Sodium in PDB 8gf9: Cryo-Em Structure of Human TRPV1 in CNW11 Nanodisc and Popc:Pope:Popg Lipids

The binding sites of Sodium atom in the Cryo-Em Structure of Human TRPV1 in CNW11 Nanodisc and Popc:Pope:Popg Lipids (pdb code 8gf9). 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 CNW11 Nanodisc and Popc:Pope:Popg Lipids, PDB code: 8gf9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cryo-Em Structure of Human TRPV1 in CNW11 Nanodisc and Popc:Pope:Popg Lipids


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 CNW11 Nanodisc and Popc:Pope:Popg Lipids within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1211 b:12.5 occ:1.00 O D:GLY644 2.4 32.7 1.0 O B:GLY644 2.4 33.4 1.0 O C:GLY644 2.4 33.4 1.0 O A:GLY644 2.4 31.1 1.0 SD B:MET645 3.1 34.3 1.0 SD D:MET645 3.1 36.0 1.0 SD A:MET645 3.1 32.4 1.0 SD C:MET645 3.1 34.1 1.0 C D:GLY644 3.6 32.7 1.0 C B:GLY644 3.6 33.4 1.0 C C:GLY644 3.6 33.4 1.0 C A:GLY644 3.6 31.1 1.0 HA D:MET645 3.8 36.0 1.0 HA B:MET645 3.8 34.3 1.0 HA C:MET645 3.8 34.1 1.0 HA A:MET645 3.8 32.4 1.0 HG2 B:MET645 4.1 34.3 1.0 HG2 D:MET645 4.1 36.0 1.0 HG2 A:MET645 4.1 32.4 1.0 HG2 C:MET645 4.1 34.1 1.0 HA3 D:GLY644 4.2 32.7 1.0 HA3 B:GLY644 4.2 33.4 1.0 HA3 A:GLY644 4.2 31.1 1.0 HA3 C:GLY644 4.2 33.4 1.0 CG D:MET645 4.2 36.0 1.0 CG B:MET645 4.2 34.3 1.0 CG A:MET645 4.2 32.4 1.0 CG C:MET645 4.3 34.1 1.0 CA D:GLY644 4.5 32.7 1.0 CA B:GLY644 4.5 33.4 1.0 N D:MET645 4.5 36.0 1.0 N B:MET645 4.5 34.3 1.0 CA D:MET645 4.5 36.0 1.0 CA B:MET645 4.5 34.3 1.0 CA C:GLY644 4.5 33.4 1.0 CA A:GLY644 4.5 31.1 1.0 N A:MET645 4.5 32.4 1.0 N C:MET645 4.5 34.1 1.0 CA A:MET645 4.5 32.4 1.0 CA C:MET645 4.5 34.1 1.0 CE B:MET645 4.6 34.3 1.0 CE D:MET645 4.6 36.0 1.0 CE A:MET645 4.6 32.4 1.0 HE1 A:MET645 4.6 32.4 1.0 HE1 B:MET645 4.6 34.3 1.0 CE C:MET645 4.6 34.1 1.0 HE1 D:MET645 4.6 36.0 1.0 HE1 C:MET645 4.6 34.1 1.0 HA2 B:GLY644 4.9 33.4 1.0 HA2 D:GLY644 4.9 32.7 1.0 HA2 C:GLY644 4.9 33.4 1.0 HA2 A:GLY644 4.9 31.1 1.0 HG3 B:MET645 5.0 34.3 1.0 HG3 D:MET645 5.0 36.0 1.0 HG3 A:MET645 5.0 32.4 1.0 HG3 C:MET645 5.0 34.1 1.0

Sodium binding site 2 out of 2 in the Cryo-Em Structure of Human TRPV1 in CNW11 Nanodisc and Popc:Pope:Popg Lipids


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 CNW11 Nanodisc and Popc:Pope:Popg Lipids within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1212 b:12.5 occ:1.00 HA3 D:GLY644 2.9 32.7 1.0 HA3 B:GLY644 2.9 33.4 1.0 HA3 A:GLY644 3.0 31.1 1.0 HA3 C:GLY644 3.0 33.4 1.0 O D:HOH1302 3.0 32.6 1.0 O A:HOH1301 3.1 31.8 1.0 O B:HOH1301 3.1 29.5 1.0 O C:HOH1301 3.1 31.6 1.0 CA D:GLY644 3.8 32.7 1.0 CA B:GLY644 3.8 33.4 1.0 CA A:GLY644 3.8 31.1 1.0 CA C:GLY644 3.8 33.4 1.0 HA2 D:GLY644 3.9 32.7 1.0 HA2 B:GLY644 3.9 33.4 1.0 HA2 A:GLY644 3.9 31.1 1.0 HA2 C:GLY644 3.9 33.4 1.0 OH D:TYR672 4.3 32.3 1.0 OH B:TYR672 4.3 33.6 1.0 OH C:TYR672 4.3 33.2 1.0 OH A:TYR672 4.3 33.1 1.0 N D:GLY644 4.5 32.7 1.0 N B:GLY644 4.6 33.4 1.0 N A:GLY644 4.6 31.1 1.0 N C:GLY644 4.6 33.4 1.0 O D:GLY644 4.6 32.7 1.0 O B:GLY644 4.6 33.4 1.0 O A:GLY644 4.6 31.1 1.0 O C:GLY644 4.6 33.4 1.0 HH D:TYR672 4.7 32.3 1.0 HH B:TYR672 4.7 33.6 1.0 HH C:TYR672 4.7 33.2 1.0 HH A:TYR672 4.7 33.1 1.0 HE1 D:TYR672 4.7 32.3 1.0 O D:ILE643 4.7 34.0 1.0 C D:GLY644 4.7 32.7 1.0 HE1 B:TYR672 4.7 33.6 1.0 O B:ILE643 4.8 33.1 1.0 C B:GLY644 4.8 33.4 1.0 O A:ILE643 4.8 31.3 1.0 HE1 A:TYR672 4.8 33.1 1.0 HE1 C:TYR672 4.8 33.2 1.0 C A:GLY644 4.8 31.1 1.0 C C:GLY644 4.8 33.4 1.0 O C:ILE643 4.8 33.0 1.0 C D:ILE643 4.9 34.0 1.0 C B:ILE643 4.9 33.1 1.0 C A:ILE643 4.9 31.3 1.0 C C:ILE643 5.0 33.0 1.0 H D:GLY644 5.0 32.7 1.0 H B:GLY644 5.0 33.4 1.0 H A:GLY644 5.0 31.1 1.0 H C:GLY644 5.0 33.4 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