Sodium in PDB 8u3j: TRPV1 in Nanodisc Bound with Empty Vanilloid Binding Pocket at 4C

The binding sites of Sodium atom in the TRPV1 in Nanodisc Bound with Empty Vanilloid Binding Pocket at 4C (pdb code 8u3j). 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 Empty Vanilloid Binding Pocket at 4C, PDB code: 8u3j:

Sodium binding site 1 out of 1 in the TRPV1 in Nanodisc Bound with Empty Vanilloid Binding Pocket at 4C


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 Empty Vanilloid Binding Pocket at 4C within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:67.1 occ:1.00 O D:GLY643 2.8 38.2 1.0 O C:GLY643 2.8 38.2 1.0 O B:GLY643 2.8 38.2 1.0 O A:GLY643 2.8 38.2 1.0 HA3 D:GLY643 3.4 38.2 1.0 HA3 B:GLY643 3.4 38.2 1.0 HA3 A:GLY643 3.4 38.2 1.0 HA3 C:GLY643 3.4 38.2 1.0 C D:GLY643 3.8 38.2 1.0 C B:GLY643 3.8 38.2 1.0 C C:GLY643 3.8 38.2 1.0 C A:GLY643 3.8 38.2 1.0 CA D:GLY643 4.1 38.2 1.0 CA B:GLY643 4.1 38.2 1.0 CA C:GLY643 4.1 38.2 1.0 CA A:GLY643 4.1 38.2 1.0 HA2 D:GLY643 4.3 38.2 1.0 HA2 B:GLY643 4.3 38.2 1.0 HA2 C:GLY643 4.3 38.2 1.0 HA2 A:GLY643 4.3 38.2 1.0 HA D:MET644 4.8 37.6 1.0 HA C:MET644 4.8 37.6 1.0 HA B:MET644 4.8 37.6 1.0 HA A:MET644 4.8 37.6 1.0 HG2 D:MET644 4.8 37.6 1.0 HG2 C:MET644 4.8 37.6 1.0 HG2 B:MET644 4.8 37.6 1.0 HG2 A:MET644 4.8 37.6 1.0 SD C:MET644 4.9 37.6 1.0 SD D:MET644 4.9 37.6 1.0 SD A:MET644 4.9 37.6 1.0 SD B:MET644 4.9 37.6 1.0 N D:MET644 5.0 37.6 1.0 N C:MET644 5.0 37.6 1.0 N B:MET644 5.0 37.6 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