Sodium in PDB 5w3s: Cryo-Electron Microscopy Structure of A TRPML3 Ion Channel

The binding sites of Sodium atom in the Cryo-Electron Microscopy Structure of A TRPML3 Ion Channel (pdb code 5w3s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Cryo-Electron Microscopy Structure of A TRPML3 Ion Channel, PDB code: 5w3s:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Cryo-Electron Microscopy Structure of A TRPML3 Ion Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryo-Electron Microscopy Structure of A TRPML3 Ion Channel within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:38.8 occ:1.00 NA C:NA603 2.8 41.5 1.0 HA3 C:GLY457 3.2 20.2 1.0 HA3 D:GLY457 3.3 20.2 1.0 HA3 A:GLY457 3.3 20.2 1.0 NA C:NA604 3.3 37.5 1.0 HA3 B:GLY457 3.3 20.2 1.0 O C:ASN456 4.1 20.2 1.0 O D:ASN456 4.1 20.2 1.0 O A:ASN456 4.1 20.2 1.0 O B:ASN456 4.1 20.2 1.0 CA C:GLY457 4.2 20.2 1.0 CA D:GLY457 4.2 20.2 1.0 CA A:GLY457 4.2 20.2 1.0 CA B:GLY457 4.3 20.2 1.0 C C:GLY457 4.4 20.2 1.0 C A:GLY457 4.5 20.2 1.0 O C:GLY457 4.5 20.2 1.0 C B:GLY457 4.5 20.2 1.0 C D:GLY457 4.5 20.2 1.0 O A:GLY457 4.6 20.2 1.0 O B:GLY457 4.6 20.2 1.0 O D:GLY457 4.7 20.2 1.0 HA2 C:GLY457 4.7 20.2 1.0 HA2 D:GLY457 4.7 20.2 1.0 HA2 A:GLY457 4.7 20.2 1.0 HA2 B:GLY457 4.8 20.2 1.0 C C:ASN456 4.8 20.2 1.0 C D:ASN456 4.8 20.2 1.0 C A:ASN456 4.9 20.2 1.0 C B:ASN456 4.9 20.2 1.0 N C:GLY457 4.9 20.2 1.0 N D:GLY457 5.0 20.2 1.0 N A:GLY457 5.0 20.2 1.0

Sodium binding site 2 out of 6 in the Cryo-Electron Microscopy Structure of A TRPML3 Ion Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryo-Electron Microscopy Structure of A TRPML3 Ion Channel within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:43.2 occ:1.00 HD11 D:ILE498 3.7 24.3 1.0 HD11 B:ILE498 3.8 24.3 1.0 HD11 A:ILE498 3.8 24.3 1.0 HD11 C:ILE498 3.8 24.3 1.0 HD13 D:ILE498 4.0 24.3 1.0 HD13 A:ILE498 4.1 24.3 1.0 HD13 B:ILE498 4.1 24.3 1.0 HD13 C:ILE498 4.1 24.3 1.0 CD1 D:ILE498 4.3 24.3 1.0 NA C:NA605 4.3 37.8 1.0 CD1 B:ILE498 4.4 24.3 1.0 CD1 A:ILE498 4.4 24.3 1.0 CD1 C:ILE498 4.4 24.3 1.0 HD12 D:ILE498 4.6 24.3 1.0 HD12 B:ILE498 4.7 24.3 1.0 HD12 A:ILE498 4.7 24.3 1.0 HD12 C:ILE498 4.7 24.3 1.0

Sodium binding site 3 out of 6 in the Cryo-Electron Microscopy Structure of A TRPML3 Ion Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cryo-Electron Microscopy Structure of A TRPML3 Ion Channel within 5.0Å range: probe atom residue distance (Å) B Occ C:Na603 b:41.5 occ:1.00 NA A:NA602 2.8 38.8 1.0 HA C:ASP458 3.6 22.2 1.0 HA D:ASP458 3.7 22.2 1.0 HA A:ASP458 3.7 22.2 1.0 HA B:ASP458 3.7 22.2 1.0 O C:GLY457 3.9 20.2 1.0 O D:GLY457 4.0 20.2 1.0 O A:GLY457 4.0 20.2 1.0 O B:GLY457 4.1 20.2 1.0 C C:GLY457 4.2 20.2 1.0 C D:GLY457 4.3 20.2 1.0 HA3 D:GLY457 4.3 20.2 1.0 C A:GLY457 4.3 20.2 1.0 C B:GLY457 4.4 20.2 1.0 HA3 C:GLY457 4.4 20.2 1.0 HA3 A:GLY457 4.4 20.2 1.0 CA C:ASP458 4.4 22.2 1.0 HA3 B:GLY457 4.5 20.2 1.0 NA D:NA601 4.5 53.5 1.0 CA D:ASP458 4.5 22.2 1.0 CA A:ASP458 4.6 22.2 1.0 CA B:ASP458 4.6 22.2 1.0 N C:ASP458 4.6 22.2 1.0 N D:ASP458 4.6 22.2 1.0 N A:ASP458 4.7 22.2 1.0 N B:ASP458 4.7 22.2 1.0 H C:ASP459 4.8 22.7 1.0 CA D:GLY457 4.9 20.2 1.0 O D:ASN456 4.9 20.2 1.0 H A:ASP459 4.9 22.7 1.0 CA C:GLY457 4.9 20.2 1.0 H D:ASP459 4.9 22.7 1.0 H B:ASP459 4.9 22.7 1.0 CA A:GLY457 5.0 20.2 1.0 O C:ASN456 5.0 20.2 1.0

Sodium binding site 4 out of 6 in the Cryo-Electron Microscopy Structure of A TRPML3 Ion Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cryo-Electron Microscopy Structure of A TRPML3 Ion Channel within 5.0Å range: probe atom residue distance (Å) B Occ C:Na604 b:37.5 occ:1.00 NA C:NA605 2.1 37.8 1.0 NA A:NA602 3.3 38.8 1.0 HA3 C:GLY457 4.6 20.2 1.0 HA3 B:GLY457 4.6 20.2 1.0 HA3 A:GLY457 4.6 20.2 1.0 HA3 D:GLY457 4.7 20.2 1.0

Sodium binding site 5 out of 6 in the Cryo-Electron Microscopy Structure of A TRPML3 Ion Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Cryo-Electron Microscopy Structure of A TRPML3 Ion Channel within 5.0Å range: probe atom residue distance (Å) B Occ C:Na605 b:37.8 occ:1.00 NA C:NA604 2.1 37.5 1.0 NA A:NA603 4.3 43.2 1.0

Sodium binding site 6 out of 6 in the Cryo-Electron Microscopy Structure of A TRPML3 Ion Channel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Cryo-Electron Microscopy Structure of A TRPML3 Ion Channel within 5.0Å range: probe atom residue distance (Å) B Occ D:Na601 b:53.5 occ:1.00 OD1 D:ASP458 4.0 22.2 1.0 OD1 A:ASP458 4.0 22.2 1.0 OD1 C:ASP458 4.0 22.2 1.0 OD1 B:ASP458 4.0 22.2 1.0 H D:ASP459 4.3 22.7 1.0 H C:ASP459 4.3 22.7 1.0 H B:ASP459 4.3 22.7 1.0 H A:ASP459 4.3 22.7 1.0 NA C:NA603 4.5 41.5 1.0 HA D:ASP458 4.7 22.2 1.0 HA A:ASP458 4.8 22.2 1.0 HA B:ASP458 4.8 22.2 1.0 HA C:ASP458 4.8 22.2 1.0 O C:HOH701 4.9 84.1 1.0 O A:HOH701 4.9 84.1 1.0 O B:HOH701 4.9 84.1 1.0 O D:HOH701 4.9 84.1 1.0 N D:ASP459 5.0 22.7 1.0

M.Hirschi, M.A.Herzik, J.Wie, Y.Suo, W.F.Borschel, D.Ren, G.C.Lander, S.Y.Lee. Cryo-Electron Microscopy Structure of the Lysosomal Calcium-Permeable Channel TRPML3. Nature V. 550 411 2017.
ISSN: ESSN 1476-4687
PubMed: 29019979
DOI: 10.1038/NATURE24055