Sodium in PDB 7mzc: Cryo-Em Structure of Minimal TRPV1 with Rtx Bound in C1 State

The binding sites of Sodium atom in the Cryo-Em Structure of Minimal TRPV1 with Rtx Bound in C1 State (pdb code 7mzc). 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 Minimal TRPV1 with Rtx Bound in C1 State, PDB code: 7mzc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cryo-Em Structure of Minimal TRPV1 with Rtx Bound in C1 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 Minimal TRPV1 with Rtx Bound in C1 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:44.5 occ:1.00 O B:GLY643 2.3 54.9 1.0 O C:GLY643 2.3 54.3 1.0 O D:GLY643 2.4 54.5 1.0 O A:GLY643 2.4 54.5 1.0 C B:GLY643 3.4 54.9 1.0 C C:GLY643 3.4 54.3 1.0 C D:GLY643 3.5 54.5 1.0 C A:GLY643 3.5 54.5 1.0 NA A:NA903 3.5 45.9 1.0 CA C:GLY643 3.9 54.3 1.0 CA B:GLY643 3.9 54.9 1.0 CA A:GLY643 3.9 54.5 1.0 CA D:GLY643 4.0 54.5 1.0 SD A:MET644 4.6 55.8 1.0 N B:MET644 4.6 55.8 1.0 N C:MET644 4.6 55.3 1.0 SD C:MET644 4.6 55.3 1.0 SD D:MET644 4.6 55.6 1.0 SD B:MET644 4.6 55.8 1.0 N D:MET644 4.6 55.6 1.0 N A:MET644 4.6 55.8 1.0 O A:ILE642 4.7 55.2 1.0 O B:ILE642 4.7 54.9 1.0 O C:ILE642 4.7 54.7 1.0 O D:ILE642 4.7 55.0 1.0 CG B:MET644 4.9 55.8 1.0 CG C:MET644 4.9 55.3 1.0 CG D:MET644 4.9 55.6 1.0 CG A:MET644 4.9 55.8 1.0 CA B:MET644 5.0 55.8 1.0 CA C:MET644 5.0 55.3 1.0

Sodium binding site 2 out of 2 in the Cryo-Em Structure of Minimal TRPV1 with Rtx Bound in C1 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 Minimal TRPV1 with Rtx Bound in C1 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na903 b:45.9 occ:1.00 NA A:NA902 3.5 44.5 1.0 CA B:GLY643 4.0 54.9 1.0 CA A:GLY643 4.0 54.5 1.0 CA D:GLY643 4.0 54.5 1.0 CA C:GLY643 4.0 54.3 1.0 OH D:TYR671 4.2 61.2 1.0 OH A:TYR671 4.2 60.9 1.0 OH B:TYR671 4.3 61.3 1.0 OH C:TYR671 4.3 60.8 1.0 O B:GLY643 4.5 54.9 1.0 O D:GLY643 4.5 54.5 1.0 O C:GLY643 4.5 54.3 1.0 O A:GLY643 4.6 54.5 1.0 O A:ILE642 4.7 55.2 1.0 O B:ILE642 4.8 54.9 1.0 C B:GLY643 4.8 54.9 1.0 N A:GLY643 4.8 54.5 1.0 C D:GLY643 4.8 54.5 1.0 O C:ILE642 4.8 54.7 1.0 O D:ILE642 4.8 55.0 1.0 N B:GLY643 4.8 54.9 1.0 C C:GLY643 4.8 54.3 1.0 C A:GLY643 4.8 54.5 1.0 N D:GLY643 4.9 54.5 1.0 N C:GLY643 4.9 54.3 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