Sodium in PDB 6o72: Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Tc-I 2014-Bound State

The structure of Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Tc-I 2014-Bound State also contains other interesting chemical elements:

Fluorine

(F)

24 atoms

The binding sites of Sodium atom in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Tc-I 2014-Bound State (pdb code 6o72). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Tc-I 2014-Bound State, PDB code: 6o72:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Tc-I 2014-Bound 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, Tc-I 2014-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1306 b:44.8 occ:1.00 N A:LEU961 4.3 39.9 1.0 CB A:LEU960 4.4 43.2 1.0 CA A:LEU961 4.5 39.9 1.0 C A:LEU960 4.6 43.2 1.0 CB A:LEU961 4.7 39.9 1.0 OG1 A:THR957 4.7 49.6 1.0 O A:LEU960 4.8 43.2 1.0 CD1 A:LEU961 4.9 39.9 1.0

Sodium binding site 2 out of 8 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Tc-I 2014-Bound 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, Tc-I 2014-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1307 b:51.0 occ:1.00 OG1 A:THR957 3.5 49.6 1.0 CH2 A:TRP867 4.2 47.4 1.0 CD2 A:TYR953 4.2 61.9 1.0 N A:THR957 4.3 49.6 1.0 CB A:SER956 4.3 49.2 1.0 CE2 A:TYR953 4.4 61.9 1.0 CZ3 A:TRP867 4.5 47.4 1.0 CZ2 A:TRP867 4.5 47.4 1.0 CB A:THR957 4.8 49.6 1.0 CD1 A:LEU960 4.8 43.2 1.0 C A:SER956 4.8 49.2 1.0 CA A:THR957 4.9 49.6 1.0

Sodium binding site 3 out of 8 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Tc-I 2014-Bound 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, Tc-I 2014-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1305 b:44.8 occ:1.00 N B:LEU961 4.3 39.9 1.0 CB B:LEU960 4.4 43.2 1.0 CA B:LEU961 4.5 39.9 1.0 C B:LEU960 4.6 43.2 1.0 CB B:LEU961 4.7 39.9 1.0 OG1 B:THR957 4.7 49.6 1.0 O B:LEU960 4.8 43.2 1.0 CD1 B:LEU961 4.9 39.9 1.0

Sodium binding site 4 out of 8 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Tc-I 2014-Bound 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, Tc-I 2014-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1306 b:51.0 occ:1.00 OG1 B:THR957 3.5 49.6 1.0 CH2 B:TRP867 4.2 47.4 1.0 CD2 B:TYR953 4.2 61.9 1.0 N B:THR957 4.3 49.6 1.0 CB B:SER956 4.3 49.2 1.0 CE2 B:TYR953 4.4 61.9 1.0 CZ3 B:TRP867 4.5 47.4 1.0 CZ2 B:TRP867 4.5 47.4 1.0 CB B:THR957 4.8 49.6 1.0 CD1 B:LEU960 4.8 43.2 1.0 C B:SER956 4.8 49.2 1.0 CA B:THR957 4.9 49.6 1.0

Sodium binding site 5 out of 8 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Tc-I 2014-Bound State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Tc-I 2014-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1306 b:44.8 occ:1.00 N C:LEU961 4.3 39.9 1.0 CB C:LEU960 4.4 43.2 1.0 CA C:LEU961 4.5 39.9 1.0 C C:LEU960 4.5 43.2 1.0 CB C:LEU961 4.7 39.9 1.0 OG1 C:THR957 4.7 49.6 1.0 O C:LEU960 4.8 43.2 1.0 CD1 C:LEU961 4.9 39.9 1.0

Sodium binding site 6 out of 8 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Tc-I 2014-Bound State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Tc-I 2014-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1307 b:51.0 occ:1.00 OG1 C:THR957 3.5 49.6 1.0 CH2 C:TRP867 4.2 47.4 1.0 CD2 C:TYR953 4.2 61.9 1.0 N C:THR957 4.3 49.6 1.0 CB C:SER956 4.3 49.2 1.0 CE2 C:TYR953 4.4 61.9 1.0 CZ3 C:TRP867 4.5 47.4 1.0 CZ2 C:TRP867 4.5 47.4 1.0 CB C:THR957 4.8 49.6 1.0 CD1 C:LEU960 4.8 43.2 1.0 C C:SER956 4.8 49.2 1.0 CA C:THR957 4.9 49.6 1.0

Sodium binding site 7 out of 8 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Tc-I 2014-Bound State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Tc-I 2014-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1306 b:44.8 occ:1.00 N D:LEU961 4.3 39.9 1.0 CB D:LEU960 4.4 43.2 1.0 CA D:LEU961 4.5 39.9 1.0 C D:LEU960 4.5 43.2 1.0 CB D:LEU961 4.7 39.9 1.0 OG1 D:THR957 4.7 49.6 1.0 O D:LEU960 4.8 43.2 1.0 CD1 D:LEU961 4.9 39.9 1.0

Sodium binding site 8 out of 8 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Tc-I 2014-Bound State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Tc-I 2014-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1307 b:51.0 occ:1.00 OG1 D:THR957 3.5 49.6 1.0 CH2 D:TRP867 4.2 47.4 1.0 CD2 D:TYR953 4.2 61.9 1.0 N D:THR957 4.3 49.6 1.0 CB D:SER956 4.3 49.2 1.0 CE2 D:TYR953 4.4 61.9 1.0 CZ3 D:TRP867 4.5 47.4 1.0 CZ2 D:TRP867 4.5 47.4 1.0 CB D:THR957 4.8 49.6 1.0 CD1 D:LEU960 4.8 43.2 1.0 C D:SER956 4.8 49.2 1.0 CA D:THR957 4.9 49.6 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