Sodium in PDB 8u3c: TRPV1 in Nanodisc Bound with Pi-BR4 Bound in Conformation 2 (Monomer)

The structure of TRPV1 in Nanodisc Bound with Pi-BR4 Bound in Conformation 2 (Monomer) also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

The binding sites of Sodium atom in the TRPV1 in Nanodisc Bound with Pi-BR4 Bound in Conformation 2 (Monomer) (pdb code 8u3c). 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 Bound in Conformation 2 (Monomer), PDB code: 8u3c:

Sodium binding site 1 out of 1 in the TRPV1 in Nanodisc Bound with Pi-BR4 Bound in Conformation 2 (Monomer)


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 Bound in Conformation 2 (Monomer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na904 b:56.4 occ:1.00 O A:GLY643 2.5 36.0 1.0 O D:GLY643 2.5 36.0 1.0 H1 D:HOH903 2.6 0.0 1.0 O A:HOH1007 2.8 39.4 1.0 O D:HOH903 2.8 33.5 1.0 HA3 A:GLY643 3.2 36.0 1.0 HA3 D:GLY643 3.2 36.0 1.0 H1 A:HOH1007 3.3 0.0 1.0 H2 A:HOH1007 3.3 0.0 1.0 C A:GLY643 3.5 36.0 1.0 C D:GLY643 3.5 36.0 1.0 H2 D:HOH903 3.7 0.0 1.0 CA A:GLY643 3.8 36.0 1.0 CA D:GLY643 3.8 36.0 1.0 HA2 D:GLY643 4.1 36.0 1.0 HA2 A:GLY643 4.1 36.0 1.0 HG2 D:MET644 4.3 34.5 1.0 HG2 A:MET644 4.4 34.5 1.0 HA A:MET644 4.6 34.5 1.0 HA D:MET644 4.6 34.5 1.0 N A:MET644 4.6 34.5 1.0 N D:MET644 4.7 34.5 1.0 O A:ILE642 4.7 37.2 1.0 O D:ILE642 4.7 37.2 1.0 SD D:MET644 4.8 34.5 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