Sodium in PDB 8t3m: TRPV1 in Nanodisc Bound with 3 Lpa Molecules

The binding sites of Sodium atom in the TRPV1 in Nanodisc Bound with 3 Lpa Molecules (pdb code 8t3m). 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 3 Lpa Molecules, PDB code: 8t3m:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the TRPV1 in Nanodisc Bound with 3 Lpa Molecules


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 3 Lpa Molecules within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:33.9 occ:1.00 O A:GLY643 2.3 38.4 1.0 O C:GLY643 2.3 39.7 1.0 O D:GLY643 2.3 37.5 1.0 O B:GLY643 2.4 38.3 1.0 C A:GLY643 3.5 38.4 1.0 C C:GLY643 3.5 39.7 1.0 C D:GLY643 3.6 37.5 1.0 C B:GLY643 3.6 38.3 1.0 HA3 A:GLY643 3.8 38.4 1.0 HA D:MET644 3.9 39.3 1.0 HA3 C:GLY643 3.9 39.7 1.0 HA3 B:GLY643 3.9 38.3 1.0 HA A:MET644 4.0 38.8 1.0 HA C:MET644 4.0 41.7 1.0 HA3 D:GLY643 4.0 37.5 1.0 HA B:MET644 4.0 38.5 1.0 CA A:GLY643 4.2 38.4 1.0 CA C:GLY643 4.3 39.7 1.0 CA B:GLY643 4.3 38.3 1.0 CA D:GLY643 4.4 37.5 1.0 N A:MET644 4.5 38.8 1.0 N D:MET644 4.5 39.3 1.0 N C:MET644 4.5 41.7 1.0 HA2 A:GLY643 4.6 38.4 1.0 N B:MET644 4.6 38.5 1.0 CA D:MET644 4.6 39.3 1.0 NA A:NA803 4.6 26.7 1.0 HA2 C:GLY643 4.6 39.7 1.0 HB2 D:MET644 4.7 39.3 1.0 CA A:MET644 4.7 38.8 1.0 HA2 B:GLY643 4.7 38.3 1.0 CA C:MET644 4.7 41.7 1.0 SD C:MET644 4.7 41.7 1.0 CA B:MET644 4.7 38.5 1.0 SD D:MET644 4.7 39.3 1.0 SD A:MET644 4.8 38.8 1.0 SD B:MET644 4.8 38.5 1.0 HB2 B:MET644 4.8 38.5 1.0 HA2 D:GLY643 4.9 37.5 1.0 O D:ILE642 4.9 37.4 1.0 HB2 C:MET644 5.0 41.7 1.0

Sodium binding site 2 out of 2 in the TRPV1 in Nanodisc Bound with 3 Lpa Molecules


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 3 Lpa Molecules within 5.0Å range: probe atom residue distance (Å) B Occ A:Na803 b:26.7 occ:1.00 HA3 A:GLY643 2.9 38.4 1.0 HA3 D:GLY643 3.3 37.5 1.0 HA3 B:GLY643 3.5 38.3 1.0 HA3 C:GLY643 3.7 39.7 1.0 CA A:GLY643 3.8 38.4 1.0 HA2 A:GLY643 4.0 38.4 1.0 CA D:GLY643 4.2 37.5 1.0 HA2 D:GLY643 4.3 37.5 1.0 CA B:GLY643 4.4 38.3 1.0 N A:GLY643 4.6 38.4 1.0 NA A:NA802 4.6 33.9 1.0 CA C:GLY643 4.6 39.7 1.0 HA2 B:GLY643 4.6 38.3 1.0 O A:GLY643 4.7 38.4 1.0 O D:GLY643 4.7 37.5 1.0 HH A:TYR671 4.7 36.2 1.0 O A:ILE642 4.7 36.5 1.0 HA2 C:GLY643 4.7 39.7 1.0 C A:GLY643 4.8 38.4 1.0 C A:ILE642 4.9 36.5 1.0 O B:GLY643 5.0 38.3 1.0 C D:GLY643 5.0 37.5 1.0 H A:GLY643 5.0 38.4 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