Sodium in PDB 8gi9: Cation Channelrhodopsin From Hyphochytrium Catenoides (Hcccr) Embedded in Peptidisc

The binding sites of Sodium atom in the Cation Channelrhodopsin From Hyphochytrium Catenoides (Hcccr) Embedded in Peptidisc (pdb code 8gi9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Cation Channelrhodopsin From Hyphochytrium Catenoides (Hcccr) Embedded in Peptidisc, PDB code: 8gi9:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Cation Channelrhodopsin From Hyphochytrium Catenoides (Hcccr) Embedded in Peptidisc


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cation Channelrhodopsin From Hyphochytrium Catenoides (Hcccr) Embedded in Peptidisc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:69.4 occ:1.00 CB A:SER166 3.4 44.2 1.0 O A:PHE195 3.5 52.6 1.0 CD1 A:PHE196 3.7 46.9 1.0 CZ A:PHE162 3.8 38.6 1.0 CB A:TRP199 3.9 45.2 1.0 CA A:SER166 4.1 43.0 1.0 CD A:PRO200 4.2 39.9 1.0 CE1 A:PHE162 4.2 41.9 1.0 CA A:PHE196 4.2 48.5 1.0 CE1 A:PHE196 4.3 50.1 1.0 CD1 A:PHE195 4.3 45.5 1.0 CE1 A:PHE195 4.4 45.7 1.0 C A:PHE195 4.5 44.1 1.0 OG A:SER166 4.5 52.0 1.0 CG A:TRP199 4.6 49.3 1.0 CE2 A:PHE162 4.6 37.6 1.0 CG A:PHE196 4.7 49.6 1.0 CE2 A:PHE165 4.7 39.6 1.0 N A:PHE196 4.8 50.2 1.0 CE3 A:TRP199 4.8 45.9 1.0 N A:PRO200 4.8 45.7 1.0 CB A:PHE196 4.9 46.0 1.0 CD2 A:TRP199 4.9 49.6 1.0 CG A:PRO200 5.0 30.4 1.0

Sodium binding site 2 out of 3 in the Cation Channelrhodopsin From Hyphochytrium Catenoides (Hcccr) Embedded in Peptidisc


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cation Channelrhodopsin From Hyphochytrium Catenoides (Hcccr) Embedded in Peptidisc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:52.7 occ:1.00 CG1 A:VAL117 3.6 47.8 1.0 CB A:PHE195 3.7 42.1 1.0 CG A:PHE195 3.9 45.8 1.0 CG2 A:VAL117 3.9 45.7 1.0 CE2 A:PHE196 4.0 49.1 1.0 SG A:CYS192 4.0 75.5 1.0 O A:ALA191 4.0 57.9 1.0 CA A:CYS192 4.1 51.9 1.0 N A:CYS192 4.2 55.5 1.0 C A:ALA191 4.2 53.5 1.0 CD2 A:PHE195 4.3 49.7 1.0 CB A:VAL117 4.4 45.5 1.0 CD1 A:PHE195 4.4 45.5 1.0 CE1 A:PHE236 4.4 49.5 1.0 CZ A:PHE236 4.4 50.8 1.0 CZ A:PHE196 4.6 49.4 1.0 CD2 A:PHE196 4.6 53.3 1.0 CG2 A:VAL173 4.6 47.8 1.0 CB A:ALA191 4.6 55.8 1.0 CB A:CYS192 4.7 52.4 1.0 CD1 A:LEU121 4.8 53.9 1.0 CG1 A:VAL173 4.9 57.8 1.0 CD1 A:LEU188 5.0 61.9 1.0

Sodium binding site 3 out of 3 in the Cation Channelrhodopsin From Hyphochytrium Catenoides (Hcccr) Embedded in Peptidisc


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cation Channelrhodopsin From Hyphochytrium Catenoides (Hcccr) Embedded in Peptidisc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:54.7 occ:1.00 C25 A:PEE312 3.5 72.6 1.0 CE2 A:PHE131 3.7 47.7 1.0 CD2 A:PHE131 3.8 47.9 1.0 C42 A:PEE313 3.9 71.0 1.0 C43 A:PEE313 4.2 73.8 1.0 C26 A:PEE312 4.3 71.5 1.0 CG1 A:ILE135 4.3 42.7 1.0 CG2 A:ILE134 4.6 38.4 1.0 C41 A:PEE313 4.6 69.0 1.0 CD1 A:ILE135 4.7 46.2 1.0 C24 A:PEE312 4.7 69.8 1.0 C23 A:PEE312 4.8 67.5 1.0 CZ A:PHE131 4.8 49.9 1.0 CG A:PHE131 4.9 51.6 1.0

T.Morizumi, K.Kim, H.Li, E.G.Govorunova, O.A.Sineshchekov, Y.Wang, L.Zheng, E.Bertalan, A.N.Bondar, A.Askari, L.S.Brown, J.L.Spudich, O.P.Ernst. Structures of Channelrhodopsin Paralogs in Peptidiscs Explain Their Contrasting K+ and Na+ Selectivities Nat Commun V. 14 4365 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-40041-2