Sodium in PDB 7y6i: Cryo-Em Structure of Human Sodium-Chloride Cotransporter

The structure of Cryo-Em Structure of Human Sodium-Chloride Cotransporter also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Cryo-Em Structure of Human Sodium-Chloride Cotransporter (pdb code 7y6i). 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 Human Sodium-Chloride Cotransporter, PDB code: 7y6i:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Cryo-Em Structure of Human Sodium-Chloride Cotransporter


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 Sodium-Chloride Cotransporter within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:31.5 occ:1.00 O A:ILE150 2.8 41.3 1.0 O A:PRO349 2.8 19.9 1.0 O A:ASN149 2.9 39.9 1.0 CL A:CL1101 3.1 56.1 1.0 O A:THR352 3.2 31.3 1.0 C A:ILE150 3.5 28.5 1.0 CA A:ILE150 3.7 17.0 1.0 NE2 A:HIS234 3.8 28.4 1.0 C A:ASN149 3.9 33.3 1.0 C A:PRO349 4.0 21.4 1.0 OG1 A:THR352 4.1 29.7 1.0 C A:THR352 4.2 26.4 1.0 CE1 A:HIS234 4.3 34.5 1.0 O A:HOH1203 4.3 30.0 1.0 N A:ILE150 4.3 25.8 1.0 CA A:SER350 4.3 21.7 1.0 O A:SER350 4.4 28.9 1.0 C A:SER350 4.4 27.4 1.0 N A:TRP151 4.5 26.4 1.0 N A:GLY152 4.5 34.3 1.0 C A:TRP151 4.6 24.1 1.0 OG A:SER468 4.6 33.1 1.0 CA A:GLY152 4.6 28.2 1.0 N A:SER350 4.6 24.1 1.0 O A:TRP151 4.8 34.9 1.0 N A:THR352 4.8 27.4 1.0 O A:HOH1201 4.9 30.0 1.0

Sodium binding site 2 out of 4 in the Cryo-Em Structure of Human Sodium-Chloride Cotransporter


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 Sodium-Chloride Cotransporter within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1104 b:46.9 occ:1.00 O A:LEU148 2.2 34.7 1.0 O A:TRP151 2.3 34.9 1.0 OG A:SER467 2.3 26.8 1.0 O A:ALA464 2.3 44.8 1.0 OG A:SER468 2.4 33.1 1.0 C A:ALA464 3.1 30.8 1.0 CA A:ALA464 3.2 26.9 1.0 N A:SER468 3.3 29.9 1.0 C A:LEU148 3.4 24.9 1.0 C A:TRP151 3.5 24.1 1.0 CB A:SER468 3.5 30.2 1.0 CB A:SER467 3.7 21.3 1.0 CB A:ALA464 3.8 29.7 1.0 CA A:SER468 3.8 21.3 1.0 C A:SER467 4.1 35.9 1.0 CA A:LEU148 4.2 23.6 1.0 CA A:GLY152 4.3 28.2 1.0 N A:GLY152 4.3 34.3 1.0 CA A:SER467 4.3 30.0 1.0 N A:THR465 4.4 32.7 1.0 O A:GLY463 4.4 45.3 1.0 CA A:TRP151 4.4 22.2 1.0 N A:ASN149 4.5 25.2 1.0 CB A:TRP151 4.5 22.5 1.0 N A:ALA464 4.5 32.6 1.0 N A:SER467 4.6 32.9 1.0 CA A:ASN149 4.7 25.8 1.0 CD1 A:ILE293 4.7 40.1 1.0 N A:TRP151 4.7 26.4 1.0 CB A:LEU148 4.7 33.5 1.0 C A:ASN149 4.9 33.3 1.0 C A:GLY463 4.9 33.4 1.0 O A:ASN149 5.0 39.9 1.0 CA A:THR465 5.0 33.6 1.0

Sodium binding site 3 out of 4 in the Cryo-Em Structure of Human Sodium-Chloride Cotransporter


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 Human Sodium-Chloride Cotransporter within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1104 b:33.1 occ:1.00 O B:ILE150 2.7 36.1 1.0 O B:ASN149 2.7 39.3 1.0 O B:PRO349 2.9 21.5 1.0 CL B:CL1103 3.1 50.0 1.0 O B:THR352 3.3 29.5 1.0 C B:ILE150 3.3 27.4 1.0 CA B:ILE150 3.6 15.7 1.0 C B:ASN149 3.8 32.3 1.0 NE2 B:HIS234 3.9 25.8 1.0 C B:PRO349 4.1 23.8 1.0 OG1 B:THR352 4.1 33.9 1.0 N B:ILE150 4.2 24.2 1.0 C B:THR352 4.3 26.7 1.0 CE1 B:HIS234 4.3 31.6 1.0 N B:TRP151 4.4 24.0 1.0 O B:SER350 4.4 25.0 1.0 O B:HOH1203 4.4 44.5 1.0 C B:TRP151 4.5 27.5 1.0 CA B:SER350 4.5 14.0 1.0 C B:SER350 4.5 23.3 1.0 N B:GLY152 4.6 30.6 1.0 O B:TRP151 4.6 38.0 1.0 OG B:SER468 4.6 24.4 1.0 CA B:GLY152 4.7 23.6 1.0 N B:SER350 4.7 25.0 1.0 O B:HOH1201 4.8 19.9 1.0 N B:THR352 4.8 23.5 1.0 CA B:TRP151 4.9 21.3 1.0 ND2 B:ASN149 4.9 38.0 1.0 CB B:ILE150 4.9 17.4 1.0 CB B:SER468 5.0 26.2 1.0

Sodium binding site 4 out of 4 in the Cryo-Em Structure of Human Sodium-Chloride Cotransporter


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 Human Sodium-Chloride Cotransporter within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1106 b:39.5 occ:1.00 O B:LEU148 2.2 33.1 1.0 O B:TRP151 2.3 38.0 1.0 O B:ALA464 2.3 41.4 1.0 OG B:SER467 2.3 28.9 1.0 OG B:SER468 2.4 24.4 1.0 C B:ALA464 3.1 28.7 1.0 CA B:ALA464 3.2 24.9 1.0 N B:SER468 3.3 29.1 1.0 C B:TRP151 3.4 27.5 1.0 C B:LEU148 3.4 24.1 1.0 CB B:SER468 3.5 26.2 1.0 CB B:SER467 3.7 19.9 1.0 CB B:ALA464 3.8 27.1 1.0 CA B:SER468 3.9 19.5 1.0 CA B:LEU148 4.1 26.8 1.0 C B:SER467 4.1 34.3 1.0 N B:GLY152 4.3 30.6 1.0 CA B:GLY152 4.3 23.6 1.0 CA B:TRP151 4.3 21.3 1.0 CB B:TRP151 4.3 19.2 1.0 N B:THR465 4.4 33.8 1.0 CA B:SER467 4.4 27.6 1.0 O B:GLY463 4.4 45.7 1.0 N B:ASN149 4.4 18.0 1.0 N B:ALA464 4.5 33.8 1.0 CD1 B:ILE293 4.5 41.4 1.0 CA B:ASN149 4.6 22.2 1.0 N B:TRP151 4.6 24.0 1.0 N B:SER467 4.6 32.8 1.0 CD2 B:LEU148 4.7 40.4 1.0 CB B:LEU148 4.8 29.5 1.0 C B:ASN149 4.8 32.3 1.0 O B:ASN149 4.9 39.3 1.0 C B:GLY463 4.9 35.8 1.0 O B:MET147 4.9 40.2 1.0

J.Nan, Y.Yuan, X.Yang, Z.Shan, H.Liu, F.Wei, W.Zhang, Y.Zhang. Cryo-Em Structure of the Human Sodium-Chloride Cotransporter Ncc. Sci Adv V. 8 D7176 2022.
ISSN: ESSN 2375-2548
PubMed: 36351028
DOI: 10.1126/SCIADV.ADD7176