Sodium in PDB 8t3l: TRPV1 in Nanodisc Bound with 2 Lpa Molecules in Neighboring Monomers

The binding sites of Sodium atom in the TRPV1 in Nanodisc Bound with 2 Lpa Molecules in Neighboring Monomers (pdb code 8t3l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the TRPV1 in Nanodisc Bound with 2 Lpa Molecules in Neighboring Monomers, PDB code: 8t3l:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the TRPV1 in Nanodisc Bound with 2 Lpa Molecules in Neighboring Monomers


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 2 Lpa Molecules in Neighboring Monomers within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:25.9 occ:1.00 O A:GLY643 2.3 38.1 1.0 O C:GLY643 2.3 40.4 1.0 O D:GLY643 2.4 36.8 1.0 O B:GLY643 2.5 38.4 1.0 C A:GLY643 3.4 38.1 1.0 C C:GLY643 3.5 40.4 1.0 HG2 D:MET644 3.6 37.8 1.0 HG2 C:MET644 3.7 42.4 1.0 NA B:NA802 3.7 36.6 1.0 C D:GLY643 3.7 36.8 1.0 C B:GLY643 3.7 38.4 1.0 HA3 A:GLY643 3.7 38.1 1.0 HA D:MET644 3.8 37.8 1.0 HA3 C:GLY643 3.9 40.4 1.0 HA3 B:GLY643 3.9 38.4 1.0 HA C:MET644 4.0 42.4 1.0 HA A:MET644 4.0 38.1 1.0 SD D:MET644 4.1 37.8 1.0 CA A:GLY643 4.1 38.1 1.0 SD A:MET644 4.2 38.1 1.0 HA3 D:GLY643 4.2 36.8 1.0 HG2 B:MET644 4.2 41.7 1.0 HA B:MET644 4.2 41.7 1.0 CG D:MET644 4.3 37.8 1.0 HG2 A:MET644 4.3 38.1 1.0 CA C:GLY643 4.3 40.4 1.0 SD C:MET644 4.4 42.4 1.0 CA B:GLY643 4.4 38.4 1.0 HA2 A:GLY643 4.4 38.1 1.0 CG C:MET644 4.4 42.4 1.0 N C:MET644 4.5 42.4 1.0 N A:MET644 4.5 38.1 1.0 CA D:GLY643 4.5 36.8 1.0 N D:MET644 4.6 37.8 1.0 CA D:MET644 4.6 37.8 1.0 HA2 B:GLY643 4.6 38.4 1.0 CA C:MET644 4.7 42.4 1.0 CA A:MET644 4.7 38.1 1.0 N B:MET644 4.7 41.7 1.0 HA2 C:GLY643 4.8 40.4 1.0 CG A:MET644 4.8 38.1 1.0 O C:ILE642 4.8 41.5 1.0 HA2 D:GLY643 4.9 36.8 1.0 CA B:MET644 5.0 41.7 1.0

Sodium binding site 2 out of 2 in the TRPV1 in Nanodisc Bound with 2 Lpa Molecules in Neighboring Monomers


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of TRPV1 in Nanodisc Bound with 2 Lpa Molecules in Neighboring Monomers within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:36.6 occ:1.00 HA3 C:GLY643 2.4 40.4 1.0 HA3 B:GLY643 2.6 38.4 1.0 HA2 B:GLY643 3.1 38.4 1.0 CA B:GLY643 3.3 38.4 1.0 CA C:GLY643 3.3 40.4 1.0 HA3 A:GLY643 3.5 38.1 1.0 O C:ILE642 3.6 41.5 1.0 NA A:NA802 3.7 25.9 1.0 O C:GLY643 3.7 40.4 1.0 HA3 D:GLY643 3.7 36.8 1.0 O B:GLY643 3.8 38.4 1.0 HA2 C:GLY643 3.9 40.4 1.0 C C:GLY643 3.9 40.4 1.0 C B:GLY643 4.0 38.4 1.0 N C:GLY643 4.0 40.4 1.0 C C:ILE642 4.1 41.5 1.0 HA2 A:GLY643 4.2 38.1 1.0 O D:GLY643 4.3 36.8 1.0 CA A:GLY643 4.3 38.1 1.0 HH A:TYR671 4.4 41.1 1.0 N B:GLY643 4.5 38.4 1.0 O A:GLY643 4.5 38.1 1.0 CA D:GLY643 4.6 36.8 1.0 H C:GLY643 4.7 40.4 1.0 H B:GLY643 4.8 38.4 1.0 OH A:TYR671 4.9 41.1 1.0 C A:GLY643 4.9 38.1 1.0 C D:GLY643 4.9 36.8 1.0 HA2 D:GLY643 4.9 36.8 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