Sodium in PDB 8wfi: Human Glycine Transporter 1 in Complex with Glycine in Occluded Conformation

The structure of Human Glycine Transporter 1 in Complex with Glycine in Occluded Conformation also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Human Glycine Transporter 1 in Complex with Glycine in Occluded Conformation (pdb code 8wfi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Glycine Transporter 1 in Complex with Glycine in Occluded Conformation, PDB code: 8wfi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Glycine Transporter 1 in Complex with Glycine in Occluded Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Glycine Transporter 1 in Complex with Glycine in Occluded Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:25.6 occ:1.00 O A:VAL64 2.4 23.2 1.0 O A:GLY61 2.5 25.6 1.0 O A:HOH827 2.6 27.9 1.0 O A:LEU414 2.7 24.2 1.0 OG1 A:THR418 2.9 24.3 1.0 N A:THR418 3.2 24.3 1.0 C A:VAL64 3.5 23.2 1.0 C A:GLY417 3.6 24.8 1.0 C A:GLY61 3.7 25.6 1.0 CA A:GLY417 3.7 24.8 1.0 C A:LEU414 3.7 24.2 1.0 CA A:GLY65 3.8 21.6 1.0 CB A:THR418 3.9 24.3 1.0 CA A:THR418 3.9 24.3 1.0 CA A:LEU414 4.1 24.2 1.0 N A:GLY65 4.1 21.6 1.0 O A:HOH826 4.2 30.0 1.0 N A:GLY417 4.2 24.8 1.0 CA A:GLY61 4.3 25.6 1.0 O A:GLY417 4.5 24.8 1.0 CD2 A:LEU414 4.5 24.2 1.0 O A:TYR62 4.6 24.1 1.0 O A:LEU413 4.6 26.8 1.0 O A:HOH835 4.7 32.6 1.0 CA A:VAL64 4.7 23.2 1.0 N A:TYR62 4.7 24.1 1.0 N A:VAL64 4.7 23.2 1.0 C A:TYR62 4.8 24.1 1.0 CB A:LEU414 4.8 24.2 1.0 CA A:TYR62 4.9 24.1 1.0 N A:GLY415 4.9 23.2 1.0

Sodium binding site 2 out of 2 in the Human Glycine Transporter 1 in Complex with Glycine in Occluded Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Glycine Transporter 1 in Complex with Glycine in Occluded Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:22.0 occ:1.00 OD1 A:ASN68 2.4 21.9 1.0 O A:ALA63 2.5 22.7 1.0 OG A:SER317 2.6 21.3 1.0 OD1 A:ASN349 2.7 23.2 1.0 O A:SER317 2.7 21.3 1.0 O A:GLY701 2.7 21.9 0.0 CG A:ASN68 3.5 21.9 1.0 C A:SER317 3.5 21.3 1.0 C A:ALA63 3.5 22.7 1.0 C A:GLY701 3.5 21.9 0.0 CA A:SER317 3.5 21.3 1.0 CG A:ASN349 3.6 23.2 1.0 CB A:SER317 3.6 21.3 1.0 ND2 A:ASN349 3.7 23.2 1.0 N A:GLY701 3.8 21.9 0.0 ND2 A:ASN68 3.9 21.9 1.0 CA A:VAL64 3.9 23.2 1.0 N A:GLY65 4.1 21.6 1.0 CA A:GLY701 4.1 21.9 0.0 N A:VAL64 4.1 23.2 1.0 OXT A:GLY701 4.3 21.9 0.0 C A:VAL64 4.5 23.2 1.0 CA A:ALA63 4.6 22.7 1.0 N A:ASN68 4.6 21.9 1.0 N A:LEU318 4.7 21.4 1.0 C A:GLY67 4.7 21.4 1.0 CB A:ASN68 4.8 21.9 1.0 N A:SER317 4.9 21.3 1.0 CA A:GLY67 5.0 21.4 1.0 CB A:ALA63 5.0 22.7 1.0 CB A:ASN349 5.0 23.2 1.0

Y.Wei, R.Li, Y.Meng, T.Hu, J.Zhao, Y.Gao, Q.Bai, N.Li, Y.Zhao. Transport Mechanism and Pharmacology of the Human GLYT1. Cell 2024.
ISSN: ISSN 1097-4172
PubMed: 38513663
DOI: 10.1016/J.CELL.2024.02.026