Sodium in PDB 2qw1: Glucose/Galactose Binding Protein Bound to 3-O-Methyl D-Glucose

The structure of Glucose/Galactose Binding Protein Bound to 3-O-Methyl D-Glucose, PDB code: 2qw1 was solved by M.J.Borrok, L.L.Kiessling, K.T.Forest, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.930, 74.660, 110.070, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.4

The structure of Glucose/Galactose Binding Protein Bound to 3-O-Methyl D-Glucose also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Glucose/Galactose Binding Protein Bound to 3-O-Methyl D-Glucose (pdb code 2qw1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Glucose/Galactose Binding Protein Bound to 3-O-Methyl D-Glucose, PDB code: 2qw1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Glucose/Galactose Binding Protein Bound to 3-O-Methyl D-Glucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Glucose/Galactose Binding Protein Bound to 3-O-Methyl D-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na312 b:14.8 occ:1.00 O A:HOH428 2.2 12.8 1.0 O A:HOH603 2.4 15.3 1.0 O A:THR110 2.4 10.6 1.0 O A:HOH429 2.5 13.4 1.0 O A:HOH339 2.5 14.1 1.0 OH A:TYR295 2.6 8.6 1.0 C A:THR110 3.6 9.8 1.0 CZ A:TYR295 3.7 9.3 1.0 N A:THR110 4.0 8.7 1.0 OD1 A:ASN91 4.1 13.1 1.0 CE1 A:TYR295 4.1 8.4 1.0 CA A:THR110 4.1 9.2 1.0 CB A:THR110 4.2 9.4 1.0 ND2 A:ASN256 4.2 11.7 1.0 O A:HOH349 4.3 17.9 1.0 OD1 A:ASN256 4.4 9.0 1.0 N A:SER112 4.4 11.2 1.0 C A:ASP111 4.5 10.8 1.0 O A:HOH357 4.6 10.3 1.0 N A:ASP111 4.7 10.4 1.0 CA A:SER112 4.7 12.4 1.0 CE2 A:TYR295 4.7 8.8 1.0 O A:ASP111 4.7 9.1 1.0 CG A:ASN256 4.7 10.1 1.0 O A:HOH359 4.8 14.9 1.0 O A:HOH383 4.9 19.1 1.0 OG1 A:THR110 4.9 9.8 1.0 CA A:ASP111 5.0 10.8 1.0

Sodium binding site 2 out of 2 in the Glucose/Galactose Binding Protein Bound to 3-O-Methyl D-Glucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Glucose/Galactose Binding Protein Bound to 3-O-Methyl D-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na313 b:14.0 occ:1.00 O A:HOH414 2.3 16.2 1.0 O A:SER228 2.3 13.0 1.0 O A:ILE230 2.3 6.8 1.0 O A:HOH412 2.4 19.6 1.0 O A:HOH415 2.6 27.2 1.0 O A:HOH413 2.7 11.1 1.0 C A:ILE230 3.2 7.6 1.0 C A:SER228 3.4 13.6 1.0 O A:ALA249 3.8 10.4 1.0 CA A:PRO231 3.9 7.0 1.0 N A:PRO231 3.9 7.3 1.0 N A:ILE230 3.9 9.5 1.0 C A:SER229 4.1 11.4 1.0 O A:HOH392 4.1 14.8 1.0 CA A:SER228 4.2 13.6 1.0 CA A:ILE230 4.2 8.0 1.0 N A:SER229 4.3 13.1 1.0 N A:VAL232 4.4 6.6 1.0 CA A:SER229 4.5 12.8 1.0 C A:PRO231 4.5 7.4 1.0 O A:SER229 4.5 11.5 1.0 CG2 A:VAL232 4.6 7.1 1.0 O A:HOH539 4.6 10.8 1.0 C A:ALA249 4.6 9.8 1.0 O A:GLY248 4.8 11.7 1.0 CD1 A:LEU222 4.8 8.7 1.0 CB A:SER228 4.9 14.2 1.0 O A:HOH510 4.9 19.1 1.0 O A:LYS227 5.0 10.9 1.0

M.J.Borrok, Y.Zhu, K.T.Forest, L.L.Kiessling. Structure-Based Design of A Periplasmic Binding Protein Antagonist That Prevents Domain Closure. Acs Chem.Biol. V. 4 447 2009.
ISSN: ISSN 1554-8929
PubMed: 19348466
DOI: 10.1021/CB900021Q