Sodium in PDB 9p6b: Cryo-Em Structure of Full-Length Human TRPV1 in the Presence of Alpha- Humulene

The binding sites of Sodium atom in the Cryo-Em Structure of Full-Length Human TRPV1 in the Presence of Alpha- Humulene (pdb code 9p6b). 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 Full-Length Human TRPV1 in the Presence of Alpha- Humulene, PDB code: 9p6b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cryo-Em Structure of Full-Length Human TRPV1 in the Presence of Alpha- Humulene


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 Full-Length Human TRPV1 in the Presence of Alpha- Humulene within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1211 b:111.9 occ:1.00 O D:GLY644 2.4 23.8 1.0 O B:GLY644 2.4 34.6 1.0 O A:GLY644 2.5 30.8 1.0 O C:GLY644 2.5 23.7 1.0 C B:GLY644 3.4 34.6 1.0 C D:GLY644 3.4 23.8 1.0 C A:GLY644 3.5 30.8 1.0 C C:GLY644 3.5 23.7 1.0 NA D:NA1210 3.8 111.9 1.0 CA A:GLY644 3.8 30.8 1.0 CA B:GLY644 3.8 34.6 1.0 CA D:GLY644 3.9 23.8 1.0 CA C:GLY644 3.9 23.7 1.0 SD D:MET645 4.0 26.1 1.0 SD B:MET645 4.1 36.8 1.0 SD C:MET645 4.2 25.8 1.0 SD A:MET645 4.3 32.7 1.0 N B:MET645 4.6 36.8 1.0 N D:MET645 4.6 26.1 1.0 O A:ILE643 4.6 30.0 1.0 O B:ILE643 4.7 34.0 1.0 N A:MET645 4.7 32.7 1.0 N C:MET645 4.7 25.8 1.0 O D:ILE643 4.7 23.3 1.0 O C:ILE643 4.8 23.0 1.0 CG D:MET645 4.8 26.1 1.0 CG B:MET645 4.9 36.8 1.0 CA D:MET645 5.0 26.1 1.0

Sodium binding site 2 out of 2 in the Cryo-Em Structure of Full-Length Human TRPV1 in the Presence of Alpha- Humulene


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 Full-Length Human TRPV1 in the Presence of Alpha- Humulene within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1210 b:111.9 occ:1.00 NA A:NA1211 3.8 111.9 1.0 CA D:GLY644 4.0 23.8 1.0 CA B:GLY644 4.2 34.6 1.0 CA C:GLY644 4.2 23.7 1.0 OH A:TYR672 4.3 27.4 1.0 CA A:GLY644 4.3 30.8 1.0 OH B:TYR672 4.4 32.2 1.0 OH C:TYR672 4.4 21.5 1.0 OH D:TYR672 4.5 21.6 1.0 O D:ILE643 4.7 23.3 1.0 O D:GLY644 4.7 23.8 1.0 N D:GLY644 4.8 23.8 1.0 O A:HOH1302 4.8 0.1 1.0 O B:ILE643 4.8 34.0 1.0 O C:ILE643 4.8 23.0 1.0 O C:HOH1305 4.9 1.6 1.0 N B:GLY644 4.9 34.6 1.0 O B:HOH1305 4.9 18.4 1.0 O B:GLY644 4.9 34.6 1.0 O C:GLY644 4.9 23.7 1.0 N C:GLY644 4.9 23.7 1.0 C D:GLY644 4.9 23.8 1.0 O A:ILE643 4.9 30.0 1.0 C D:ILE643 5.0 23.3 1.0 N A:GLY644 5.0 30.8 1.0

R.Sanchez-Hernandez, M.Benitez-Angeles, I.A.Talyzina, I.Llorente, M.Gonzalez-Avendano, F.Sierra, A.Mendez-Resendiz, F.Mercado, A.Vergara-Jaque, A.I.Sobolevsky, L.D.Islas, T.Rosenbaum. Structural Basis of the Inhibition of TRPV1 By Analgesic Sesquiterpenes Proc.Natl.Acad.Sci.Usa V. 122 2025.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.2506560122