Sodium in PDB 9d69: Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Cysteine in An Intermediate Outward Facing State (Slight Upper Position)

The structure of Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Cysteine in An Intermediate Outward Facing State (Slight Upper Position) also contains other interesting chemical elements:

Mercury

(Hg)

1 atom

The binding sites of Sodium atom in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Cysteine in An Intermediate Outward Facing State (Slight Upper Position) (pdb code 9d69). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Cysteine in An Intermediate Outward Facing State (Slight Upper Position), PDB code: 9d69:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Cysteine in An Intermediate Outward Facing State (Slight Upper Position)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Cysteine in An Intermediate Outward Facing State (Slight Upper Position) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:54.4 occ:1.00 OD2 A:ASP455 2.2 64.5 1.0 O A:ASN366 2.3 66.7 1.0 O A:GLY362 2.3 63.4 1.0 CG A:ASP455 3.0 64.5 1.0 CA A:ALA363 3.1 58.7 1.0 OD1 A:ASP455 3.2 61.0 1.0 C A:GLY362 3.2 62.8 1.0 C A:ALA363 3.3 56.9 1.0 C A:ASN366 3.4 61.3 1.0 O A:ALA363 3.4 58.4 1.0 O A:ASN451 3.6 60.9 1.0 N A:ALA363 3.6 62.7 1.0 CG A:MET367 3.9 60.1 1.0 N A:THR364 4.0 48.8 1.0 C A:ASN451 4.1 55.0 1.0 CB A:ASN451 4.1 61.0 1.0 OG A:SER333 4.2 64.7 1.0 N A:MET367 4.3 59.4 1.0 CA A:MET367 4.4 63.9 1.0 CA A:ASN366 4.4 61.3 1.0 CB A:SER333 4.4 61.7 1.0 CB A:ALA363 4.4 56.4 1.0 CB A:ASP455 4.4 58.6 1.0 CB A:ASN366 4.5 62.0 1.0 CA A:ASN451 4.5 58.0 1.0 CA A:GLY362 4.5 58.9 1.0 N A:ASN366 4.5 62.7 1.0 CB A:MET367 4.7 67.0 1.0 CE A:MET367 4.8 62.1 1.0 N A:VAL452 4.9 55.4 1.0 CA A:THR364 4.9 51.8 1.0 CG A:ASN451 4.9 58.6 1.0

Sodium binding site 2 out of 3 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Cysteine in An Intermediate Outward Facing State (Slight Upper Position)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Cysteine in An Intermediate Outward Facing State (Slight Upper Position) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:75.0 occ:1.00 O A:SER405 2.1 69.6 1.0 O A:THR364 2.1 60.9 1.0 O A:ALA408 2.3 64.4 1.0 SD A:MET367 3.0 66.2 1.0 C A:ALA408 3.1 69.7 1.0 N A:ALA408 3.1 65.9 1.0 CB A:ALA408 3.2 65.3 1.0 O A:ILE406 3.2 63.5 1.0 CA A:ALA408 3.3 69.7 1.0 C A:SER405 3.3 68.1 1.0 C A:THR364 3.3 55.5 1.0 C A:ILE406 3.5 65.7 1.0 CG A:MET367 3.8 60.1 1.0 C A:GLY407 3.9 62.2 1.0 CA A:ILE406 4.0 63.1 1.0 CE A:MET367 4.1 62.1 1.0 N A:ILE406 4.1 61.7 1.0 N A:GLY407 4.1 65.5 1.0 CA A:THR364 4.2 51.8 1.0 N A:ILE365 4.3 59.3 1.0 CA A:SER405 4.3 70.0 1.0 CA A:ILE365 4.3 60.5 1.0 N A:ALA409 4.3 59.9 1.0 CB A:MET367 4.4 67.0 1.0 OG1 A:THR364 4.4 55.7 1.0 CA A:GLY407 4.5 62.6 1.0 O A:GLY407 4.6 65.7 1.0 C A:ILE365 4.6 63.0 1.0 O A:ILE365 4.7 58.6 1.0 O A:ALA404 4.7 72.6 1.0 CA A:ALA409 5.0 54.6 1.0 CB A:THR364 5.0 52.9 1.0

Sodium binding site 3 out of 3 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Cysteine in An Intermediate Outward Facing State (Slight Upper Position)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Cysteine in An Intermediate Outward Facing State (Slight Upper Position) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:75.5 occ:1.00 OG1 A:THR102 2.1 63.7 1.0 OD1 A:ASP368 2.1 66.1 1.0 OD1 A:ASN366 2.2 63.2 1.0 O A:TYR98 2.2 61.4 1.0 OG1 A:THR101 2.5 55.0 1.0 N A:THR102 3.0 59.5 1.0 C A:TYR98 3.1 58.3 1.0 CG A:ASN366 3.2 62.5 1.0 CB A:THR102 3.3 60.6 1.0 CG A:ASP368 3.4 61.8 1.0 CA A:TYR98 3.4 56.2 1.0 CA A:THR102 3.5 61.3 1.0 CB A:THR101 3.6 56.7 1.0 C A:THR101 3.8 60.7 1.0 ND2 A:ASN366 3.9 60.6 1.0 OD2 A:ASP368 4.0 63.2 1.0 CA A:THR101 4.1 61.7 1.0 CB A:TYR98 4.1 54.7 1.0 CB A:ASN366 4.2 62.0 1.0 CA A:ASN366 4.3 61.3 1.0 O A:TYR97 4.3 57.0 1.0 N A:PHE99 4.3 55.4 1.0 N A:THR101 4.3 64.0 1.0 CG2 A:THR102 4.4 61.3 1.0 CB A:ASP368 4.5 58.6 1.0 N A:ASP368 4.6 65.3 1.0 N A:MET367 4.6 59.4 1.0 CA A:ASP368 4.7 59.7 1.0 O A:THR101 4.7 62.2 1.0 N A:TYR98 4.7 60.3 1.0 C A:ASN366 4.7 61.3 1.0 CG2 A:THR101 4.8 57.0 1.0 CA A:PHE99 4.8 56.9 1.0 CG A:TYR98 4.9 58.0 1.0 C A:TYR97 5.0 59.1 1.0 CD1 A:TYR98 5.0 60.0 1.0 C A:THR102 5.0 61.0 1.0

B.Qiu, O.Boudker. Structural Basis of the Excitatory Amino Acid Transporter 3 Substrate Recognition. Biorxiv 2024.
ISSN: ISSN 2692-8205
PubMed: 39282329
DOI: 10.1101/2024.09.05.611541