Sodium in PDB 7rqu: Cryo-Em Structure of the Full-Length TRPV1 with Rtx at 4 Degrees Celsius, in A Closed State, Class I

The binding sites of Sodium atom in the Cryo-Em Structure of the Full-Length TRPV1 with Rtx at 4 Degrees Celsius, in A Closed State, Class I (pdb code 7rqu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Cryo-Em Structure of the Full-Length TRPV1 with Rtx at 4 Degrees Celsius, in A Closed State, Class I, PDB code: 7rqu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cryo-Em Structure of the Full-Length TRPV1 with Rtx at 4 Degrees Celsius, in A Closed State, Class I


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryo-Em Structure of the Full-Length TRPV1 with Rtx at 4 Degrees Celsius, in A Closed State, Class I within 5.0Å range: probe atom residue distance (Å) B Occ A:Na910 b:31.8 occ:1.00 O B:GLY643 2.4 31.8 1.0 O C:GLY643 2.4 31.8 1.0 O D:GLY643 2.4 31.8 1.0 O A:GLY643 2.4 31.8 1.0 C B:GLY643 3.6 31.8 1.0 C C:GLY643 3.6 31.8 1.0 C A:GLY643 3.6 31.8 1.0 C D:GLY643 3.6 31.8 1.0 HA3 B:GLY643 3.9 31.8 1.0 HA3 A:GLY643 3.9 31.8 1.0 HA3 C:GLY643 3.9 31.8 1.0 HA3 D:GLY643 3.9 31.8 1.0 HG2 B:MET644 4.0 22.3 1.0 HG2 C:MET644 4.0 22.3 1.0 HG2 D:MET644 4.0 22.3 1.0 HG2 A:MET644 4.0 22.3 1.0 HA B:MET644 4.2 22.3 1.0 HA C:MET644 4.2 22.3 1.0 HA D:MET644 4.2 22.3 1.0 HA A:MET644 4.2 22.3 1.0 CA B:GLY643 4.3 31.8 1.0 CA A:GLY643 4.3 31.8 1.0 CA C:GLY643 4.3 31.8 1.0 CA D:GLY643 4.3 31.8 1.0 SD C:MET644 4.4 22.3 1.0 SD B:MET644 4.4 22.3 1.0 SD D:MET644 4.4 22.3 1.0 SD A:MET644 4.4 22.3 1.0 NA A:NA911 4.5 22.1 1.0 HA2 B:GLY643 4.6 31.8 1.0 HA2 A:GLY643 4.6 31.8 1.0 CG B:MET644 4.6 22.3 1.0 CG C:MET644 4.6 22.3 1.0 HA2 D:GLY643 4.6 31.8 1.0 HA2 C:GLY643 4.6 31.8 1.0 CG D:MET644 4.7 22.3 1.0 N B:MET644 4.7 22.3 1.0 CG A:MET644 4.7 22.3 1.0 N C:MET644 4.7 22.3 1.0 N D:MET644 4.7 22.3 1.0 N A:MET644 4.7 22.3 1.0 CA B:MET644 4.9 22.3 1.0 CA C:MET644 4.9 22.3 1.0 CA D:MET644 4.9 22.3 1.0 CA A:MET644 4.9 22.3 1.0

Sodium binding site 2 out of 2 in the Cryo-Em Structure of the Full-Length TRPV1 with Rtx at 4 Degrees Celsius, in A Closed State, Class I


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryo-Em Structure of the Full-Length TRPV1 with Rtx at 4 Degrees Celsius, in A Closed State, Class I within 5.0Å range: probe atom residue distance (Å) B Occ A:Na911 b:22.1 occ:1.00 HA3 B:GLY643 3.4 31.8 1.0 HA3 C:GLY643 3.4 31.8 1.0 HA3 D:GLY643 3.4 31.8 1.0 HA3 A:GLY643 3.4 31.8 1.0 OH B:TYR671 4.1 21.5 1.0 OH D:TYR671 4.1 21.5 1.0 OH C:TYR671 4.1 21.5 1.0 OH A:TYR671 4.1 21.5 1.0 HH B:TYR671 4.2 21.5 1.0 HH D:TYR671 4.2 21.5 1.0 HH A:TYR671 4.2 21.5 1.0 HH C:TYR671 4.2 21.5 1.0 CA B:GLY643 4.3 31.8 1.0 CA C:GLY643 4.3 31.8 1.0 CA D:GLY643 4.3 31.8 1.0 CA A:GLY643 4.3 31.8 1.0 HA2 B:GLY643 4.5 31.8 1.0 HA2 C:GLY643 4.5 31.8 1.0 HA2 D:GLY643 4.5 31.8 1.0 NA A:NA910 4.5 31.8 1.0 HA2 A:GLY643 4.5 31.8 1.0 O C:GLY643 4.9 31.8 1.0 O B:GLY643 4.9 31.8 1.0 O D:GLY643 4.9 31.8 1.0 O A:GLY643 4.9 31.8 1.0

D.H.Kwon, F.Zhang, J.G.Fedor, Y.Suo, S.Y.Lee. Vanilloid-Dependent TRPV1 Opening Trajectory From Cryoem Ensemble Analysis. Nat Commun V. 13 2874 2022.
ISSN: ESSN 2041-1723
PubMed: 35610228
DOI: 10.1038/S41467-022-30602-2