Magnesium in PDB 6vpb: A Novel Membrane-Bound 6-Phosphogluconate Dehydrogenase From the Acetic Acid Bacteria Gluconacetobacter Diazotrophicus (GD6PGD)

The structure of A Novel Membrane-Bound 6-Phosphogluconate Dehydrogenase From the Acetic Acid Bacteria Gluconacetobacter Diazotrophicus (GD6PGD), PDB code: 6vpb was solved by A.Rodriguez-Romero, A.Rodriguez-Hernandez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.48 / 1.87
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	91.760, 82.097, 81.831, 90.00, 103.41, 90.00
R / Rfree (%)	18.3 / 22.2

The binding sites of Magnesium atom in the A Novel Membrane-Bound 6-Phosphogluconate Dehydrogenase From the Acetic Acid Bacteria Gluconacetobacter Diazotrophicus (GD6PGD) (pdb code 6vpb). 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 A Novel Membrane-Bound 6-Phosphogluconate Dehydrogenase From the Acetic Acid Bacteria Gluconacetobacter Diazotrophicus (GD6PGD), PDB code: 6vpb:

Magnesium binding site 1 out of 1 in the A Novel Membrane-Bound 6-Phosphogluconate Dehydrogenase From the Acetic Acid Bacteria Gluconacetobacter Diazotrophicus (GD6PGD)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A Novel Membrane-Bound 6-Phosphogluconate Dehydrogenase From the Acetic Acid Bacteria Gluconacetobacter Diazotrophicus (GD6PGD) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:50.9 occ:1.00 O B:SER276 2.2 50.0 1.0 OD1 B:ASP275 2.9 57.5 1.0 N B:ARG280 3.0 24.4 1.0 N B:GLY279 3.2 28.0 1.0 CB B:ASP275 3.2 43.9 1.0 OH B:TYR204 3.3 48.8 1.0 CG B:ARG280 3.4 39.0 1.0 C B:SER276 3.4 50.1 1.0 CA B:GLY279 3.5 28.6 1.0 CG B:ASP275 3.5 46.4 1.0 CD1 B:LEU300 3.7 34.8 1.0 C B:GLY279 3.7 30.3 1.0 C B:GLY277 3.8 39.8 1.0 C B:ASP275 3.8 52.4 1.0 O B:GLY277 3.9 31.2 1.0 N B:SER276 3.9 51.8 1.0 CB B:ARG280 4.0 27.1 1.0 N B:GLU278 4.1 31.5 1.0 CA B:ASP275 4.1 42.9 1.0 CE1 B:TYR204 4.1 45.6 1.0 CA B:ARG280 4.1 18.6 1.0 CZ B:TYR204 4.1 46.6 1.0 O B:ASP275 4.2 53.0 1.0 NH1 B:ARG280 4.2 49.7 1.0 CA B:GLY277 4.2 43.7 1.0 CD B:ARG280 4.2 43.3 1.0 N B:GLY277 4.2 51.3 1.0 C B:GLU278 4.3 29.0 1.0 CA B:SER276 4.3 50.8 1.0 NE B:ARG280 4.6 52.0 1.0 CZ B:ARG280 4.7 55.1 1.0 OD2 B:ASP275 4.7 49.0 1.0 CA B:GLU278 4.8 29.9 1.0 O B:GLY279 4.9 27.5 1.0

P.D.Sarmiento-Pavia, A.Rodriguez-Hernandez, A.Rodriguez-Romero, M.E.Sosa-Torres. The Structure of A Novel Membrane-Associated 6-Phosphogluconate Dehydrogenase From Gluconacetobacter Diazotrophicus (GD6PGD) Reveals A Subfamily of Short-Chain 6PGDS. Febs J. 2020.
ISSN: ISSN 1742-464X
PubMed: 32621793
DOI: 10.1111/FEBS.15472