Sodium in PDB 2nwx: Crystal Structure of Gltph in Complex with L-Aspartate and Sodium Ions

The structure of Crystal Structure of Gltph in Complex with L-Aspartate and Sodium Ions, PDB code: 2nwx was solved by E.Gouaux, O.Boudker, R.Ryan, D.Yernool, K.Shimamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 3.29
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	115.473, 115.473, 324.227, 90.00, 90.00, 120.00
R / Rfree (%)	26.3 / 28.6

The binding sites of Sodium atom in the Crystal Structure of Gltph in Complex with L-Aspartate and Sodium Ions (pdb code 2nwx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Gltph in Complex with L-Aspartate and Sodium Ions, PDB code: 2nwx:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Crystal Structure of Gltph in Complex with L-Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Gltph in Complex with L-Aspartate and Sodium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na423 b:57.5 occ:1.00 O A:SER349 2.0 0.3 1.0 O A:THR352 2.5 0.4 1.0 O A:THR308 2.8 0.1 1.0 CE A:MET311 3.0 0.5 1.0 C A:SER349 3.1 0.6 1.0 O A:ILE350 3.2 98.7 1.0 C A:ILE350 3.4 0.7 1.0 SD A:MET311 3.4 0.6 1.0 C A:THR352 3.5 0.4 1.0 CB A:MET311 3.5 0.4 1.0 C A:THR308 3.6 0.7 1.0 N A:THR352 3.6 0.0 1.0 CG A:MET311 3.8 0.4 1.0 CA A:ILE350 3.8 0.5 1.0 CB A:THR352 3.8 0.4 1.0 N A:ILE350 3.9 0.0 1.0 CA A:THR352 3.9 0.1 1.0 C A:GLY351 4.0 1.0 1.0 N A:GLY351 4.0 0.1 1.0 CA A:SER349 4.2 0.9 1.0 N A:ILE309 4.2 0.6 1.0 CA A:ILE309 4.3 0.8 1.0 O A:ILE309 4.3 0.0 1.0 C A:ILE309 4.4 0.5 1.0 CA A:THR308 4.4 0.4 1.0 O A:GLY351 4.4 0.6 1.0 OG1 A:THR352 4.5 0.8 1.0 N A:MET311 4.6 0.8 1.0 CA A:GLY351 4.6 0.5 1.0 N A:ALA353 4.6 0.5 1.0 CA A:MET311 4.7 0.9 1.0 O A:ALA348 4.7 0.0 1.0 CG2 A:THR352 4.9 0.7 1.0 CB A:SER349 5.0 0.0 1.0 CA A:ALA353 5.0 0.6 1.0

Sodium binding site 2 out of 6 in the Crystal Structure of Gltph in Complex with L-Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Gltph in Complex with L-Aspartate and Sodium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na424 b:84.8 occ:1.00 O A:ASN310 2.6 0.8 1.0 O A:GLY306 2.7 0.5 1.0 OD1 A:ASP405 2.7 0.2 1.0 O A:ASN401 2.7 0.3 1.0 OD2 A:ASP405 2.8 0.6 1.0 CG A:ASP405 3.1 0.3 1.0 C A:ASN310 3.4 1.0 1.0 C A:ASN401 3.4 0.7 1.0 C A:GLY306 3.5 0.8 1.0 OG A:SER278 3.6 0.7 1.0 CA A:ALA307 3.6 0.6 1.0 C A:ALA307 3.9 0.7 1.0 N A:ALA307 3.9 0.2 1.0 CB A:ASN401 4.0 0.2 1.0 CE A:MET311 4.0 0.5 1.0 CA A:ASN310 4.1 1.0 1.0 N A:VAL402 4.1 0.6 1.0 N A:ASN310 4.2 0.8 1.0 CA A:ASN401 4.2 0.5 1.0 O A:ALA307 4.2 0.9 1.0 CB A:ASN310 4.3 0.1 1.0 N A:MET311 4.3 0.8 1.0 CA A:VAL402 4.3 0.7 1.0 N A:THR308 4.4 0.4 1.0 CB A:ASP405 4.6 0.0 1.0 CA A:MET311 4.6 0.9 1.0 CA A:GLY306 4.7 0.5 1.0 CB A:ALA307 4.9 0.6 1.0 CB A:SER278 4.9 0.1 1.0

Sodium binding site 3 out of 6 in the Crystal Structure of Gltph in Complex with L-Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Gltph in Complex with L-Aspartate and Sodium Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Na423 b:65.5 occ:1.00 O B:SER349 2.0 0.7 1.0 O B:THR352 2.3 0.8 1.0 O B:THR308 2.9 0.2 1.0 CE B:MET311 2.9 0.3 1.0 C B:SER349 3.2 0.3 1.0 C B:THR352 3.3 0.5 1.0 SD B:MET311 3.3 0.9 1.0 O B:ILE350 3.4 1.0 1.0 N B:THR352 3.5 0.0 1.0 CB B:MET311 3.5 0.6 1.0 C B:ILE350 3.6 0.4 1.0 CA B:THR352 3.7 0.8 1.0 CB B:THR352 3.7 0.6 1.0 C B:THR308 3.7 0.3 1.0 CG B:MET311 3.8 0.2 1.0 C B:GLY351 3.9 0.4 1.0 CA B:ILE350 3.9 0.1 1.0 N B:ILE350 4.0 0.3 1.0 N B:GLY351 4.2 0.6 1.0 CA B:SER349 4.3 0.5 1.0 OG1 B:THR352 4.3 0.0 1.0 O B:GLY351 4.3 0.8 1.0 O B:ILE309 4.4 0.8 1.0 N B:ALA353 4.4 0.6 1.0 CA B:THR308 4.4 0.2 1.0 N B:ILE309 4.4 0.6 1.0 CA B:ILE309 4.5 0.5 1.0 C B:ILE309 4.5 0.2 1.0 N B:MET311 4.6 0.4 1.0 CA B:GLY351 4.6 0.7 1.0 CA B:MET311 4.7 0.7 1.0 O B:ALA348 4.8 0.8 1.0 CA B:ALA353 4.8 0.7 1.0 CG2 B:THR352 4.9 1.0 1.0 O B:ALA353 4.9 0.4 1.0 C B:ALA353 5.0 0.7 1.0

Sodium binding site 4 out of 6 in the Crystal Structure of Gltph in Complex with L-Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Gltph in Complex with L-Aspartate and Sodium Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Na424 b:0.9 occ:1.00 O B:ASN310 2.6 0.6 1.0 O B:GLY306 2.8 0.0 1.0 OD2 B:ASP405 2.8 0.9 1.0 O B:ASN401 2.8 0.8 1.0 OD1 B:ASP405 2.9 0.1 1.0 CG B:ASP405 3.2 0.8 1.0 C B:ASN310 3.3 0.9 1.0 C B:ASN401 3.4 0.9 1.0 C B:GLY306 3.6 0.5 1.0 OG B:SER278 3.7 0.8 1.0 CA B:ALA307 3.7 0.9 1.0 CE B:MET311 3.9 0.3 1.0 CB B:ASN401 3.9 0.0 1.0 C B:ALA307 4.0 0.2 1.0 N B:ALA307 4.0 0.8 1.0 CA B:ASN310 4.0 0.7 1.0 N B:VAL402 4.1 1.0 1.0 N B:ASN310 4.1 0.1 1.0 CA B:ASN401 4.1 0.7 1.0 N B:MET311 4.2 0.4 1.0 CB B:ASN310 4.2 0.5 1.0 O B:ALA307 4.4 0.4 1.0 CA B:VAL402 4.4 0.5 1.0 N B:THR308 4.4 0.2 1.0 CA B:MET311 4.5 0.7 1.0 CB B:ASP405 4.6 0.3 1.0 CA B:GLY306 4.8 0.9 1.0 CB B:SER278 4.9 0.3 1.0

Sodium binding site 5 out of 6 in the Crystal Structure of Gltph in Complex with L-Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Gltph in Complex with L-Aspartate and Sodium Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Na423 b:78.6 occ:1.00 O C:SER349 2.1 0.6 1.0 O C:THR352 2.2 0.1 1.0 O C:THR308 2.6 0.5 1.0 CE C:MET311 3.1 0.3 1.0 O C:ILE350 3.2 0.7 1.0 C C:THR352 3.2 0.1 1.0 C C:SER349 3.3 0.6 1.0 N C:THR352 3.4 0.5 1.0 C C:ILE350 3.4 0.8 1.0 SD C:MET311 3.5 0.2 1.0 C C:THR308 3.5 1.0 1.0 CA C:THR352 3.7 0.7 1.0 C C:GLY351 3.7 0.8 1.0 CB C:THR352 3.8 1.0 1.0 CA C:ILE350 3.9 0.1 1.0 CB C:MET311 3.9 0.2 1.0 N C:ILE350 4.0 0.8 1.0 N C:GLY351 4.0 0.1 1.0 CG C:MET311 4.1 0.1 1.0 O C:GLY351 4.1 0.1 1.0 N C:ILE309 4.2 0.2 1.0 CA C:THR308 4.3 0.2 1.0 CA C:ILE309 4.3 0.3 1.0 CA C:GLY351 4.4 0.5 1.0 N C:ALA353 4.4 0.9 1.0 CA C:SER349 4.4 0.9 1.0 O C:ILE309 4.5 0.7 1.0 OG1 C:THR352 4.5 0.4 1.0 C C:ILE309 4.6 0.3 1.0 O C:ALA348 4.8 0.6 1.0 CA C:ALA353 4.8 0.7 1.0 N C:MET311 4.9 0.4 1.0 CG2 C:THR352 5.0 0.1 1.0 C C:ALA353 5.0 0.8 1.0

Sodium binding site 6 out of 6 in the Crystal Structure of Gltph in Complex with L-Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Gltph in Complex with L-Aspartate and Sodium Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Na424 b:90.4 occ:1.00 O C:ASN310 2.7 1.0 1.0 O C:ASN401 2.7 0.9 1.0 OD2 C:ASP405 2.8 0.7 1.0 O C:GLY306 2.8 0.8 1.0 OD1 C:ASP405 3.0 0.8 1.0 CG C:ASP405 3.3 0.6 1.0 C C:ASN401 3.3 0.8 1.0 C C:ASN310 3.4 0.2 1.0 OG C:SER278 3.5 0.6 1.0 CA C:ALA307 3.7 0.3 1.0 C C:GLY306 3.7 0.3 1.0 CB C:ASN401 3.8 0.9 1.0 C C:ALA307 3.9 0.1 1.0 N C:VAL402 4.0 0.5 1.0 CE C:MET311 4.0 0.3 1.0 CA C:ASN401 4.0 0.8 1.0 N C:ALA307 4.1 0.8 1.0 CA C:ASN310 4.2 0.4 1.0 N C:MET311 4.2 0.4 1.0 O C:ALA307 4.2 0.9 1.0 CA C:VAL402 4.2 0.5 1.0 N C:ASN310 4.3 0.7 1.0 CB C:ASN310 4.4 0.6 1.0 N C:THR308 4.5 0.1 1.0 CA C:MET311 4.5 1.0 1.0 CB C:ASP405 4.7 0.5 1.0 CB C:SER278 4.7 0.5 1.0 CB C:ALA307 4.9 0.7 1.0 CA C:GLY306 4.9 0.7 1.0 CG C:ASN401 4.9 0.3 1.0

O.Boudker, R.M.Ryan, D.Yernool, K.Shimamoto, E.Gouaux. Coupling Substrate and Ion Binding to Extracellular Gate of A Sodium-Dependent Aspartate Transporter. Nature V. 445 387 2007.
ISSN: ISSN 0028-0836
PubMed: 17230192
DOI: 10.1038/NATURE05455