Sodium in PDB 8t10: TRPV1 in Nanodisc Bound with Two Lpa Molecules in Opposite Monomers

The binding sites of Sodium atom in the TRPV1 in Nanodisc Bound with Two Lpa Molecules in Opposite Monomers (pdb code 8t10). 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 Two Lpa Molecules in Opposite Monomers, PDB code: 8t10:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the TRPV1 in Nanodisc Bound with Two Lpa Molecules in Opposite 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 Two Lpa Molecules in Opposite Monomers within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:48.5 occ:1.00 HA3 D:GLY643 3.0 41.5 1.0 HA3 B:GLY643 3.1 41.0 1.0 HA3 A:GLY643 3.1 40.9 1.0 HH D:TYR671 3.2 41.3 1.0 NA A:NA902 3.2 36.1 1.0 HA3 C:GLY643 3.3 40.5 1.0 HH B:TYR671 3.3 41.1 1.0 OH B:TYR671 3.8 41.1 1.0 OH D:TYR671 3.9 41.3 1.0 CA D:GLY643 4.0 41.5 1.0 CA A:GLY643 4.0 40.9 1.0 CA B:GLY643 4.0 41.0 1.0 HA2 A:GLY643 4.0 40.9 1.0 CA C:GLY643 4.2 40.5 1.0 HA2 B:GLY643 4.2 41.0 1.0 HA2 C:GLY643 4.2 40.5 1.0 HA2 D:GLY643 4.2 41.5 1.0 O D:GLY643 4.4 41.5 1.0 OH C:TYR671 4.4 41.2 1.0 O D:ILE642 4.7 41.2 1.0 C D:GLY643 4.7 41.5 1.0 O B:GLY643 4.7 41.0 1.0 HH C:TYR671 4.7 41.2 1.0 N A:GLY643 4.7 40.9 1.0 N B:GLY643 4.7 41.0 1.0 O B:ILE642 4.8 41.2 1.0 N D:GLY643 4.8 41.5 1.0 O C:GLY643 4.9 40.5 1.0 HE2 D:TYR671 4.9 41.3 1.0 C B:GLY643 4.9 41.0 1.0 O A:GLY643 4.9 40.9 1.0 C A:GLY643 5.0 40.9 1.0 HE1 A:TYR671 5.0 41.3 1.0 O C:ILE642 5.0 40.9 1.0

Sodium binding site 2 out of 2 in the TRPV1 in Nanodisc Bound with Two Lpa Molecules in Opposite 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 Two Lpa Molecules in Opposite Monomers within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:36.1 occ:1.00 O D:GLY643 2.3 41.5 1.0 O B:GLY643 2.3 41.0 1.0 O A:GLY643 2.5 40.9 1.0 O C:GLY643 2.5 40.5 1.0 HA3 A:GLY643 2.8 40.9 1.0 HA3 B:GLY643 2.9 41.0 1.0 HA3 C:GLY643 3.0 40.5 1.0 C B:GLY643 3.2 41.0 1.0 NA B:NA902 3.2 48.5 1.0 HA3 D:GLY643 3.3 41.5 1.0 C A:GLY643 3.3 40.9 1.0 C D:GLY643 3.3 41.5 1.0 C C:GLY643 3.4 40.5 1.0 CA A:GLY643 3.4 40.9 1.0 CA B:GLY643 3.5 41.0 1.0 CA C:GLY643 3.7 40.5 1.0 HA2 A:GLY643 3.8 40.9 1.0 CA D:GLY643 3.8 41.5 1.0 HA2 B:GLY643 3.9 41.0 1.0 HA2 C:GLY643 4.0 40.5 1.0 HG2 B:MET644 4.2 41.0 1.0 O B:ILE642 4.3 41.2 1.0 HA2 D:GLY643 4.3 41.5 1.0 HA D:MET644 4.3 42.6 1.0 O D:ILE642 4.4 41.2 1.0 N B:MET644 4.4 41.0 1.0 HA B:MET644 4.4 41.0 1.0 N D:MET644 4.5 42.6 1.0 O A:ILE642 4.5 41.1 1.0 O C:ILE642 4.5 40.9 1.0 N A:MET644 4.6 41.5 1.0 SD C:MET644 4.6 41.4 1.0 HB2 D:MET644 4.7 42.6 1.0 N B:GLY643 4.7 41.0 1.0 N A:GLY643 4.7 40.9 1.0 N C:MET644 4.7 41.4 1.0 HA C:MET644 4.8 41.4 1.0 HA A:MET644 4.8 41.5 1.0 CA D:MET644 4.9 42.6 1.0 N C:GLY643 4.9 40.5 1.0 C B:ILE642 5.0 41.2 1.0 CA B:MET644 5.0 41.0 1.0 N D:GLY643 5.0 41.5 1.0 SD A:MET644 5.0 41.5 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