Sodium in PDB 8u4d: TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure

The structure of TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure also contains other interesting chemical elements:

Bromine

(Br)

8 atoms

The binding sites of Sodium atom in the TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure (pdb code 8u4d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure, PDB code: 8u4d:

Sodium binding site 1 out of 1 in the TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of TRPV1 in Nanodisc Bound with Pi-BR4, Consensus Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:33.7 occ:1.00 H1 D:HOH901 2.1 33.7 1.0 H1 A:HOH901 2.2 22.1 1.0 O A:GLY643 2.4 19.5 1.0 O B:GLY643 2.4 19.5 1.0 O D:GLY643 2.4 19.5 1.0 O C:GLY643 2.4 19.5 1.0 O A:HOH901 2.4 22.1 1.0 O D:HOH901 2.5 33.7 1.0 HA3 A:GLY643 3.4 19.5 1.0 HA3 B:GLY643 3.4 19.5 1.0 HA3 D:GLY643 3.4 19.5 1.0 HA3 C:GLY643 3.4 19.5 1.0 C A:GLY643 3.4 19.5 1.0 C B:GLY643 3.4 19.5 1.0 C D:GLY643 3.4 19.5 1.0 C C:GLY643 3.4 19.5 1.0 CA A:GLY643 3.9 19.5 1.0 CA B:GLY643 3.9 19.5 1.0 CA D:GLY643 3.9 19.5 1.0 CA C:GLY643 3.9 19.5 1.0 HA2 A:GLY643 4.2 19.5 1.0 HA2 D:GLY643 4.2 19.5 1.0 HA2 B:GLY643 4.2 19.5 1.0 HA2 C:GLY643 4.2 19.5 1.0 HA A:MET644 4.2 18.7 1.0 HA B:MET644 4.2 18.7 1.0 HA D:MET644 4.2 18.7 1.0 HA C:MET644 4.2 18.7 1.0 HG2 B:MET644 4.4 18.7 1.0 HG2 A:MET644 4.4 18.7 1.0 HG2 C:MET644 4.4 18.7 1.0 HG2 D:MET644 4.4 18.7 1.0 SD B:MET644 4.4 18.7 1.0 SD A:MET644 4.4 18.7 1.0 SD C:MET644 4.4 18.7 1.0 SD D:MET644 4.4 18.7 1.0 N A:MET644 4.5 18.7 1.0 N B:MET644 4.5 18.7 1.0 N D:MET644 4.5 18.7 1.0 N C:MET644 4.5 18.7 1.0 O B:ILE642 4.9 20.4 1.0 O A:ILE642 4.9 20.4 1.0 O C:ILE642 4.9 20.4 1.0 O D:ILE642 4.9 20.4 1.0 CA A:MET644 4.9 18.7 1.0 CA B:MET644 4.9 18.7 1.0 CA D:MET644 4.9 18.7 1.0 CA C:MET644 4.9 18.7 1.0 CG B:MET644 4.9 18.7 1.0 CG A:MET644 4.9 18.7 1.0 CG C:MET644 4.9 18.7 1.0 CG D:MET644 4.9 18.7 1.0

W.R.Arnold, M.Mancino, F.R.Moss Iii, A.Frost, D.Julius, Y.Cheng. Structural Basis of TRPV1 Modulation By Endogenous Bioactive Lipids Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-024-01299-2