Sodium in PDB 7rqv: Cryo-Em Structure of the Full-Length TRPV1 with Rtx at 4 Degrees Celsius, in An Intermediate-Closed State, Class II

The binding sites of Sodium atom in the Cryo-Em Structure of the Full-Length TRPV1 with Rtx at 4 Degrees Celsius, in An Intermediate-Closed State, Class II (pdb code 7rqv). 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 An Intermediate-Closed State, Class II, PDB code: 7rqv:
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 An Intermediate-Closed State, Class II


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 An Intermediate-Closed State, Class II within 5.0Å range: probe atom residue distance (Å) B Occ A:Na907 b:30.1 occ:1.00 O B:GLY643 2.9 9.4 1.0 O C:GLY643 2.9 9.4 1.0 O D:GLY643 2.9 9.4 1.0 O A:GLY643 3.0 9.4 1.0 C B:GLY643 4.1 9.4 1.0 C C:GLY643 4.1 9.4 1.0 C D:GLY643 4.1 9.4 1.0 C A:GLY643 4.2 9.4 1.0 HA C:MET644 4.4 12.3 1.0 HA B:MET644 4.4 12.3 1.0 NA A:NA908 4.4 30.1 1.0 HA3 B:GLY643 4.4 9.4 1.0 HA D:MET644 4.5 12.3 1.0 HA3 D:GLY643 4.5 9.4 1.0 HA3 C:GLY643 4.5 9.4 1.0 HA A:MET644 4.5 12.3 1.0 HA3 A:GLY643 4.5 9.4 1.0 SD C:MET644 4.8 12.3 1.0 SD B:MET644 4.9 12.3 1.0 SD D:MET644 4.9 12.3 1.0 CA B:GLY643 4.9 9.4 1.0 SD A:MET644 4.9 12.3 1.0 CA C:GLY643 4.9 9.4 1.0 CA D:GLY643 4.9 9.4 1.0 CA A:GLY643 5.0 9.4 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 An Intermediate-Closed State, Class II


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 An Intermediate-Closed State, Class II within 5.0Å range: probe atom residue distance (Å) B Occ A:Na908 b:30.1 occ:1.00 OH B:TYR671 4.0 11.5 1.0 OH D:TYR671 4.0 11.5 1.0 OH C:TYR671 4.0 11.5 1.0 OH A:TYR671 4.0 11.5 1.0 HH B:TYR671 4.2 11.5 1.0 HH D:TYR671 4.2 11.5 1.0 HH C:TYR671 4.2 11.5 1.0 HH A:TYR671 4.2 11.5 1.0 HA3 C:GLY643 4.3 9.4 1.0 HA3 B:GLY643 4.3 9.4 1.0 HA3 D:GLY643 4.3 9.4 1.0 HA3 A:GLY643 4.3 9.4 1.0 NA A:NA907 4.4 30.1 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