Sodium in PDB 8v6k: Apo-State Cryo-Em Structure of Human TRPV3 in CNW30 Nanodiscs

The binding sites of Sodium atom in the Apo-State Cryo-Em Structure of Human TRPV3 in CNW30 Nanodiscs (pdb code 8v6k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Apo-State Cryo-Em Structure of Human TRPV3 in CNW30 Nanodiscs, PDB code: 8v6k:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Apo-State Cryo-Em Structure of Human TRPV3 in CNW30 Nanodiscs


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apo-State Cryo-Em Structure of Human TRPV3 in CNW30 Nanodiscs within 5.0Å range: probe atom residue distance (Å) B Occ A:Na909 b:45.2 occ:1.00 O B:GLY638 3.1 26.6 1.0 O D:GLY638 3.2 27.5 1.0 O C:GLY638 3.2 27.9 1.0 NA A:NA910 3.3 48.9 1.0 O A:GLY638 3.3 27.7 1.0 H B:GLY640 3.5 31.6 1.0 H D:GLY640 3.5 32.4 1.0 HA B:LEU639 3.5 27.9 1.0 H C:GLY640 3.6 32.9 1.0 HA D:LEU639 3.6 28.6 1.0 H A:GLY640 3.6 32.9 1.0 HA C:LEU639 3.6 29.1 1.0 HA A:LEU639 3.8 29.1 1.0 O A:GLY640 4.0 32.9 1.0 O B:GLY640 4.0 31.6 1.0 O C:GLY640 4.1 32.9 1.0 N B:GLY640 4.1 31.6 1.0 O D:GLY640 4.1 32.4 1.0 N D:GLY640 4.2 32.4 1.0 N C:GLY640 4.2 32.9 1.0 N A:GLY640 4.2 32.9 1.0 C B:GLY638 4.2 26.6 1.0 HD13 D:LEU639 4.3 28.6 1.0 C D:GLY638 4.3 27.5 1.0 HD13 B:LEU639 4.3 27.9 1.0 C C:GLY638 4.3 27.9 1.0 CA B:LEU639 4.4 27.9 1.0 HD13 C:LEU639 4.4 29.1 1.0 CA D:LEU639 4.4 28.6 1.0 C A:GLY638 4.4 27.7 1.0 CA C:LEU639 4.5 29.1 1.0 HD13 A:LEU639 4.5 29.1 1.0 CA A:LEU639 4.6 29.1 1.0 C B:LEU639 4.6 27.9 1.0 C D:LEU639 4.7 28.6 1.0 C C:LEU639 4.7 29.1 1.0 N B:LEU639 4.8 27.9 1.0 C A:LEU639 4.8 29.1 1.0 N D:LEU639 4.8 28.6 1.0 N C:LEU639 4.8 29.1 1.0 C A:GLY640 4.9 32.9 1.0 C B:GLY640 4.9 31.6 1.0 N A:LEU639 5.0 29.1 1.0 C C:GLY640 5.0 32.9 1.0

Sodium binding site 2 out of 4 in the Apo-State Cryo-Em Structure of Human TRPV3 in CNW30 Nanodiscs


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Apo-State Cryo-Em Structure of Human TRPV3 in CNW30 Nanodiscs within 5.0Å range: probe atom residue distance (Å) B Occ A:Na910 b:48.9 occ:1.00 NA B:NA909 2.1 53.7 1.0 O D:GLY638 2.4 27.5 1.0 O B:GLY638 2.4 26.6 1.0 O A:GLY638 2.4 27.7 1.0 O C:GLY638 2.4 27.9 1.0 HA3 B:GLY638 3.2 26.6 1.0 HA3 D:GLY638 3.2 27.5 1.0 HA3 C:GLY638 3.2 27.9 1.0 HA3 A:GLY638 3.3 27.7 1.0 NA A:NA909 3.3 45.2 1.0 C B:GLY638 3.4 26.6 1.0 C D:GLY638 3.4 27.5 1.0 C C:GLY638 3.4 27.9 1.0 C A:GLY638 3.4 27.7 1.0 CA B:GLY638 3.7 26.6 1.0 CA D:GLY638 3.7 27.5 1.0 CA C:GLY638 3.8 27.9 1.0 CA A:GLY638 3.8 27.7 1.0 HA2 B:GLY638 3.9 26.6 1.0 HA2 A:GLY638 3.9 27.7 1.0 HA2 D:GLY638 4.0 27.5 1.0 HA2 C:GLY638 4.0 27.9 1.0 HD22 D:LEU639 4.4 28.6 1.0 HA D:LEU639 4.5 28.6 1.0 HD22 B:LEU639 4.5 27.9 1.0 HA B:LEU639 4.5 27.9 1.0 HD22 C:LEU639 4.5 29.1 1.0 HA C:LEU639 4.5 29.1 1.0 HA A:LEU639 4.5 29.1 1.0 N D:LEU639 4.6 28.6 1.0 N B:LEU639 4.6 27.9 1.0 N C:LEU639 4.6 29.1 1.0 N A:LEU639 4.6 29.1 1.0 HD22 A:LEU639 4.7 29.1 1.0 O D:ILE637 4.9 29.0 1.0 O B:ILE637 4.9 28.2 1.0 O D:HOH1084 5.0 34.4 1.0 O A:HOH1081 5.0 32.0 1.0 O C:HOH1083 5.0 34.5 1.0 O C:ILE637 5.0 29.3 1.0 O B:HOH1081 5.0 34.1 1.0

Sodium binding site 3 out of 4 in the Apo-State Cryo-Em Structure of Human TRPV3 in CNW30 Nanodiscs


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Apo-State Cryo-Em Structure of Human TRPV3 in CNW30 Nanodiscs within 5.0Å range: probe atom residue distance (Å) B Occ B:Na909 b:53.7 occ:1.00 NA A:NA910 2.1 48.9 1.0 HA3 B:GLY638 2.9 26.6 1.0 HA3 C:GLY638 3.0 27.9 1.0 HA3 D:GLY638 3.0 27.5 1.0 HA3 A:GLY638 3.1 27.7 1.0 O B:HOH1081 3.2 34.1 1.0 O C:HOH1083 3.2 34.5 1.0 O D:HOH1084 3.2 34.4 1.0 O A:HOH1081 3.2 32.0 1.0 O B:GLY638 3.8 26.6 1.0 O A:GLY638 3.8 27.7 1.0 O C:GLY638 3.8 27.9 1.0 O D:GLY638 3.8 27.5 1.0 CA B:GLY638 3.8 26.6 1.0 CA C:GLY638 3.9 27.9 1.0 CA D:GLY638 3.9 27.5 1.0 CA A:GLY638 3.9 27.7 1.0 HA2 B:GLY638 4.1 26.6 1.0 HA2 C:GLY638 4.1 27.9 1.0 HA2 A:GLY638 4.1 27.7 1.0 HA2 D:GLY638 4.2 27.5 1.0 C B:GLY638 4.3 26.6 1.0 C C:GLY638 4.3 27.9 1.0 C A:GLY638 4.3 27.7 1.0 C D:GLY638 4.3 27.5 1.0 O D:HOH1044 4.5 37.4 1.0 O B:ILE637 4.5 28.2 1.0 O C:HOH1036 4.5 40.1 1.0 O B:HOH1029 4.5 39.1 1.0 O A:HOH1040 4.5 38.1 1.0 O D:ILE637 4.6 29.0 1.0 O C:ILE637 4.6 29.3 1.0 O A:ILE637 4.7 29.2 1.0 N B:GLY638 4.9 26.6 1.0 O A:HOH1093 4.9 34.6 1.0 O B:HOH1094 4.9 33.8 1.0 O C:HOH1094 4.9 36.0 1.0 N C:GLY638 4.9 27.9 1.0 O D:HOH1095 4.9 34.1 1.0 N D:GLY638 5.0 27.5 1.0

Sodium binding site 4 out of 4 in the Apo-State Cryo-Em Structure of Human TRPV3 in CNW30 Nanodiscs


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Apo-State Cryo-Em Structure of Human TRPV3 in CNW30 Nanodiscs within 5.0Å range: probe atom residue distance (Å) B Occ B:Na910 b:104.8 occ:1.00 O D:HOH1063 2.6 35.3 1.0 O C:HOH1062 2.6 37.2 1.0 O B:HOH1059 2.6 36.9 1.0 O A:HOH1069 2.6 36.8 1.0 O D:HOH1062 3.2 31.8 1.0 O C:HOH1063 3.2 32.8 1.0 O B:HOH1095 3.3 112.5 1.0 O A:HOH1063 3.3 32.8 1.0 O D:HOH1064 3.4 35.0 1.0 O B:HOH1010 4.4 43.2 1.0 O C:HOH1011 4.4 45.4 1.0 O D:HOH1011 4.5 44.1 1.0 O A:HOH1014 4.6 43.1 1.0 O C:HOH1049 4.7 24.8 1.0 O B:HOH1048 4.7 24.8 1.0 O D:HOH1046 4.7 25.5 1.0 OE1 B:GLU682 4.8 33.9 1.0 O A:HOH1041 4.8 24.9 1.0 OE1 D:GLU682 4.8 35.1 1.0 OE1 C:GLU682 4.8 34.9 1.0

K.D.Nadezhdin, A.I.Sobolevsky. TRPV3 Activation By Different Agonists Accompanied By Lipid Dissociation From the Vanilloid Site To Be Published.