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Sodium in PDB 6o6r: Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Amtb-Bound State

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Amtb-Bound State (pdb code 6o6r). 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, Amtb-Bound State, PDB code: 6o6r:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 6o6r

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Sodium binding site 1 out of 8 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Amtb-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, Amtb-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1306

b:53.6
occ:1.00
 CB A:LEU960 4.4 36.0 1.0
N A:LEU961 4.7 34.1 1.0
NA A:NA1307 4.7 43.7 1.0
C A:LEU960 4.8 36.0 1.0
O A:LEU960 4.9 36.0 1.0
CA A:LEU961 4.9 34.1 1.0
CZ A:PHE860 5.0 29.1 1.0

Sodium binding site 2 out of 8 in 6o6r

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Sodium binding site 2 out of 8 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Amtb-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, Amtb-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1307

b:43.7
occ:1.00
 CH2 A:TRP867 3.6 39.4 1.0
CZ3 A:TRP867 3.9 39.4 1.0
CZ2 A:TRP867 4.2 39.4 1.0
OG A:SER956 4.4 42.4 1.0
CD1 A:LEU960 4.5 36.0 1.0
CE3 A:TRP867 4.6 39.4 1.0
O A:SER956 4.6 42.4 1.0
OG1 A:THR957 4.6 40.7 1.0
CE2 A:TYR953 4.7 58.6 1.0
NA A:NA1306 4.7 53.6 1.0
CE2 A:TRP867 4.8 39.4 1.0
CA A:THR957 4.8 40.7 1.0
C A:SER956 4.8 42.4 1.0
CD2 A:TYR953 4.9 58.6 1.0
CE1 A:PHE864 4.9 34.1 1.0
N A:THR957 4.9 40.7 1.0

Sodium binding site 3 out of 8 in 6o6r

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Sodium binding site 3 out of 8 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Amtb-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, Amtb-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1306

b:53.6
occ:1.00
 CB B:LEU960 4.4 36.0 1.0
N B:LEU961 4.7 34.1 1.0
NA B:NA1307 4.7 43.7 1.0
C B:LEU960 4.8 36.0 1.0
O B:LEU960 4.9 36.0 1.0
CA B:LEU961 4.9 34.1 1.0
CZ B:PHE860 5.0 29.1 1.0

Sodium binding site 4 out of 8 in 6o6r

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Sodium binding site 4 out of 8 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Amtb-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, Amtb-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1307

b:43.7
occ:1.00
 CH2 B:TRP867 3.6 39.4 1.0
CZ3 B:TRP867 3.9 39.4 1.0
CZ2 B:TRP867 4.2 39.4 1.0
OG B:SER956 4.4 42.4 1.0
CD1 B:LEU960 4.5 36.0 1.0
CE3 B:TRP867 4.6 39.4 1.0
O B:SER956 4.6 42.4 1.0
OG1 B:THR957 4.6 40.7 1.0
CE2 B:TYR953 4.7 58.6 1.0
NA B:NA1306 4.7 53.6 1.0
CE2 B:TRP867 4.8 39.4 1.0
CA B:THR957 4.8 40.7 1.0
C B:SER956 4.8 42.4 1.0
CD2 B:TYR953 4.9 58.6 1.0
CE1 B:PHE864 4.9 34.1 1.0
N B:THR957 4.9 40.7 1.0

Sodium binding site 5 out of 8 in 6o6r

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Sodium binding site 5 out of 8 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Amtb-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, Amtb-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1306

b:53.6
occ:1.00
 CB C:LEU960 4.4 36.0 1.0
N C:LEU961 4.7 34.1 1.0
NA C:NA1307 4.7 43.7 1.0
C C:LEU960 4.8 36.0 1.0
O C:LEU960 4.9 36.0 1.0
CA C:LEU961 4.9 34.1 1.0
CZ C:PHE860 5.0 29.1 1.0

Sodium binding site 6 out of 8 in 6o6r

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Sodium binding site 6 out of 8 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Amtb-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, Amtb-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1307

b:43.7
occ:1.00
 CH2 C:TRP867 3.6 39.4 1.0
CZ3 C:TRP867 3.9 39.4 1.0
CZ2 C:TRP867 4.2 39.4 1.0
OG C:SER956 4.4 42.4 1.0
CD1 C:LEU960 4.5 36.0 1.0
CE3 C:TRP867 4.6 39.4 1.0
O C:SER956 4.6 42.4 1.0
OG1 C:THR957 4.6 40.7 1.0
CE2 C:TYR953 4.7 58.6 1.0
NA C:NA1306 4.7 53.6 1.0
CE2 C:TRP867 4.8 39.4 1.0
CA C:THR957 4.8 40.7 1.0
C C:SER956 4.8 42.4 1.0
CD2 C:TYR953 4.9 58.6 1.0
CE1 C:PHE864 4.9 34.1 1.0
N C:THR957 4.9 40.7 1.0

Sodium binding site 7 out of 8 in 6o6r

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Sodium binding site 7 out of 8 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Amtb-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, Amtb-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1306

b:53.6
occ:1.00
 CB D:LEU960 4.4 36.0 1.0
N D:LEU961 4.7 34.1 1.0
NA D:NA1307 4.7 43.7 1.0
C D:LEU960 4.8 36.0 1.0
O D:LEU960 4.9 36.0 1.0
CA D:LEU961 4.9 34.1 1.0
CZ D:PHE860 5.0 29.1 1.0

Sodium binding site 8 out of 8 in 6o6r

Go back to Sodium Binding Sites List in 6o6r
Sodium binding site 8 out of 8 in the Structure of the TRPM8 Cold Receptor By Single Particle Electron Cryo- Microscopy, Amtb-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, Amtb-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1307

b:43.7
occ:1.00
 CH2 D:TRP867 3.6 39.4 1.0
CZ3 D:TRP867 3.9 39.4 1.0
CZ2 D:TRP867 4.2 39.4 1.0
OG D:SER956 4.4 42.4 1.0
CD1 D:LEU960 4.5 36.0 1.0
CE3 D:TRP867 4.6 39.4 1.0
O D:SER956 4.6 42.4 1.0
OG1 D:THR957 4.6 40.7 1.0
CE2 D:TYR953 4.7 58.6 1.0
NA D:NA1306 4.7 53.6 1.0
CE2 D:TRP867 4.8 39.4 1.0
CA D:THR957 4.8 40.7 1.0
C D:SER956 4.8 42.4 1.0
CD2 D:TYR953 4.9 58.6 1.0
CE1 D:PHE864 4.9 34.1 1.0
N D:THR957 4.9 40.7 1.0

Reference:

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
Page generated: Tue Oct 8 12:28:21 2024

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