Sodium in PDB 8y56: Cryo-Em Reveals Cholesterol Binding in the Lysosomal Gpcr-Like Protein Lychos

The binding sites of Sodium atom in the Cryo-Em Reveals Cholesterol Binding in the Lysosomal Gpcr-Like Protein Lychos (pdb code 8y56). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Cryo-Em Reveals Cholesterol Binding in the Lysosomal Gpcr-Like Protein Lychos, PDB code: 8y56:

Sodium binding site 1 out of 1 in the Cryo-Em Reveals Cholesterol Binding in the Lysosomal Gpcr-Like Protein Lychos


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryo-Em Reveals Cholesterol Binding in the Lysosomal Gpcr-Like Protein Lychos within 5.0Å range: probe atom residue distance (Å) B Occ R:Na901 b:62.2 occ:1.00 OG1 R:THR142 3.0 53.8 1.0 CB R:THR142 3.5 53.8 1.0 OG R:SER176 3.6 57.4 1.0 CD1 R:LEU180 3.7 58.7 1.0 N R:GLN143 3.7 57.3 1.0 C R:THR142 3.8 53.8 1.0 CG R:GLN143 3.8 57.3 1.0 CB R:LEU180 3.9 58.7 1.0 OD1 R:ASN181 4.0 60.8 1.0 CA R:GLN143 4.1 57.3 1.0 O R:THR142 4.1 53.8 1.0 O R:SER176 4.2 57.4 1.0 CA R:THR142 4.3 53.8 1.0 CB R:GLN143 4.3 57.3 1.0 CG R:LEU180 4.4 58.7 1.0 O R:ILE139 4.7 56.7 1.0 C R:SER176 4.7 57.4 1.0 CG2 R:THR142 4.7 53.8 1.0 CG R:ASN181 4.7 60.8 1.0 CB R:SER176 4.8 57.4 1.0 CD R:LYS110 4.9 52.5 1.0 N R:ASN181 4.9 60.8 1.0 CA R:ILE139 4.9 56.7 1.0

J.Zhao, Q.Shen, X.Yong, X.Li, X.Tian, S.Sun, Z.Xu, X.Zhang, L.Zhang, H.Yang, Z.Shao, H.Xu, Y.Jiang, Y.Zhang, W.Yan. Cryo-Em Reveals Cholesterol Binding in the Lysosomal Gpcr-Like Protein Lychos. Nat.Struct.Mol.Biol. 2025.
ISSN: ESSN 1545-9985
PubMed: 39824976
DOI: 10.1038/S41594-024-01470-9