Sodium in PDB 8gz1: Cryo-Em Structure of Human NAV1.6/BETA1/BETA2,Apo State

The binding sites of Sodium atom in the Cryo-Em Structure of Human NAV1.6/BETA1/BETA2,Apo State (pdb code 8gz1). 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 Human NAV1.6/BETA1/BETA2,Apo State, PDB code: 8gz1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cryo-Em Structure of Human NAV1.6/BETA1/BETA2,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 Human NAV1.6/BETA1/BETA2,Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2002 b:38.4 occ:1.00 OE2 B:GLU939 4.0 38.7 1.0 CG B:MET1416 4.3 42.9 1.0 NA B:NA2003 4.4 40.3 1.0 OE2 B:GLU373 4.6 40.1 1.0 O B:PHE1412 4.7 33.9 1.0 OE2 B:GLU936 4.8 40.0 1.0 CD1 B:TYR371 4.8 34.7 1.0 OD2 B:ASP1708 4.8 37.3 1.0 NE1 B:TRP1415 4.8 38.0 1.0 N B:GLY1414 4.9 38.0 1.0 CG B:GLU936 5.0 40.0 1.0

Sodium binding site 2 out of 2 in the Cryo-Em Structure of Human NAV1.6/BETA1/BETA2,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 Human NAV1.6/BETA1/BETA2,Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2003 b:40.3 occ:1.00 OE1 B:GLU373 2.5 40.1 1.0 OE2 B:GLU373 2.6 40.1 1.0 CD B:GLU373 2.9 40.1 1.0 CA B:TYR371 3.5 34.7 1.0 CE B:LYS1413 3.6 34.9 1.0 N B:TYR371 3.7 34.7 1.0 CD1 B:TYR371 4.0 34.7 1.0 N B:GLY1706 4.3 36.0 1.0 CG B:GLU373 4.3 40.1 1.0 CG B:LYS1413 4.4 34.9 1.0 NA B:NA2002 4.4 38.4 1.0 C B:TYR371 4.4 34.7 1.0 CB B:TYR371 4.4 34.7 1.0 OE2 B:GLU936 4.4 40.0 1.0 N B:TRP372 4.6 35.6 1.0 CD B:LYS1413 4.6 34.9 1.0 NZ B:LYS1413 4.7 34.9 1.0 CG B:TYR371 4.7 34.7 1.0 CB B:ALA1705 4.7 36.0 1.0 CA B:ALA1705 4.7 36.0 1.0 O B:GLN369 4.9 40.9 1.0 CE1 B:TYR371 4.9 34.7 1.0 C B:ALA1705 4.9 36.0 1.0 C B:ASP370 5.0 38.1 1.0

Y.Li, T.Yuan, B.Huang, F.Zhou, C.Peng, X.Li, Y.Qiu, B.Yang, Y.Zhao, Z.Huang, D.Jiang. Structure of Human Na V 1.6 Channel Reveals Na + Selectivity and Pore Blockade By 4,9-Anhydro-Tetrodotoxin. Nat Commun V. 14 1030 2023.
ISSN: ESSN 2041-1723
PubMed: 36823201
DOI: 10.1038/S41467-023-36766-9