Sodium in PDB 7mzd: Cryo-Em Structure of Minimal TRPV1 with Rtx Bound in C2 State

The binding sites of Sodium atom in the Cryo-Em Structure of Minimal TRPV1 with Rtx Bound in C2 State (pdb code 7mzd). 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 C2 State, PDB code: 7mzd:
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 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 Minimal TRPV1 with Rtx Bound in C2 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:31.2 occ:1.00 O A:GLY643 2.3 45.1 1.0 O B:GLY643 2.3 45.6 1.0 O C:GLY643 2.3 45.4 1.0 O D:GLY643 2.3 45.8 1.0 C B:GLY643 3.4 45.6 1.0 C C:GLY643 3.4 45.4 1.0 C D:GLY643 3.4 45.8 1.0 C A:GLY643 3.4 45.1 1.0 NA A:NA903 3.7 35.0 1.0 CA B:GLY643 3.9 45.6 1.0 CA D:GLY643 4.0 45.8 1.0 CA C:GLY643 4.0 45.4 1.0 CA A:GLY643 4.0 45.1 1.0 SD C:MET644 4.5 45.5 1.0 SD A:MET644 4.5 45.7 1.0 SD D:MET644 4.5 45.5 1.0 SD B:MET644 4.5 46.2 1.0 N B:MET644 4.6 46.2 1.0 N C:MET644 4.6 45.5 1.0 N D:MET644 4.6 45.5 1.0 N A:MET644 4.6 45.7 1.0 O A:ILE642 4.8 47.4 1.0 CG C:MET644 4.8 45.5 1.0 CG D:MET644 4.8 45.5 1.0 CG A:MET644 4.8 45.7 1.0 O D:ILE642 4.8 47.8 1.0 CG B:MET644 4.8 46.2 1.0 O C:ILE642 4.8 47.7 1.0 O B:ILE642 4.8 48.0 1.0 CA B:MET644 4.9 46.2 1.0 CA C:MET644 4.9 45.5 1.0 CA D:MET644 4.9 45.5 1.0 CA A:MET644 4.9 45.7 1.0

Sodium binding site 2 out of 2 in the Cryo-Em Structure of Minimal TRPV1 with Rtx Bound 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 Minimal TRPV1 with Rtx Bound in C2 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na903 b:35.0 occ:1.00 NA A:NA902 3.7 31.2 1.0 CA B:GLY643 4.0 45.6 1.0 CA A:GLY643 4.0 45.1 1.0 CA C:GLY643 4.0 45.4 1.0 CA D:GLY643 4.0 45.8 1.0 O B:HOH1001 4.3 51.4 1.0 O A:HOH1001 4.3 52.2 1.0 O D:HOH1001 4.3 50.8 1.0 O C:HOH1001 4.4 51.5 1.0 O A:GLY643 4.6 45.1 1.0 O B:GLY643 4.6 45.6 1.0 O C:GLY643 4.6 45.4 1.0 O D:GLY643 4.6 45.8 1.0 O B:ILE642 4.8 48.0 1.0 N A:GLY643 4.8 45.1 1.0 O C:ILE642 4.8 47.7 1.0 O D:ILE642 4.8 47.8 1.0 N B:GLY643 4.8 45.6 1.0 O A:ILE642 4.8 47.4 1.0 C B:GLY643 4.8 45.6 1.0 N C:GLY643 4.8 45.4 1.0 C A:GLY643 4.8 45.1 1.0 C C:GLY643 4.8 45.4 1.0 N D:GLY643 4.8 45.8 1.0 C D:GLY643 4.8 45.8 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