Sodium in PDB 7qoa: Structure of Codb, A Cytosine Transporter in An Outward-Facing Conformation

The structure of Structure of Codb, A Cytosine Transporter in An Outward-Facing Conformation, PDB code: 7qoa was solved by C.E.Hatton, A.D.Cameron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.16 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	108.246, 209.027, 102.452, 90, 90, 90
R / Rfree (%)	21.8 / 26.5

The binding sites of Sodium atom in the Structure of Codb, A Cytosine Transporter in An Outward-Facing Conformation (pdb code 7qoa). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Codb, A Cytosine Transporter in An Outward-Facing Conformation, PDB code: 7qoa:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Codb, A Cytosine Transporter in An Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Codb, A Cytosine Transporter in An Outward-Facing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:35.4 occ:1.00 OG1 A:THR279 2.3 28.7 1.0 O A:ASN275 2.3 38.2 1.0 O A:GLY29 2.4 37.7 1.0 O A:PHE32 2.4 35.4 1.0 OG1 A:THR278 2.5 34.7 1.0 N A:THR279 2.9 35.9 1.0 CB A:THR279 3.2 33.8 1.0 C A:PHE32 3.4 37.1 1.0 C A:ASN275 3.4 35.2 1.0 CA A:THR279 3.4 34.9 1.0 CB A:THR278 3.5 35.1 1.0 C A:GLY29 3.5 35.7 1.0 C A:THR278 3.7 36.0 1.0 O A:LEU30 3.8 38.1 1.0 CA A:ASN275 3.8 33.1 1.0 CA A:THR278 4.0 36.6 1.0 CA A:PHE32 4.2 31.7 1.0 C A:LEU30 4.2 36.9 1.0 N A:PHE33 4.2 35.5 1.0 N A:PHE32 4.3 35.4 1.0 CA A:PHE33 4.3 35.9 1.0 CA A:GLY29 4.3 31.4 1.0 CB A:PHE32 4.3 34.8 1.0 CB A:PHE33 4.4 26.9 1.0 N A:THR278 4.4 34.0 1.0 N A:LEU30 4.4 36.9 1.0 CA A:LEU30 4.4 35.0 1.0 CB A:ASN275 4.5 38.2 1.0 O A:LEU274 4.5 36.5 1.0 N A:ILE276 4.5 34.3 1.0 CD1 A:PHE33 4.6 26.4 1.0 CG2 A:THR279 4.6 27.5 1.0 O A:THR278 4.6 33.8 1.0 CG2 A:THR278 4.8 28.7 1.0 OD1 A:ASN275 4.8 38.5 1.0 O A:ILE276 4.9 31.5 1.0 C A:THR279 4.9 33.5 1.0 CG A:PHE33 4.9 30.2 1.0 CA A:ILE276 4.9 34.8 1.0 O A:LEU28 4.9 36.9 1.0 C A:ILE276 5.0 34.4 1.0 N A:THR31 5.0 33.7 1.0 C A:THR31 5.0 33.5 1.0

Sodium binding site 2 out of 2 in the Structure of Codb, A Cytosine Transporter in An Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Codb, A Cytosine Transporter in An Outward-Facing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:35.9 occ:1.00 O B:GLY29 2.2 40.2 1.0 O B:ASN275 2.3 36.7 1.0 OG1 B:THR279 2.3 33.9 1.0 OG1 B:THR278 2.4 36.7 1.0 O B:PHE32 2.4 32.8 1.0 N B:THR279 3.0 37.8 1.0 C B:ASN275 3.2 35.5 1.0 CB B:THR279 3.4 34.4 1.0 C B:PHE32 3.4 37.1 1.0 C B:GLY29 3.4 36.7 1.0 CB B:THR278 3.4 34.0 1.0 CA B:THR279 3.6 35.2 1.0 CA B:ASN275 3.7 33.2 1.0 C B:THR278 3.7 37.9 1.0 CA B:THR278 4.0 36.8 1.0 O B:LEU30 4.1 40.7 1.0 CA B:PHE32 4.2 39.2 1.0 CB B:PHE32 4.2 35.2 1.0 CA B:GLY29 4.2 35.8 1.0 N B:THR278 4.2 33.8 1.0 N B:PHE32 4.3 36.9 1.0 O B:LEU274 4.3 33.1 1.0 N B:PHE33 4.3 33.7 1.0 C B:LEU30 4.4 39.2 1.0 N B:ILE276 4.4 37.9 1.0 N B:LEU30 4.4 37.6 1.0 CB B:ASN275 4.4 29.6 1.0 CA B:PHE33 4.5 32.5 1.0 CA B:LEU30 4.5 41.1 1.0 CB B:PHE33 4.5 32.8 1.0 CD1 B:PHE33 4.7 28.2 1.0 O B:THR278 4.7 36.4 1.0 CG2 B:THR279 4.7 33.3 1.0 CG2 B:THR278 4.7 34.5 1.0 OD1 B:ASN275 4.8 34.9 1.0 CA B:ILE276 4.8 33.2 1.0 N B:ASN275 4.9 32.1 1.0 O B:LEU28 5.0 34.0 1.0 C B:ILE276 5.0 33.5 1.0

C.E.Hatton, D.H.Brotherton, M.Spencer, A.D.Cameron. Structure of Cytosine Transport Protein Codb Provides Insight Into Nucleobase-Cation Symporter 1 Mechanism. Embo J. V. 41 10527 2022.
ISSN: ESSN 1460-2075
PubMed: 35775318
DOI: 10.15252/EMBJ.2021110527