Atomistry » Sodium » PDB 3fvs-3gdg » 3ga5
Atomistry »
  Sodium »
    PDB 3fvs-3gdg »
      3ga5 »

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

Protein crystallography data

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

Other elements in 3ga5:

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

Sodium Binding Sites:

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 3ga5

Go back to Sodium Binding Sites List in 3ga5
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 3ga5

Go back to Sodium Binding Sites List in 3ga5
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

Reference:

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
Page generated: Tue Dec 15 06:12:17 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy