Sodium in PDB 8tz6: Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Psi-6206

The structure of Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Psi-6206 also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Sodium atom in the Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Psi-6206 (pdb code 8tz6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Psi-6206, PDB code: 8tz6:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Psi-6206


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Psi-6206 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:40.0 occ:1.00 O A:ILE345 2.4 43.3 1.0 O A:ASN342 2.6 43.4 1.0 OG1 A:THR376 2.6 40.5 1.0 OD1 A:ASN342 2.9 43.4 1.0 O A:ILE377 3.1 39.2 1.0 HB3 A:ASN342 3.1 43.4 1.0 HA2 A:GLY346 3.2 43.1 1.0 HG1 A:THR376 3.2 40.5 1.0 HB A:THR376 3.3 40.5 1.0 HA A:ASN342 3.4 43.4 1.0 C A:ASN342 3.5 43.4 1.0 C A:ILE345 3.5 43.3 1.0 CB A:THR376 3.5 40.5 1.0 CG A:ASN342 3.6 43.4 1.0 CB A:ASN342 3.6 43.4 1.0 CA A:ASN342 3.7 43.4 1.0 C A:ILE377 3.7 39.2 1.0 CA A:GLY346 3.8 43.1 1.0 C A:THR376 3.9 40.5 1.0 C A:GLY346 3.9 43.1 1.0 O A:THR376 4.0 40.5 1.0 N A:ILE377 4.0 39.2 1.0 N A:GLN347 4.0 45.0 1.0 HA2 A:GLY373 4.1 42.9 1.0 H A:GLN347 4.1 45.0 1.0 N A:GLY346 4.1 43.1 1.0 HA A:ALA378 4.3 38.5 1.0 HA A:ILE377 4.3 39.2 1.0 H A:ILE345 4.3 43.3 1.0 CA A:THR376 4.3 40.5 1.0 CA A:ILE377 4.3 39.2 1.0 H A:ILE377 4.3 39.2 1.0 O A:GLY346 4.4 43.1 1.0 HA A:GLN347 4.4 45.0 1.0 O A:GLY373 4.5 42.9 1.0 N A:ALA378 4.5 38.5 1.0 HB2 A:ASN342 4.5 43.4 1.0 H A:THR376 4.6 40.5 1.0 HB3 A:GLN347 4.6 45.0 1.0 N A:ILE345 4.6 43.3 1.0 HG21 A:THR376 4.7 40.5 1.0 HA3 A:GLY346 4.7 43.1 1.0 CA A:ILE345 4.7 43.3 1.0 N A:ILE343 4.7 41.1 1.0 O A:ALA372 4.7 42.5 1.0 HB2 A:ALA378 4.7 38.5 1.0 CG2 A:THR376 4.7 40.5 1.0 CA A:GLN347 4.8 45.0 1.0 ND2 A:ASN342 4.8 43.4 1.0 CA A:ALA378 4.8 38.5 1.0 HE2 A:PHE569 4.9 40.3 1.0 HD2 A:PHE569 4.9 40.3 1.0 N A:THR376 4.9 40.5 1.0 CA A:GLY373 5.0 42.9 1.0 H A:GLY346 5.0 43.1 1.0

Sodium binding site 2 out of 3 in the Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Psi-6206


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Psi-6206 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:39.3 occ:1.00 O B:ILE345 2.4 42.7 1.0 O B:ASN342 2.6 42.8 1.0 OG1 B:THR376 2.6 40.2 1.0 OD1 B:ASN342 2.9 42.8 1.0 O B:ILE377 3.1 39.1 1.0 HB3 B:ASN342 3.1 42.8 1.0 HA2 B:GLY346 3.2 42.8 1.0 HG1 B:THR376 3.2 40.2 1.0 HB B:THR376 3.3 40.2 1.0 HA B:ASN342 3.4 42.8 1.0 C B:ASN342 3.5 42.8 1.0 C B:ILE345 3.5 42.7 1.0 CB B:THR376 3.5 40.2 1.0 CG B:ASN342 3.6 42.8 1.0 CB B:ASN342 3.6 42.8 1.0 CA B:ASN342 3.7 42.8 1.0 C B:ILE377 3.7 39.1 1.0 CA B:GLY346 3.8 42.8 1.0 C B:THR376 3.9 40.2 1.0 C B:GLY346 3.9 42.8 1.0 O B:THR376 4.0 40.2 1.0 N B:ILE377 4.0 39.1 1.0 N B:GLN347 4.0 44.4 1.0 HA2 B:GLY373 4.1 41.9 1.0 H B:GLN347 4.1 44.4 1.0 N B:GLY346 4.1 42.8 1.0 HA B:ALA378 4.3 38.1 1.0 HA B:ILE377 4.3 39.1 1.0 H B:ILE345 4.3 42.7 1.0 CA B:THR376 4.3 40.2 1.0 CA B:ILE377 4.3 39.1 1.0 H B:ILE377 4.3 39.1 1.0 O B:GLY346 4.4 42.8 1.0 HA B:GLN347 4.4 44.4 1.0 O B:GLY373 4.5 41.9 1.0 N B:ALA378 4.5 38.1 1.0 HB2 B:ASN342 4.5 42.8 1.0 H B:THR376 4.6 40.2 1.0 HB3 B:GLN347 4.6 44.4 1.0 N B:ILE345 4.6 42.7 1.0 HG21 B:THR376 4.7 40.2 1.0 HA3 B:GLY346 4.7 42.8 1.0 CA B:ILE345 4.7 42.7 1.0 N B:ILE343 4.7 41.0 1.0 O B:ALA372 4.7 41.7 1.0 HB2 B:ALA378 4.7 38.1 1.0 CG2 B:THR376 4.7 40.2 1.0 CA B:GLN347 4.8 44.4 1.0 ND2 B:ASN342 4.8 42.8 1.0 CA B:ALA378 4.8 38.1 1.0 HE2 B:PHE569 4.9 40.3 1.0 HD2 B:PHE569 4.9 40.3 1.0 N B:THR376 4.9 40.2 1.0 CA B:GLY373 5.0 41.9 1.0 H B:GLY346 5.0 42.8 1.0

Sodium binding site 3 out of 3 in the Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Psi-6206


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Psi-6206 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na802 b:39.6 occ:1.00 O C:ILE345 2.4 43.2 1.0 O C:ASN342 2.6 43.2 1.0 OG1 C:THR376 2.6 40.3 1.0 OD1 C:ASN342 2.9 43.2 1.0 O C:ILE377 3.1 39.1 1.0 HB3 C:ASN342 3.1 43.2 1.0 HA2 C:GLY346 3.2 43.0 1.0 HG1 C:THR376 3.2 40.3 1.0 HB C:THR376 3.3 40.3 1.0 HA C:ASN342 3.4 43.2 1.0 C C:ASN342 3.5 43.2 1.0 C C:ILE345 3.5 43.2 1.0 CB C:THR376 3.5 40.3 1.0 CG C:ASN342 3.6 43.2 1.0 CB C:ASN342 3.6 43.2 1.0 CA C:ASN342 3.7 43.2 1.0 C C:ILE377 3.7 39.1 1.0 CA C:GLY346 3.8 43.0 1.0 C C:THR376 3.9 40.3 1.0 C C:GLY346 3.9 43.0 1.0 O C:THR376 4.0 40.3 1.0 N C:ILE377 4.0 39.1 1.0 N C:GLN347 4.0 44.5 1.0 HA2 C:GLY373 4.1 42.3 1.0 H C:GLN347 4.1 44.5 1.0 N C:GLY346 4.1 43.0 1.0 HA C:ALA378 4.3 38.6 1.0 HA C:ILE377 4.3 39.1 1.0 H C:ILE345 4.3 43.2 1.0 CA C:THR376 4.3 40.3 1.0 CA C:ILE377 4.3 39.1 1.0 H C:ILE377 4.3 39.1 1.0 O C:GLY346 4.4 43.0 1.0 HA C:GLN347 4.4 44.5 1.0 O C:GLY373 4.5 42.3 1.0 N C:ALA378 4.5 38.6 1.0 HB2 C:ASN342 4.5 43.2 1.0 H C:THR376 4.6 40.3 1.0 HB3 C:GLN347 4.6 44.5 1.0 N C:ILE345 4.6 43.2 1.0 HG21 C:THR376 4.7 40.3 1.0 HA3 C:GLY346 4.7 43.0 1.0 CA C:ILE345 4.7 43.2 1.0 N C:ILE343 4.7 41.4 1.0 O C:ALA372 4.7 42.2 1.0 HB2 C:ALA378 4.7 38.6 1.0 CG2 C:THR376 4.7 40.3 1.0 CA C:GLN347 4.8 44.5 1.0 ND2 C:ASN342 4.8 43.2 1.0 CA C:ALA378 4.8 38.6 1.0 HE2 C:PHE569 4.9 40.2 1.0 HD2 C:PHE569 4.9 40.2 1.0 N C:THR376 4.9 40.3 1.0 CA C:GLY373 5.0 42.3 1.0 H C:GLY346 5.0 43.0 1.0

N.J.Wright, F.Zhang, Y.Suo, L.Kong, Y.Yin, J.G.Fedor, K.Sharma, M.J.Borgnia, W.Im, S.Y.Lee. Antiviral Drug Recognition and Elevator-Type Transport Motions of CNT3. Nat.Chem.Biol. 2024.
ISSN: ESSN 1552-4469
PubMed: 38418906
DOI: 10.1038/S41589-024-01559-8