Sodium in PDB 3ga5: X-Ray Structure of Glucose/Galactose Receptor From Salmonella Typhimurium in Complex with (2R)-Glyceryl-Beta- D-Galactopyranoside

The structure of X-Ray Structure of Glucose/Galactose Receptor From Salmonella Typhimurium in Complex with (2R)-Glyceryl-Beta- D-Galactopyranoside, PDB code: 3ga5 was solved by S.Sooriyaarachchi, W.Ubhayasekera, S.L.Mowbray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.74 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.458, 109.275, 150.703, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 22.2

The structure of X-Ray Structure of Glucose/Galactose Receptor From Salmonella Typhimurium in Complex with (2R)-Glyceryl-Beta- D-Galactopyranoside also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the X-Ray Structure of Glucose/Galactose Receptor From Salmonella Typhimurium in Complex with (2R)-Glyceryl-Beta- D-Galactopyranoside (pdb code 3ga5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of Glucose/Galactose Receptor From Salmonella Typhimurium in Complex with (2R)-Glyceryl-Beta- D-Galactopyranoside, PDB code: 3ga5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of Glucose/Galactose Receptor From Salmonella Typhimurium in Complex with (2R)-Glyceryl-Beta- D-Galactopyranoside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Glucose/Galactose Receptor From Salmonella Typhimurium in Complex with (2R)-Glyceryl-Beta- D-Galactopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Na700 b:11.5 occ:1.00 O A:GLY28 2.2 17.2 1.0 O A:VAL34 2.3 14.1 1.0 O A:ALA31 2.3 16.7 1.0 O A:HOH566 2.4 18.0 1.0 C A:GLY28 3.3 17.5 1.0 C A:VAL34 3.5 14.2 1.0 C A:ALA31 3.5 17.5 1.0 O A:LYS29 3.7 20.0 1.0 C A:LYS29 3.9 19.6 1.0 CA A:LYS29 4.0 19.6 1.0 O A:HOH531 4.1 17.0 1.0 N A:VAL34 4.1 15.6 1.0 N A:LYS29 4.1 18.4 1.0 CA A:VAL34 4.2 14.5 1.0 N A:ALA31 4.2 18.6 1.0 CA A:ALA31 4.3 17.8 1.0 CA A:GLY28 4.4 16.9 1.0 N A:PRO32 4.4 17.1 1.0 CA A:PRO32 4.5 17.3 1.0 C A:PRO32 4.5 17.4 1.0 CB A:VAL34 4.5 14.5 1.0 N A:GLN35 4.5 13.4 1.0 CB A:ALA31 4.5 17.7 1.0 O A:PRO32 4.5 17.3 1.0 N A:SER30 4.7 19.8 1.0 CA A:GLN35 4.7 13.0 1.0 C A:SER30 5.0 19.6 1.0 N A:ASP33 5.0 17.2 1.0 CG1 A:VAL34 5.0 14.7 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of Glucose/Galactose Receptor From Salmonella Typhimurium in Complex with (2R)-Glyceryl-Beta- D-Galactopyranoside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of Glucose/Galactose Receptor From Salmonella Typhimurium in Complex with (2R)-Glyceryl-Beta- D-Galactopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Na701 b:8.8 occ:1.00 O B:VAL34 2.3 10.8 1.0 O B:ALA31 2.3 10.2 1.0 O B:GLY28 2.4 10.6 1.0 O B:HOH359 2.5 9.4 1.0 O B:HOH353 2.5 8.9 1.0 O B:HOH318 2.5 20.6 1.0 C B:ALA31 3.4 10.7 1.0 C B:VAL34 3.5 11.5 1.0 C B:GLY28 3.6 10.8 1.0 N B:VAL34 4.1 12.1 1.0 CA B:PRO32 4.1 10.9 1.0 O B:HOH513 4.1 16.6 1.0 N B:PRO32 4.1 10.6 1.0 C B:PRO32 4.2 11.7 1.0 CA B:VAL34 4.2 11.7 1.0 N B:ALA31 4.2 11.3 1.0 O B:PRO32 4.3 11.2 1.0 CA B:ALA31 4.3 10.6 1.0 O B:LYS29 4.3 12.0 1.0 CA B:LYS29 4.3 11.3 1.0 C B:LYS29 4.4 11.5 1.0 N B:LYS29 4.4 10.9 1.0 NE2 B:GLN35 4.4 23.0 1.0 O B:HOH399 4.5 23.2 1.0 CB B:VAL34 4.5 11.9 1.0 N B:GLN35 4.5 10.9 1.0 CA B:GLY28 4.5 11.0 1.0 CB B:ALA31 4.7 10.8 1.0 CA B:GLN35 4.7 11.1 1.0 N B:ASP33 4.8 12.1 1.0 N B:SER30 5.0 11.6 1.0

S.Sooriyaarachchi, W.Ubhayasekera, W.Boos, S.L.Mowbray. X-Ray Structure of Glucose/Galactose Receptor From Salmonella Typhimurium in Complex with the Physiological Ligand, (2R)-Glyceryl-Beta-D-Galactopyranoside Febs J. V. 276 2116 2009.
ISSN: ISSN 1742-464X
PubMed: 19292879
DOI: 10.1111/J.1742-4658.2009.06945.X