Sodium in PDB 8tz1: Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Ribavirin

The binding sites of Sodium atom in the Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Ribavirin (pdb code 8tz1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Ribavirin, PDB code: 8tz1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Ribavirin


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 Ribavirin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:73.6 occ:1.00 OG1 A:THR376 2.4 74.1 1.0 O A:ASN342 2.4 76.7 1.0 O A:HOH901 2.4 75.8 1.0 O A:ILE377 2.6 73.6 1.0 O A:ILE345 2.6 76.2 1.0 HB A:THR376 2.8 74.1 1.0 CB A:THR376 3.1 74.1 1.0 HG1 A:THR376 3.1 74.1 1.0 C A:ILE377 3.2 73.6 1.0 HB3 A:ASN342 3.3 76.7 1.0 C A:THR376 3.4 74.1 1.0 N A:ILE377 3.4 73.6 1.0 C A:ASN342 3.5 76.7 1.0 HA2 A:GLY346 3.5 77.0 1.0 OD1 A:ASN342 3.5 76.7 1.0 HA A:ASN342 3.7 76.7 1.0 H A:ILE377 3.7 73.6 1.0 O A:THR376 3.7 74.1 1.0 CA A:ILE377 3.8 73.6 1.0 C A:ILE345 3.8 76.2 1.0 CA A:THR376 3.8 74.1 1.0 HA A:ILE377 3.8 73.6 1.0 CB A:ASN342 3.9 76.7 1.0 CA A:ASN342 3.9 76.7 1.0 HA A:ALA378 4.0 73.3 1.0 CG A:ASN342 4.1 76.7 1.0 N A:ALA378 4.1 73.3 1.0 CA A:GLY346 4.2 77.0 1.0 HA2 A:GLY373 4.3 75.6 1.0 H A:ILE345 4.3 76.2 1.0 CG2 A:THR376 4.4 74.1 1.0 HG21 A:THR376 4.4 74.1 1.0 H A:THR376 4.4 74.1 1.0 C A:GLY346 4.4 77.0 1.0 N A:GLY346 4.4 77.0 1.0 O A:GLY373 4.5 75.6 1.0 N A:GLN347 4.6 78.3 1.0 CA A:ALA378 4.6 73.3 1.0 HA A:THR376 4.6 74.1 1.0 H A:GLN347 4.6 78.3 1.0 N A:THR376 4.6 74.1 1.0 N A:ILE343 4.7 74.3 1.0 N A:ILE345 4.7 76.2 1.0 HB2 A:ALA378 4.7 73.3 1.0 HA A:ILE343 4.7 74.3 1.0 H A:ALA378 4.8 73.3 1.0 HB2 A:ASN342 4.8 76.7 1.0 O A:ALA372 4.8 75.7 1.0 O A:GLY346 4.9 77.0 1.0 CA A:ILE345 4.9 76.2 1.0 HA A:GLN347 4.9 78.3 1.0 HG23 A:THR376 4.9 74.1 1.0 HG22 A:THR376 5.0 74.1 1.0 C A:ILE343 5.0 74.3 1.0

Sodium binding site 2 out of 6 in the Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Ribavirin


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 Ribavirin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na803 b:76.5 occ:1.00 HG A:CYS608 2.2 73.9 1.0 O A:CYS567 2.3 73.0 1.0 O A:SER375 2.4 74.2 1.0 O A:HOH902 2.4 71.1 1.0 OG A:SER402 2.5 75.0 1.0 HG A:SER402 3.0 75.0 1.0 HB3 A:CYS567 3.1 73.0 1.0 HB3 A:SER402 3.2 75.0 1.0 CB A:SER402 3.4 75.0 1.0 SG A:CYS608 3.4 73.9 1.0 C A:CYS567 3.5 73.0 1.0 C A:SER375 3.5 74.2 1.0 HA A:THR376 3.6 74.1 1.0 HA A:CYS608 3.7 73.9 1.0 HB2 A:SER402 3.9 75.0 1.0 CB A:CYS567 3.9 73.0 1.0 HB2 A:SER375 4.2 74.2 1.0 HA A:SER375 4.2 74.2 1.0 HB3 A:CYS608 4.2 73.9 1.0 CA A:CYS567 4.2 73.0 1.0 CB A:CYS608 4.3 73.9 1.0 SG A:CYS567 4.3 73.0 1.0 N A:THR376 4.3 74.1 1.0 HA2 A:GLY568 4.3 73.2 1.0 CA A:THR376 4.4 74.1 1.0 CA A:SER375 4.4 74.2 1.0 HB1 A:ALA398 4.4 72.1 1.0 O A:ALA398 4.4 72.1 1.0 HG21 A:THR611 4.4 74.4 1.0 CA A:CYS608 4.5 73.9 1.0 HA A:SER402 4.5 75.0 1.0 N A:GLY568 4.5 73.2 1.0 HA3 A:GLY568 4.5 73.2 1.0 HG22 A:THR376 4.5 74.1 1.0 CA A:SER402 4.6 75.0 1.0 O A:TYR564 4.6 73.0 1.0 HG A:CYS567 4.6 73.0 1.0 H A:CYS567 4.6 73.0 1.0 HB2 A:CYS567 4.6 73.0 1.0 HA A:SER399 4.6 73.3 1.0 CA A:GLY568 4.7 73.2 1.0 CB A:SER375 4.8 74.2 1.0 HG23 A:THR376 4.8 74.1 1.0 N A:CYS567 4.9 73.0 1.0 HG1 A:THR611 5.0 74.4 1.0

Sodium binding site 3 out of 6 in the Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Ribavirin


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 Ribavirin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na802 b:73.6 occ:1.00 OG1 C:THR376 2.4 74.1 1.0 O C:ASN342 2.4 76.7 1.0 O C:HOH901 2.4 75.8 1.0 O C:ILE377 2.6 73.6 1.0 O C:ILE345 2.6 76.2 1.0 HB C:THR376 2.8 74.1 1.0 CB C:THR376 3.1 74.1 1.0 HG1 C:THR376 3.1 74.1 1.0 C C:ILE377 3.2 73.6 1.0 HB3 C:ASN342 3.3 76.7 1.0 C C:THR376 3.4 74.1 1.0 N C:ILE377 3.4 73.6 1.0 C C:ASN342 3.5 76.7 1.0 HA2 C:GLY346 3.5 77.0 1.0 OD1 C:ASN342 3.5 76.7 1.0 HA C:ASN342 3.7 76.7 1.0 H C:ILE377 3.7 73.6 1.0 O C:THR376 3.7 74.1 1.0 CA C:ILE377 3.8 73.6 1.0 C C:ILE345 3.8 76.2 1.0 CA C:THR376 3.8 74.1 1.0 HA C:ILE377 3.8 73.6 1.0 CB C:ASN342 3.9 76.7 1.0 CA C:ASN342 3.9 76.7 1.0 HA C:ALA378 4.0 73.3 1.0 CG C:ASN342 4.1 76.7 1.0 N C:ALA378 4.1 73.3 1.0 CA C:GLY346 4.2 77.0 1.0 HA2 C:GLY373 4.3 75.6 1.0 H C:ILE345 4.3 76.2 1.0 CG2 C:THR376 4.4 74.1 1.0 HG21 C:THR376 4.4 74.1 1.0 H C:THR376 4.4 74.1 1.0 C C:GLY346 4.4 77.0 1.0 N C:GLY346 4.4 77.0 1.0 O C:GLY373 4.5 75.6 1.0 N C:GLN347 4.6 78.3 1.0 CA C:ALA378 4.6 73.3 1.0 HA C:THR376 4.6 74.1 1.0 H C:GLN347 4.6 78.3 1.0 N C:THR376 4.6 74.1 1.0 N C:ILE343 4.7 74.3 1.0 N C:ILE345 4.7 76.2 1.0 HB2 C:ALA378 4.7 73.3 1.0 HA C:ILE343 4.7 74.3 1.0 H C:ALA378 4.8 73.3 1.0 HB2 C:ASN342 4.8 76.7 1.0 O C:ALA372 4.8 75.7 1.0 O C:GLY346 4.9 77.0 1.0 CA C:ILE345 4.9 76.2 1.0 HA C:GLN347 4.9 78.3 1.0 HG23 C:THR376 4.9 74.1 1.0 HG22 C:THR376 5.0 74.1 1.0 C C:ILE343 5.0 74.3 1.0

Sodium binding site 4 out of 6 in the Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Ribavirin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Ribavirin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na803 b:76.5 occ:1.00 HG C:CYS608 2.2 73.9 1.0 O C:CYS567 2.3 73.0 1.0 O C:SER375 2.4 74.2 1.0 O C:HOH902 2.4 71.1 1.0 OG C:SER402 2.5 75.0 1.0 HG C:SER402 3.0 75.0 1.0 HB3 C:CYS567 3.1 73.0 1.0 HB3 C:SER402 3.2 75.0 1.0 CB C:SER402 3.4 75.0 1.0 SG C:CYS608 3.4 73.9 1.0 C C:CYS567 3.5 73.0 1.0 C C:SER375 3.5 74.2 1.0 HA C:THR376 3.6 74.1 1.0 HA C:CYS608 3.7 73.9 1.0 HB2 C:SER402 3.9 75.0 1.0 CB C:CYS567 3.9 73.0 1.0 HB2 C:SER375 4.2 74.2 1.0 HA C:SER375 4.2 74.2 1.0 HB3 C:CYS608 4.2 73.9 1.0 CA C:CYS567 4.2 73.0 1.0 CB C:CYS608 4.3 73.9 1.0 SG C:CYS567 4.3 73.0 1.0 N C:THR376 4.3 74.1 1.0 HA2 C:GLY568 4.3 73.2 1.0 CA C:THR376 4.4 74.1 1.0 CA C:SER375 4.4 74.2 1.0 HB1 C:ALA398 4.4 72.1 1.0 O C:ALA398 4.4 72.1 1.0 HG21 C:THR611 4.4 74.4 1.0 CA C:CYS608 4.5 73.9 1.0 HA C:SER402 4.5 75.0 1.0 N C:GLY568 4.5 73.2 1.0 HA3 C:GLY568 4.5 73.2 1.0 HG22 C:THR376 4.5 74.1 1.0 CA C:SER402 4.6 75.0 1.0 O C:TYR564 4.6 73.0 1.0 HG C:CYS567 4.6 73.0 1.0 H C:CYS567 4.6 73.0 1.0 HB2 C:CYS567 4.6 73.0 1.0 HA C:SER399 4.6 73.3 1.0 CA C:GLY568 4.7 73.2 1.0 CB C:SER375 4.8 74.2 1.0 HG23 C:THR376 4.8 74.1 1.0 N C:CYS567 4.9 73.0 1.0 HG1 C:THR611 5.0 74.4 1.0

Sodium binding site 5 out of 6 in the Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Ribavirin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Ribavirin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:73.6 occ:1.00 OG1 B:THR376 2.4 74.1 1.0 O B:ASN342 2.4 76.7 1.0 O B:HOH901 2.4 75.8 1.0 O B:ILE377 2.6 73.6 1.0 O B:ILE345 2.6 76.2 1.0 HB B:THR376 2.8 74.1 1.0 CB B:THR376 3.1 74.1 1.0 HG1 B:THR376 3.1 74.1 1.0 C B:ILE377 3.2 73.6 1.0 HB3 B:ASN342 3.3 76.7 1.0 C B:THR376 3.4 74.1 1.0 N B:ILE377 3.4 73.6 1.0 C B:ASN342 3.5 76.7 1.0 HA2 B:GLY346 3.5 77.0 1.0 OD1 B:ASN342 3.5 76.7 1.0 HA B:ASN342 3.7 76.7 1.0 H B:ILE377 3.7 73.6 1.0 O B:THR376 3.7 74.1 1.0 CA B:ILE377 3.8 73.6 1.0 C B:ILE345 3.8 76.2 1.0 CA B:THR376 3.8 74.1 1.0 HA B:ILE377 3.8 73.6 1.0 CB B:ASN342 3.9 76.7 1.0 CA B:ASN342 3.9 76.7 1.0 HA B:ALA378 4.0 73.3 1.0 CG B:ASN342 4.1 76.7 1.0 N B:ALA378 4.1 73.3 1.0 CA B:GLY346 4.2 77.0 1.0 HA2 B:GLY373 4.3 75.6 1.0 H B:ILE345 4.3 76.2 1.0 CG2 B:THR376 4.4 74.1 1.0 HG21 B:THR376 4.4 74.1 1.0 H B:THR376 4.4 74.1 1.0 C B:GLY346 4.4 77.0 1.0 N B:GLY346 4.4 77.0 1.0 O B:GLY373 4.5 75.6 1.0 N B:GLN347 4.6 78.3 1.0 CA B:ALA378 4.6 73.3 1.0 HA B:THR376 4.6 74.1 1.0 H B:GLN347 4.6 78.3 1.0 N B:THR376 4.6 74.1 1.0 N B:ILE343 4.7 74.3 1.0 N B:ILE345 4.7 76.2 1.0 HB2 B:ALA378 4.7 73.3 1.0 HA B:ILE343 4.7 74.3 1.0 H B:ALA378 4.8 73.3 1.0 HB2 B:ASN342 4.8 76.7 1.0 O B:ALA372 4.8 75.7 1.0 O B:GLY346 4.9 77.0 1.0 CA B:ILE345 4.9 76.2 1.0 HA B:GLN347 4.9 78.3 1.0 HG23 B:THR376 4.9 74.1 1.0 HG22 B:THR376 5.0 74.1 1.0 C B:ILE343 5.0 74.3 1.0

Sodium binding site 6 out of 6 in the Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Ribavirin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with Ribavirin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na803 b:76.5 occ:1.00 HG B:CYS608 2.2 73.9 1.0 O B:CYS567 2.3 73.0 1.0 O B:SER375 2.4 74.2 1.0 O B:HOH902 2.4 71.1 1.0 OG B:SER402 2.5 75.0 1.0 HG B:SER402 3.0 75.0 1.0 HB3 B:CYS567 3.1 73.0 1.0 HB3 B:SER402 3.2 75.0 1.0 CB B:SER402 3.4 75.0 1.0 SG B:CYS608 3.4 73.9 1.0 C B:CYS567 3.5 73.0 1.0 C B:SER375 3.5 74.2 1.0 HA B:THR376 3.6 74.1 1.0 HA B:CYS608 3.7 73.9 1.0 HB2 B:SER402 3.9 75.0 1.0 CB B:CYS567 3.9 73.0 1.0 HB2 B:SER375 4.2 74.2 1.0 HA B:SER375 4.2 74.2 1.0 HB3 B:CYS608 4.2 73.9 1.0 CA B:CYS567 4.2 73.0 1.0 CB B:CYS608 4.3 73.9 1.0 SG B:CYS567 4.3 73.0 1.0 N B:THR376 4.3 74.1 1.0 HA2 B:GLY568 4.3 73.2 1.0 CA B:THR376 4.4 74.1 1.0 CA B:SER375 4.4 74.2 1.0 HB1 B:ALA398 4.4 72.1 1.0 O B:ALA398 4.4 72.1 1.0 HG21 B:THR611 4.4 74.4 1.0 CA B:CYS608 4.5 73.9 1.0 HA B:SER402 4.5 75.0 1.0 N B:GLY568 4.5 73.2 1.0 HA3 B:GLY568 4.5 73.2 1.0 HG22 B:THR376 4.5 74.1 1.0 CA B:SER402 4.6 75.0 1.0 O B:TYR564 4.6 73.0 1.0 HG B:CYS567 4.6 73.0 1.0 H B:CYS567 4.6 73.0 1.0 HB2 B:CYS567 4.6 73.0 1.0 HA B:SER399 4.6 73.3 1.0 CA B:GLY568 4.7 73.2 1.0 CB B:SER375 4.8 74.2 1.0 HG23 B:THR376 4.8 74.1 1.0 N B:CYS567 4.9 73.0 1.0 HG1 B:THR611 5.0 74.4 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