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

Sodium Binding Sites:

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 5w3s

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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 5w3s

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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 5w3s

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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 5w3s

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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 5w3s

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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 5w3s

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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

Reference:

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
Page generated: Tue Oct 8 00:59:47 2024

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