Sodium in PDB 9ngg: Elic Facing Ecd Inwards in Liposomes with 2:1:1 Popc:Pope:Popg

The binding sites of Sodium atom in the Elic Facing Ecd Inwards in Liposomes with 2:1:1 Popc:Pope:Popg (pdb code 9ngg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Elic Facing Ecd Inwards in Liposomes with 2:1:1 Popc:Pope:Popg, PDB code: 9ngg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Elic Facing Ecd Inwards in Liposomes with 2:1:1 Popc:Pope:Popg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Elic Facing Ecd Inwards in Liposomes with 2:1:1 Popc:Pope:Popg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:11.2 occ:1.00 NA A:NA402 4.5 11.3 1.0

Sodium binding site 2 out of 7 in the Elic Facing Ecd Inwards in Liposomes with 2:1:1 Popc:Pope:Popg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Elic Facing Ecd Inwards in Liposomes with 2:1:1 Popc:Pope:Popg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:11.3 occ:1.00 ND2 C:ASN251 4.3 12.5 1.0 ND2 B:ASN251 4.3 12.5 1.0 ND2 A:ASN251 4.3 12.5 1.0 ND2 D:ASN251 4.3 12.5 1.0 ND2 E:ASN251 4.3 12.5 1.0 NA A:NA401 4.5 11.2 1.0 OD1 B:ASN251 4.7 12.5 1.0 OD1 C:ASN251 4.7 12.5 1.0 OD1 A:ASN251 4.7 12.5 1.0 OD1 D:ASN251 4.8 12.5 1.0 OD1 E:ASN251 4.8 12.5 1.0 CG B:ASN251 4.9 12.5 1.0 CG C:ASN251 4.9 12.5 1.0 CG A:ASN251 4.9 12.5 1.0 CG D:ASN251 4.9 12.5 1.0 CG E:ASN251 5.0 12.5 1.0

Sodium binding site 3 out of 7 in the Elic Facing Ecd Inwards in Liposomes with 2:1:1 Popc:Pope:Popg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Elic Facing Ecd Inwards in Liposomes with 2:1:1 Popc:Pope:Popg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:30.0 occ:1.00 CE2 B:PHE247 2.9 11.0 0.5 CE2 C:PHE247 3.0 11.0 0.5 CE2 D:PHE247 3.0 11.0 0.5 CE2 A:PHE247 3.0 11.0 0.5 CE2 E:PHE247 3.0 11.0 0.5 CZ B:PHE247 3.6 11.0 0.5 CZ C:PHE247 3.6 11.0 0.5 CZ D:PHE247 3.7 11.0 0.5 CZ A:PHE247 3.7 11.0 0.5 CZ E:PHE247 3.7 11.0 0.5 CD2 B:PHE247 3.9 11.0 0.5 CD2 C:PHE247 3.9 11.0 0.5 CD2 D:PHE247 4.0 11.0 0.5 CD2 A:PHE247 4.0 11.0 0.5 CD2 E:PHE247 4.0 11.0 0.5 CE1 B:PHE247 4.9 11.0 0.5 CE1 C:PHE247 4.9 11.0 0.5 CE1 C:PHE247 4.9 11.0 0.5 CE1 B:PHE247 5.0 11.0 0.5 CE1 D:PHE247 5.0 11.0 0.5 CE1 D:PHE247 5.0 11.0 0.5 CD1 C:PHE247 5.0 11.0 0.5 CD1 B:PHE247 5.0 11.0 0.5 CE1 A:PHE247 5.0 11.0 0.5 CE1 A:PHE247 5.0 11.0 0.5 CD1 D:PHE247 5.0 11.0 0.5

Sodium binding site 4 out of 7 in the Elic Facing Ecd Inwards in Liposomes with 2:1:1 Popc:Pope:Popg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Elic Facing Ecd Inwards in Liposomes with 2:1:1 Popc:Pope:Popg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:11.2 occ:1.00 CZ D:PHE247 3.3 11.0 0.5 CZ B:PHE247 3.4 11.0 0.5 CZ A:PHE247 3.4 11.0 0.5 CZ C:PHE247 3.4 11.0 0.5 CZ E:PHE247 3.4 11.0 0.5 CE1 D:PHE247 3.6 11.0 0.5 CE1 A:PHE247 3.6 11.0 0.5 CE1 B:PHE247 3.6 11.0 0.5 CE1 C:PHE247 3.6 11.0 0.5 CE1 E:PHE247 3.6 11.0 0.5 CE2 D:PHE247 4.5 11.0 0.5 CE2 B:PHE247 4.5 11.0 0.5 CE2 A:PHE247 4.5 11.0 0.5 CE2 C:PHE247 4.5 11.0 0.5 CE2 E:PHE247 4.5 11.0 0.5 CD1 D:PHE247 4.9 11.0 0.5 CD1 B:PHE247 4.9 11.0 0.5 CD1 A:PHE247 4.9 11.0 0.5 CD1 C:PHE247 4.9 11.0 0.5 CD1 E:PHE247 4.9 11.0 0.5

Sodium binding site 5 out of 7 in the Elic Facing Ecd Inwards in Liposomes with 2:1:1 Popc:Pope:Popg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Elic Facing Ecd Inwards in Liposomes with 2:1:1 Popc:Pope:Popg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:30.0 occ:1.00 CD2 D:LEU240 3.3 9.2 1.0 CD2 B:LEU240 3.3 9.2 1.0 CD2 A:LEU240 3.4 9.2 1.0 CD2 C:LEU240 3.4 9.2 1.0 CD2 E:LEU240 3.4 9.2 1.0 CG D:LEU240 4.2 9.2 1.0 CG B:LEU240 4.3 9.2 1.0 CG C:LEU240 4.3 9.2 1.0 CG A:LEU240 4.3 9.2 1.0 CG E:LEU240 4.3 9.2 1.0 CD1 D:LEU240 4.7 9.2 1.0 CD1 B:LEU240 4.8 9.2 1.0 CD1 C:LEU240 4.8 9.2 1.0 CD1 A:LEU240 4.8 9.2 1.0 CD1 E:LEU240 4.8 9.2 1.0

Sodium binding site 6 out of 7 in the Elic Facing Ecd Inwards in Liposomes with 2:1:1 Popc:Pope:Popg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Elic Facing Ecd Inwards in Liposomes with 2:1:1 Popc:Pope:Popg within 5.0Å range: probe atom residue distance (Å) B Occ D:Na401 b:11.2 occ:1.00 OE1 D:GLN233 4.9 22.9 0.3 OG1 D:THR237 4.9 15.8 1.0 OE1 C:GLN233 5.0 22.9 0.3

Sodium binding site 7 out of 7 in the Elic Facing Ecd Inwards in Liposomes with 2:1:1 Popc:Pope:Popg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Elic Facing Ecd Inwards in Liposomes with 2:1:1 Popc:Pope:Popg within 5.0Å range:

V.Dalal, B.K.Tan, H.Xu, W.W.Cheng. Cryo-Em Structures of A Pentameric Ligand-Gated Ion Channel in Liposomes Elife 2025.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.106728.2