Sodium in PDB 8gfa: Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791

The structure of Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791 (pdb code 8gfa). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791, PDB code: 8gfa:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791


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 Human TRPV1 in Complex with the Analgesic Drug Sb-366791 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1212 b:19.2 occ:1.00 O C:HOH1314 2.3 24.2 1.0 O D:GLY644 2.4 18.4 1.0 O B:GLY644 2.4 18.3 1.0 O C:GLY644 2.4 18.2 1.0 O A:GLY644 2.4 18.4 1.0 NA C:NA1211 2.8 18.8 1.0 HA3 D:GLY644 3.2 18.4 1.0 HA3 C:GLY644 3.2 18.2 1.0 HA3 B:GLY644 3.2 18.3 1.0 HA3 A:GLY644 3.2 18.4 1.0 C D:GLY644 3.4 18.4 1.0 C C:GLY644 3.4 18.2 1.0 C B:GLY644 3.4 18.3 1.0 C A:GLY644 3.4 18.4 1.0 CA D:GLY644 3.7 18.4 1.0 CA B:GLY644 3.7 18.3 1.0 CA C:GLY644 3.7 18.2 1.0 CA A:GLY644 3.7 18.4 1.0 HA2 B:GLY644 4.0 18.3 1.0 HA2 D:GLY644 4.0 18.4 1.0 HA2 C:GLY644 4.0 18.2 1.0 HA2 A:GLY644 4.0 18.4 1.0 HG2 A:MET645 4.1 19.2 1.0 HG2 D:MET645 4.2 19.0 1.0 SD A:MET645 4.2 19.2 1.0 HG2 C:MET645 4.2 18.9 1.0 HG2 B:MET645 4.2 18.9 1.0 SD C:MET645 4.2 18.9 1.0 SD D:MET645 4.2 19.0 1.0 SD B:MET645 4.3 18.9 1.0 HA C:MET645 4.5 18.9 1.0 HA D:MET645 4.5 19.0 1.0 HA B:MET645 4.5 18.9 1.0 HA A:MET645 4.5 19.2 1.0 N D:MET645 4.5 19.0 1.0 N C:MET645 4.6 18.9 1.0 N B:MET645 4.6 18.9 1.0 N A:MET645 4.6 19.2 1.0 O A:ILE643 4.7 19.1 1.0 CG A:MET645 4.7 19.2 1.0 O D:ILE643 4.7 19.2 1.0 O C:ILE643 4.7 19.1 1.0 CG D:MET645 4.8 19.0 1.0 CG C:MET645 4.8 18.9 1.0 O B:ILE643 4.8 19.0 1.0 CG B:MET645 4.8 18.9 1.0 N D:GLY644 5.0 18.4 1.0 N C:GLY644 5.0 18.2 1.0 N B:GLY644 5.0 18.3 1.0 N A:GLY644 5.0 18.4 1.0

Sodium binding site 2 out of 2 in the Cryo-Em Structure of Human TRPV1 in Complex with the Analgesic Drug Sb-366791


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 Human TRPV1 in Complex with the Analgesic Drug Sb-366791 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1211 b:18.8 occ:1.00 HA3 C:GLY644 2.8 18.2 1.0 NA A:NA1212 2.8 19.2 1.0 HA3 D:GLY644 2.8 18.4 1.0 HA3 B:GLY644 2.8 18.3 1.0 HA3 A:GLY644 2.8 18.4 1.0 CA C:GLY644 3.6 18.2 1.0 CA D:GLY644 3.7 18.4 1.0 CA B:GLY644 3.7 18.3 1.0 CA A:GLY644 3.7 18.4 1.0 HA2 C:GLY644 3.7 18.2 1.0 HA2 D:GLY644 3.7 18.4 1.0 HA2 B:GLY644 3.7 18.3 1.0 HA2 A:GLY644 3.8 18.4 1.0 O C:GLY644 4.1 18.2 1.0 O B:GLY644 4.1 18.3 1.0 O A:GLY644 4.1 18.4 1.0 O D:GLY644 4.1 18.4 1.0 C C:GLY644 4.4 18.2 1.0 OH D:TYR672 4.4 20.4 1.0 C D:GLY644 4.4 18.4 1.0 OH C:TYR672 4.4 20.5 1.0 OH B:TYR672 4.4 20.3 1.0 C B:GLY644 4.4 18.3 1.0 C A:GLY644 4.4 18.4 1.0 OH A:TYR672 4.5 20.4 1.0 N C:GLY644 4.6 18.2 1.0 N D:GLY644 4.6 18.4 1.0 N B:GLY644 4.6 18.3 1.0 N A:GLY644 4.6 18.4 1.0 HH D:TYR672 4.8 20.4 1.0 HH B:TYR672 4.8 20.3 1.0 HH C:TYR672 4.8 20.5 1.0 O A:ILE643 4.8 19.1 1.0 O C:ILE643 4.8 19.1 1.0 O D:ILE643 4.8 19.2 1.0 O B:ILE643 4.8 19.0 1.0 HH A:TYR672 4.9 20.4 1.0 HE1 C:TYR672 5.0 20.5 1.0 HE1 D:TYR672 5.0 20.4 1.0 HE1 B:TYR672 5.0 20.3 1.0 C C:ILE643 5.0 19.1 1.0

A.Neuberger, M.Oda, Y.A.Nikolaev, K.D.Nadezhdin, E.O.Gracheva, S.N.Bagriantsev, A.I.Sobolevsky. Human TRPV1 Structure and Inhibition By the Analgesic Sb-366791. Nat Commun V. 14 2451 2023.
ISSN: ESSN 2041-1723
PubMed: 37117175
DOI: 10.1038/S41467-023-38162-9