole, C.Liu, P.Mariano, D.Dunaway-Mariano, K.N.Allen. Structural Analysis of Binding Determinants Ofsalmonella Typhimuriumtrehalose-6-Phosphate Phosphatase Using Ground-State Complexes. Biochemistry V. 59 3247 2020.
ISSN: ISSN 0006-2960
PubMed: 32786412
DOI: 10.1021/ACS.BIOCHEM.0C00317