Sodium in PDB 7mz5: Cryo-Em Structure of Rtx-Bound Full-Length TRPV1 in C2 State

The binding sites of Sodium atom in the Cryo-Em Structure of Rtx-Bound Full-Length TRPV1 in C2 State (pdb code 7mz5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Cryo-Em Structure of Rtx-Bound Full-Length TRPV1 in C2 State, PDB code: 7mz5:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Cryo-Em Structure of Rtx-Bound Full-Length TRPV1 in C2 State


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 Rtx-Bound Full-Length TRPV1 in C2 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:26.8 occ:1.00 CA C:GLY643 4.1 31.1 1.0 CA B:GLY643 4.1 31.3 1.0 CA D:GLY643 4.1 30.8 1.0 CA A:GLY643 4.1 30.7 1.0 N C:GLY643 4.8 31.1 1.0 N A:GLY643 4.8 30.7 1.0 N B:GLY643 4.8 31.3 1.0 N D:GLY643 4.8 30.8 1.0 O D:ILE642 4.9 32.7 1.0 O C:ILE642 4.9 32.6 1.0 O B:ILE642 4.9 32.6 1.0 O A:ILE642 4.9 32.4 1.0 O B:GLY643 5.0 31.3 1.0 O C:GLY643 5.0 31.1 1.0 O D:GLY643 5.0 30.8 1.0 O A:GLY643 5.0 30.7 1.0

Sodium binding site 2 out of 3 in the Cryo-Em Structure of Rtx-Bound Full-Length TRPV1 in C2 State


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 Rtx-Bound Full-Length TRPV1 in C2 State within 5.0Å range:

Sodium binding site 3 out of 3 in the Cryo-Em Structure of Rtx-Bound Full-Length TRPV1 in C2 State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cryo-Em Structure of Rtx-Bound Full-Length TRPV1 in C2 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na904 b:53.8 occ:1.00 SD A:MET682 3.1 60.4 1.0 SD B:MET682 3.1 60.7 1.0 SD D:MET682 3.1 60.2 1.0 SD C:MET682 3.2 60.4 1.0 CG A:MET682 3.9 60.4 1.0 CG B:MET682 3.9 60.7 1.0 CG C:MET682 3.9 60.4 1.0 CG D:MET682 4.0 60.2 1.0 CB A:MET682 4.2 60.4 1.0 CB C:MET682 4.2 60.4 1.0 CB D:MET682 4.2 60.2 1.0 CB B:MET682 4.2 60.7 1.0 CE B:MET682 4.7 60.7 1.0 CE A:MET682 4.7 60.4 1.0 CE D:MET682 4.7 60.2 1.0 CE C:MET682 4.8 60.4 1.0

K.Zhang, D.Julius, Y.Cheng. Structural Snapshots of TRPV1 Reveal Mechanism of Polymodal Functionality. Cell 2021.
ISSN: ISSN 1097-4172
PubMed: 34496225
DOI: 10.1016/J.CELL.2021.08.012