Sodium in PDB 2fw0: Apo Open Form of Glucose/Galactose Binding Protein

The structure of Apo Open Form of Glucose/Galactose Binding Protein, PDB code: 2fw0 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)	19.99 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.800, 70.300, 112.100, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 17.8

The structure of Apo Open Form of Glucose/Galactose Binding Protein also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Apo Open Form of Glucose/Galactose Binding Protein (pdb code 2fw0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Apo Open Form of Glucose/Galactose Binding Protein, PDB code: 2fw0:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Apo Open Form of Glucose/Galactose Binding Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apo Open Form of Glucose/Galactose Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:9.8 occ:1.00 O A:HOH809 2.3 9.9 1.0 O A:THR110 2.4 7.7 1.0 O A:HOH547 2.4 12.3 1.0 O A:HOH517 2.5 8.7 1.0 O A:HOH507 2.5 10.3 1.0 OH A:TYR295 2.6 7.6 1.0 C A:THR110 3.5 7.2 1.0 CZ A:TYR295 3.6 5.8 1.0 N A:THR110 4.0 6.5 1.0 O A:HOH633 4.0 18.3 1.0 CA A:THR110 4.1 8.0 1.0 ND2 A:ASN91 4.1 4.9 1.0 CE1 A:TYR295 4.1 8.5 1.0 CB A:THR110 4.1 9.2 1.0 O A:HOH553 4.2 15.5 1.0 ND2 A:ASN256 4.2 8.6 1.0 N A:SER112 4.4 10.9 1.0 C A:ASP111 4.4 10.3 1.0 O A:HOH601 4.5 20.9 1.0 OD1 A:ASN256 4.5 8.2 1.0 O A:HOH504 4.6 14.8 1.0 CA A:SER112 4.6 11.9 1.0 N A:ASP111 4.6 8.9 1.0 O A:HOH655 4.6 16.0 1.0 CE2 A:TYR295 4.7 6.4 1.0 O A:ASP111 4.7 9.4 1.0 CG A:ASN256 4.8 7.6 1.0 O A:HOH503 4.8 8.9 1.0 CA A:ASP111 4.9 10.1 1.0 OG1 A:THR110 5.0 8.2 1.0

Sodium binding site 2 out of 3 in the Apo Open Form of Glucose/Galactose Binding Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Apo Open Form of Glucose/Galactose Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na312 b:11.0 occ:1.00 O A:ILE230 2.3 6.5 1.0 O A:HOH656 2.3 11.2 1.0 O A:SER228 2.3 10.6 1.0 O A:HOH651 2.5 15.3 1.0 O A:HOH569 2.6 17.4 1.0 O A:HOH510 2.6 8.1 1.0 C A:ILE230 3.3 6.3 1.0 C A:SER228 3.4 11.0 1.0 O A:HOH786 3.6 19.4 1.0 CA A:PRO231 3.9 5.5 1.0 O A:ALA249 3.9 8.2 1.0 N A:PRO231 3.9 6.0 1.0 N A:ILE230 4.0 8.7 1.0 CA A:SER228 4.1 10.7 1.0 O A:HOH658 4.2 13.1 1.0 C A:SER229 4.2 10.2 1.0 CA A:ILE230 4.3 7.2 1.0 N A:VAL232 4.5 5.5 1.0 N A:SER229 4.5 10.4 1.0 C A:PRO231 4.5 6.5 1.0 CB A:SER228 4.5 10.1 1.0 O A:SER229 4.6 12.0 1.0 CG2 A:VAL232 4.6 7.4 1.0 C A:ALA249 4.7 7.9 1.0 CD1 A:LEU222 4.7 11.2 1.0 CA A:SER229 4.7 10.1 1.0 O A:GLY248 4.8 10.7 1.0 O A:HOH523 4.8 10.7 1.0 O A:HOH567 4.9 17.4 1.0

Sodium binding site 3 out of 3 in the Apo Open Form of Glucose/Galactose Binding Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Apo Open Form of Glucose/Galactose Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na313 b:11.2 occ:0.50 O A:HOH687 2.3 30.1 1.0 O1 A:CIT314 2.3 24.4 0.5 OD1 A:ASN15 2.4 3.8 0.5 O A:HOH822 2.5 26.8 1.0 O5 A:CIT314 2.6 23.4 0.5 O7 A:CIT314 2.7 23.3 0.5 C6 A:CIT314 3.2 26.0 0.5 O A:HOH810 3.3 24.4 1.0 CG A:ASN15 3.3 8.7 0.5 C3 A:CIT314 3.4 26.5 0.5 C1 A:CIT314 3.4 27.8 0.5 ND2 A:ASN15 3.5 4.8 0.5 O A:HOH801 3.8 37.1 1.0 C2 A:CIT314 3.9 26.4 0.5 OD1 A:ASP14 4.1 19.6 1.0 O A:HOH785 4.1 25.3 1.0 O A:HOH588 4.1 17.8 1.0 O A:HOH836 4.2 31.0 1.0 O A:HOH705 4.2 20.2 1.0 O6 A:CIT314 4.3 24.3 0.5 O2 A:CIT314 4.5 24.5 0.5 O A:HOH550 4.6 14.8 1.0 N A:PHE16 4.7 12.8 1.0 CB A:ASN15 4.8 10.6 0.5 O3 A:CIT314 4.8 27.9 0.5 C4 A:CIT314 4.8 27.1 0.5 CB A:PHE16 4.9 11.4 1.0 N A:ASN15 4.9 14.9 1.0

M.J.Borrok, L.L.Kiessling, K.T.Forest. Conformational Changes of Glucose/Galactose-Binding Protein Illuminated By Open, Unliganded, and Ultra-High-Resolution Ligand-Bound Structures. Protein Sci. V. 16 1032 2007.
ISSN: ISSN 0961-8368
PubMed: 17473016
DOI: 10.1110/PS.062707807