Sodium in PDB 7lp9: Cryo-Em Structure of Full-Length TRPV1 at 4 Degrees Celsius

The binding sites of Sodium atom in the Cryo-Em Structure of Full-Length TRPV1 at 4 Degrees Celsius (pdb code 7lp9). 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 Full-Length TRPV1 at 4 Degrees Celsius, PDB code: 7lp9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cryo-Em Structure of Full-Length TRPV1 at 4 Degrees Celsius


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 Full-Length TRPV1 at 4 Degrees Celsius within 5.0Å range: probe atom residue distance (Å) B Occ A:Na911 b:48.6 occ:1.00 O A:GLY643 2.4 63.8 1.0 O C:GLY643 2.4 63.7 1.0 O B:GLY643 2.4 63.7 1.0 O D:GLY643 2.4 63.9 1.0 C A:GLY643 3.5 63.8 1.0 C C:GLY643 3.5 63.7 1.0 C B:GLY643 3.5 63.7 1.0 C D:GLY643 3.5 63.9 1.0 NA A:NA912 4.1 58.7 1.0 CA D:GLY643 4.1 63.9 1.0 CA C:GLY643 4.1 63.7 1.0 CA A:GLY643 4.1 63.8 1.0 CA B:GLY643 4.1 63.7 1.0 SD C:MET644 4.4 64.3 1.0 SD A:MET644 4.4 64.2 1.0 SD B:MET644 4.4 64.3 1.0 SD D:MET644 4.4 64.4 1.0 N C:MET644 4.6 64.3 1.0 N B:MET644 4.6 64.3 1.0 N A:MET644 4.6 64.2 1.0 N D:MET644 4.6 64.4 1.0 CG C:MET644 4.7 64.3 1.0 CG A:MET644 4.7 64.2 1.0 CG B:MET644 4.8 64.3 1.0 CG D:MET644 4.8 64.4 1.0 CA B:MET644 4.9 64.3 1.0 CA C:MET644 4.9 64.3 1.0 CA A:MET644 4.9 64.2 1.0 CA D:MET644 4.9 64.4 1.0

Sodium binding site 2 out of 2 in the Cryo-Em Structure of Full-Length TRPV1 at 4 Degrees Celsius


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 Full-Length TRPV1 at 4 Degrees Celsius within 5.0Å range: probe atom residue distance (Å) B Occ A:Na912 b:58.7 occ:1.00 NA A:NA911 4.1 48.6 1.0 CA C:GLY643 4.2 63.7 1.0 CA D:GLY643 4.2 63.9 1.0 CA A:GLY643 4.2 63.8 1.0 CA B:GLY643 4.2 63.7 1.0 OH C:TYR671 4.3 66.6 1.0 OH B:TYR671 4.3 66.4 1.0 OH A:TYR671 4.3 66.3 1.0 OH D:TYR671 4.3 66.2 1.0 O A:GLY643 4.8 63.8 1.0 O C:GLY643 4.8 63.7 1.0 O B:GLY643 4.8 63.7 1.0 O D:GLY643 4.8 63.9 1.0

D.H.Kwon, F.Zhang, Y.Suo, J.Bouvette, M.J.Borgnia, S.Y.Lee. Heat-Dependent Opening of TRPV1 in the Presence of Capsaicin. Nat.Struct.Mol.Biol. V. 28 554 2021.
ISSN: ESSN 1545-9985
PubMed: 34239123
DOI: 10.1038/S41594-021-00616-3