Sodium in PDB 8t1b: Cryo-Em Structure of Full-Length Human TRPV4 in Apo State

The binding sites of Sodium atom in the Cryo-Em Structure of Full-Length Human TRPV4 in Apo State (pdb code 8t1b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Cryo-Em Structure of Full-Length Human TRPV4 in Apo State, PDB code: 8t1b:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Cryo-Em Structure of Full-Length Human TRPV4 in Apo 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 Full-Length Human TRPV4 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1214 b:27.7 occ:1.00 NA A:NA1215 3.6 28.9 1.0 CA D:GLY679 4.7 47.2 1.0 CA C:GLY679 4.7 46.7 1.0 O D:ILE678 4.7 45.4 1.0 O C:ILE678 4.7 45.1 1.0 O C:GLY679 4.7 46.7 1.0 O D:GLY679 4.7 47.2 1.0 O B:ILE678 4.7 45.7 1.0 CA B:GLY679 4.7 47.3 1.0 O A:ILE678 4.7 30.1 1.0 CA A:GLY679 4.8 30.8 1.0 O B:GLY679 4.8 47.3 1.0 O A:GLY679 4.8 30.8 1.0 C C:GLY679 4.9 46.7 1.0 C D:GLY679 4.9 47.2 1.0 C B:GLY679 4.9 47.3 1.0 C A:GLY679 5.0 30.8 1.0

Sodium binding site 2 out of 4 in the Cryo-Em Structure of Full-Length Human TRPV4 in Apo 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 Full-Length Human TRPV4 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1215 b:28.9 occ:1.00 O D:GLY679 3.3 47.2 1.0 O C:GLY679 3.3 46.7 1.0 O B:GLY679 3.3 47.3 1.0 O A:GLY679 3.4 30.8 1.0 NA A:NA1214 3.6 27.7 1.0 O D:HOH1311 4.0 100.1 1.0 O A:HOH1311 4.0 76.7 1.0 O B:HOH1311 4.0 119.3 1.0 O C:HOH1311 4.0 113.2 1.0 C D:GLY679 4.1 47.2 1.0 C C:GLY679 4.1 46.7 1.0 C B:GLY679 4.2 47.3 1.0 C A:GLY679 4.2 30.8 1.0 CA D:MET680 4.6 49.2 1.0 CA C:MET680 4.6 48.9 1.0 CA A:MET680 4.7 32.8 1.0 CA B:MET680 4.7 49.6 1.0 N D:MET680 4.7 49.2 1.0 N C:MET680 4.7 48.9 1.0 N B:MET680 4.8 49.6 1.0 N A:MET680 4.8 32.8 1.0 CA D:GLY679 5.0 47.2 1.0 CA C:GLY679 5.0 46.7 1.0 CA B:GLY679 5.0 47.3 1.0

Sodium binding site 3 out of 4 in the Cryo-Em Structure of Full-Length Human TRPV4 in Apo 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 Full-Length Human TRPV4 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1216 b:30.3 occ:1.00 CG2 A:ILE715 4.5 21.4 1.0 CG2 C:ILE715 4.5 34.4 1.0 CG2 D:ILE715 4.5 34.6 1.0 CG2 B:ILE715 4.6 34.9 1.0 O A:ILE715 4.7 21.4 1.0 O D:ILE715 4.8 34.6 1.0 O C:ILE715 4.8 34.4 1.0 O B:ILE715 4.8 34.9 1.0

Sodium binding site 4 out of 4 in the Cryo-Em Structure of Full-Length Human TRPV4 in Apo State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cryo-Em Structure of Full-Length Human TRPV4 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1217 b:98.2 occ:1.00 O D:HOH1310 2.5 102.8 1.0 O A:HOH1310 2.5 78.2 1.0 O C:HOH1308 2.5 116.5 1.0 O B:HOH1310 2.5 114.3 1.0 O B:HOH1311 3.1 119.3 1.0 O C:HOH1311 3.2 113.2 1.0 O A:HOH1311 3.2 76.7 1.0 O D:HOH1311 3.2 100.1 1.0 OD1 B:ASP682 4.1 55.1 1.0 OD1 C:ASP682 4.2 54.5 1.0 OD1 D:ASP682 4.2 54.5 1.0 OD1 A:ASP682 4.4 38.2 1.0 OD2 B:ASP682 4.5 55.1 1.0 OD2 C:ASP682 4.5 54.5 1.0 OD2 D:ASP682 4.6 54.5 1.0 OD2 A:ASP682 4.7 38.2 1.0 CG B:ASP682 4.8 55.1 1.0 CG C:ASP682 4.8 54.5 1.0 CG D:ASP682 4.9 54.5 1.0 CG A:ASP682 5.0 38.2 1.0

K.D.Nadezhdin, I.A.Talyzina, A.Parthasarathy, A.Neuberger, D.X.Zhang, A.I.Sobolevsky. Structure of Human TRPV4 in Complex with Gtpase Rhoa. Nat Commun V. 14 3733 2023.
ISSN: ESSN 2041-1723
PubMed: 37353478
DOI: 10.1038/S41467-023-39346-Z