Sodium in PDB 7rqx: Cryo-Em Structure of the Full-Length TRPV1 with Rtx at 25 Degrees Celsius, in An Intermediate-Open State, Class A

The binding sites of Sodium atom in the Cryo-Em Structure of the Full-Length TRPV1 with Rtx at 25 Degrees Celsius, in An Intermediate-Open State, Class A (pdb code 7rqx). 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 25 Degrees Celsius, in An Intermediate-Open State, Class A, PDB code: 7rqx:
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 25 Degrees Celsius, in An Intermediate-Open State, Class A


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 25 Degrees Celsius, in An Intermediate-Open State, Class A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na907 b:3.9 occ:1.00 O D:GLY643 2.5 9.5 1.0 O C:GLY643 2.6 9.5 1.0 O A:GLY643 3.1 9.5 1.0 O B:GLY643 3.2 9.5 1.0 C D:GLY643 3.7 9.5 1.0 HA D:MET644 3.8 12.7 1.0 C C:GLY643 3.8 9.5 1.0 HA C:MET644 3.9 12.7 1.0 HB3 D:MET644 3.9 12.7 1.0 C A:GLY643 4.3 9.5 1.0 HB3 C:MET644 4.3 12.7 1.0 HA A:MET644 4.3 12.7 1.0 HB3 A:MET644 4.3 12.7 1.0 HA B:MET644 4.4 12.7 1.0 HA3 D:GLY643 4.4 9.5 1.0 C B:GLY643 4.4 9.5 1.0 CA D:MET644 4.4 12.7 1.0 HA3 C:GLY643 4.5 9.5 1.0 N D:MET644 4.5 12.7 1.0 CB D:MET644 4.6 12.7 1.0 CA C:MET644 4.6 12.7 1.0 HB3 B:MET644 4.6 12.7 1.0 CA D:GLY643 4.7 9.5 1.0 N C:MET644 4.7 12.7 1.0 CA C:GLY643 4.8 9.5 1.0 HB2 D:MET644 4.8 12.7 1.0 HA3 A:GLY643 4.8 9.5 1.0 CB C:MET644 4.9 12.7 1.0 CA A:MET644 5.0 12.7 1.0 HA3 B:GLY643 5.0 9.5 1.0 CB A:MET644 5.0 12.7 1.0

Sodium binding site 2 out of 2 in the Cryo-Em Structure of the Full-Length TRPV1 with Rtx at 25 Degrees Celsius, in An Intermediate-Open State, Class A


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 25 Degrees Celsius, in An Intermediate-Open State, Class A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na908 b:23.1 occ:1.00 OH D:TYR671 3.5 8.2 1.0 HH D:TYR671 3.6 8.2 1.0 OH A:TYR671 3.6 8.2 1.0 HH A:TYR671 3.8 8.2 1.0 OH C:TYR671 3.8 8.2 1.0 HH C:TYR671 3.8 8.2 1.0 OH B:TYR671 3.9 8.2 1.0 HH B:TYR671 4.0 8.2 1.0 CZ D:TYR671 4.8 8.2 1.0 CZ A:TYR671 4.8 8.2 1.0 HA3 A:GLY643 4.9 9.5 1.0 HE2 A:TYR671 4.9 8.2 1.0 HE2 D:TYR671 4.9 8.2 1.0 HA3 D:GLY643 5.0 9.5 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