Sodium in PDB 6o6a: Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Ligand-Free State

The binding sites of Sodium atom in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Ligand-Free State (pdb code 6o6a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Ligand-Free State, PDB code: 6o6a:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Ligand-Free State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Ligand-Free State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1302 b:53.4 occ:1.00 CH2 A:TRP867 4.1 49.0 1.0 CE1 A:TYR953 4.2 78.8 1.0 OH A:TYR953 4.5 78.8 1.0 CZ3 A:TRP867 4.5 49.0 1.0 OG A:SER956 4.5 59.2 1.0 CZ2 A:TRP867 4.5 49.0 1.0 CZ A:TYR953 4.6 78.8 1.0 CB A:THR957 4.7 59.5 1.0 CD1 A:LEU960 4.8 52.6 1.0 CA A:THR957 4.8 59.5 1.0 OG1 A:THR957 4.9 59.5 1.0 CD1 A:TYR953 5.0 78.8 1.0

Sodium binding site 2 out of 4 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Ligand-Free State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Ligand-Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1302 b:53.4 occ:1.00 CH2 B:TRP867 4.1 49.0 1.0 CE1 B:TYR953 4.2 78.8 1.0 OH B:TYR953 4.5 78.8 1.0 CZ3 B:TRP867 4.5 49.0 1.0 OG B:SER956 4.5 59.2 1.0 CZ2 B:TRP867 4.5 49.0 1.0 CZ B:TYR953 4.6 78.8 1.0 CB B:THR957 4.7 59.5 1.0 CD1 B:LEU960 4.8 52.6 1.0 CA B:THR957 4.8 59.5 1.0 OG1 B:THR957 4.9 59.5 1.0 CD1 B:TYR953 5.0 78.8 1.0

Sodium binding site 3 out of 4 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Ligand-Free State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Ligand-Free State within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1302 b:53.4 occ:1.00 CH2 C:TRP867 4.1 49.0 1.0 CE1 C:TYR953 4.2 78.8 1.0 OH C:TYR953 4.5 78.8 1.0 CZ3 C:TRP867 4.5 49.0 1.0 OG C:SER956 4.5 59.2 1.0 CZ2 C:TRP867 4.5 49.0 1.0 CZ C:TYR953 4.6 78.8 1.0 CB C:THR957 4.7 59.5 1.0 CD1 C:LEU960 4.8 52.6 1.0 CA C:THR957 4.8 59.5 1.0 OG1 C:THR957 4.9 59.5 1.0 CD1 C:TYR953 5.0 78.8 1.0

Sodium binding site 4 out of 4 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Ligand-Free State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Ligand-Free State within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1302 b:53.4 occ:1.00 CH2 D:TRP867 4.1 49.0 1.0 CE1 D:TYR953 4.2 78.8 1.0 OH D:TYR953 4.5 78.8 1.0 CZ3 D:TRP867 4.5 49.0 1.0 OG D:SER956 4.5 59.2 1.0 CZ2 D:TRP867 4.5 49.0 1.0 CZ D:TYR953 4.6 78.8 1.0 CB D:THR957 4.7 59.5 1.0 CD1 D:LEU960 4.8 52.6 1.0 CA D:THR957 4.8 59.5 1.0 OG1 D:THR957 4.9 59.5 1.0 CD1 D:TYR953 5.0 78.8 1.0

M.M.Diver, Y.Cheng, D.Julius. Structural Insights Into TRPM8 Inhibition and Desensitization. Science V. 365 1434 2019.
ISSN: ESSN 1095-9203
PubMed: 31488702
DOI: 10.1126/SCIENCE.AAX6672