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Sodium in PDB 9d66: Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State

Other elements in 9d66:

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

Mercury (Hg) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State (pdb code 9d66). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State, PDB code: 9d66:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 9d66

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Sodium binding site 1 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State


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- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:45.2
occ:1.00
 O A:ASN366 2.2 55.0 1.0
O A:ASN451 2.7 52.3 1.0
O A:GLY362 2.8 50.5 1.0
OD2 A:ASP455 2.9 57.8 1.0
C A:ASN366 3.4 53.1 1.0
C A:ASN451 3.5 47.8 1.0
CB A:ASN451 3.6 38.1 1.0
OD1 A:ASP455 3.6 54.7 1.0
CG A:ASP455 3.7 58.5 1.0
CG A:MET367 3.7 40.9 1.0
O A:ALA363 3.7 53.6 1.0
C A:ALA363 3.7 48.3 1.0
CA A:ALA363 3.8 47.3 1.0
C A:GLY362 3.8 46.1 1.0
CA A:ASN451 3.9 44.6 1.0
CA A:MET367 4.0 40.2 1.0
N A:MET367 4.1 49.3 1.0
N A:ALA363 4.3 46.0 1.0
N A:THR364 4.3 47.5 1.0
CB A:MET367 4.4 39.1 1.0
OG A:SER333 4.4 50.1 1.0
CA A:ASN366 4.4 45.6 1.0
CB A:SER333 4.5 44.5 1.0
N A:VAL452 4.5 43.7 1.0
CG A:ASN451 4.5 37.2 1.0
N A:ASN366 4.6 41.7 1.0
CB A:ASN366 4.8 43.3 1.0
CE A:MET367 4.8 46.0 1.0
CA A:THR364 4.8 47.8 1.0
CA A:VAL452 4.9 43.7 1.0

Sodium binding site 2 out of 9 in 9d66

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Sodium binding site 2 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State


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- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:49.8
occ:1.00
 O A:THR364 2.1 45.9 1.0
O A:ALA408 2.1 45.4 1.0
O A:SER405 2.4 44.1 1.0
O A:ILE406 2.8 43.8 1.0
SD A:MET367 2.9 40.7 1.0
C A:THR364 3.2 43.5 1.0
C A:ALA408 3.3 45.3 1.0
C A:ILE406 3.3 41.3 1.0
OG1 A:THR364 3.4 47.9 1.0
C A:SER405 3.5 36.5 1.0
CA A:ILE406 3.5 42.2 1.0
CE A:MET367 3.7 46.0 1.0
CG A:MET367 3.7 40.9 1.0
N A:ALA408 3.8 43.6 1.0
CA A:THR364 3.9 47.8 1.0
CA A:ALA408 4.0 40.3 1.0
N A:ILE406 4.0 36.8 1.0
N A:ILE365 4.2 44.3 1.0
CB A:THR364 4.2 50.2 1.0
N A:GLY407 4.3 45.8 1.0
CB A:ALA408 4.3 42.6 1.0
C A:GLY407 4.3 47.8 1.0
N A:ALA409 4.4 45.6 1.0
CA A:ILE365 4.4 41.0 1.0
CB A:MET367 4.6 39.1 1.0
O A:ILE365 4.6 45.6 1.0
C A:ILE365 4.6 40.6 1.0
CA A:ALA409 4.7 42.2 1.0
CA A:SER405 4.8 39.0 1.0
CA A:GLY407 4.8 45.0 1.0
CB A:ILE406 4.9 39.7 1.0
O A:GLY407 5.0 53.8 1.0

Sodium binding site 3 out of 9 in 9d66

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Sodium binding site 3 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State


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- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:61.2
occ:1.00
 OD1 A:ASP368 2.1 56.1 1.0
OG1 A:THR102 2.2 52.9 1.0
OD1 A:ASN366 2.2 50.7 1.0
O A:TYR98 2.4 53.0 1.0
OG1 A:THR101 2.5 51.0 1.0
N A:THR102 2.8 50.1 1.0
CG A:ASP368 3.1 57.2 1.0
CB A:THR102 3.2 48.2 1.0
CA A:THR102 3.3 44.3 1.0
CG A:ASN366 3.3 50.1 1.0
C A:TYR98 3.4 51.3 1.0
OD2 A:ASP368 3.4 61.6 1.0
C A:THR101 3.4 49.6 1.0
CB A:THR101 3.4 49.9 1.0
CA A:TYR98 3.8 51.3 1.0
CA A:THR101 3.9 50.8 1.0
ND2 A:ASN366 4.0 57.7 1.0
N A:THR101 4.2 51.2 1.0
O A:THR101 4.2 53.0 1.0
O A:TYR97 4.4 56.0 1.0
CB A:ASN366 4.4 43.3 1.0
CB A:ASP368 4.4 43.4 1.0
CG2 A:THR102 4.4 47.6 1.0
CA A:ASN366 4.5 45.6 1.0
CB A:TYR98 4.6 49.5 1.0
N A:PHE99 4.6 56.6 1.0
N A:ASP368 4.6 53.2 1.0
CA A:ASP368 4.7 48.7 1.0
CG2 A:THR101 4.8 54.5 1.0
C A:THR102 4.8 48.5 1.0
N A:MET367 4.9 49.3 1.0
C A:ASN366 4.9 53.1 1.0
N A:TYR98 4.9 54.4 1.0

Sodium binding site 4 out of 9 in 9d66

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Sodium binding site 4 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:61.2
occ:1.00
 OD1 B:ASP368 2.1 56.1 1.0
OG1 B:THR102 2.2 52.9 1.0
OD1 B:ASN366 2.2 50.7 1.0
O B:TYR98 2.4 53.0 1.0
OG1 B:THR101 2.5 51.0 1.0
N B:THR102 2.8 50.1 1.0
CG B:ASP368 3.1 57.2 1.0
CB B:THR102 3.2 48.2 1.0
CA B:THR102 3.3 44.3 1.0
CG B:ASN366 3.3 50.1 1.0
C B:TYR98 3.4 51.3 1.0
OD2 B:ASP368 3.4 61.6 1.0
C B:THR101 3.4 49.6 1.0
CB B:THR101 3.4 49.9 1.0
CA B:TYR98 3.8 51.3 1.0
CA B:THR101 3.9 50.8 1.0
ND2 B:ASN366 4.0 57.7 1.0
N B:THR101 4.2 51.2 1.0
O B:THR101 4.2 53.0 1.0
O B:TYR97 4.4 56.0 1.0
CB B:ASN366 4.4 43.3 1.0
CB B:ASP368 4.4 43.4 1.0
CG2 B:THR102 4.4 47.6 1.0
CA B:ASN366 4.5 45.6 1.0
CB B:TYR98 4.6 49.5 1.0
N B:PHE99 4.6 56.6 1.0
N B:ASP368 4.6 53.2 1.0
CA B:ASP368 4.7 48.7 1.0
CG2 B:THR101 4.8 54.5 1.0
C B:THR102 4.8 48.5 1.0
N B:MET367 4.9 49.3 1.0
C B:ASN366 4.9 53.1 1.0
N B:TYR98 4.9 54.4 1.0

Sodium binding site 5 out of 9 in 9d66

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Sodium binding site 5 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:49.8
occ:1.00
 O B:THR364 2.1 45.9 1.0
O B:ALA408 2.1 45.4 1.0
O B:SER405 2.4 44.1 1.0
O B:ILE406 2.8 43.8 1.0
SD B:MET367 2.9 40.7 1.0
C B:THR364 3.2 43.5 1.0
C B:ALA408 3.3 45.3 1.0
C B:ILE406 3.3 41.3 1.0
OG1 B:THR364 3.4 47.9 1.0
C B:SER405 3.5 36.5 1.0
CA B:ILE406 3.5 42.2 1.0
CE B:MET367 3.7 46.0 1.0
CG B:MET367 3.7 40.9 1.0
N B:ALA408 3.8 43.6 1.0
CA B:THR364 3.9 47.8 1.0
CA B:ALA408 4.0 40.3 1.0
N B:ILE406 4.0 36.8 1.0
N B:ILE365 4.2 44.3 1.0
CB B:THR364 4.2 50.2 1.0
N B:GLY407 4.3 45.8 1.0
CB B:ALA408 4.3 42.6 1.0
C B:GLY407 4.3 47.8 1.0
N B:ALA409 4.4 45.6 1.0
CA B:ILE365 4.4 41.0 1.0
CB B:MET367 4.6 39.1 1.0
O B:ILE365 4.6 45.6 1.0
C B:ILE365 4.6 40.6 1.0
CA B:ALA409 4.7 42.2 1.0
CA B:SER405 4.8 39.0 1.0
CA B:GLY407 4.8 45.0 1.0
CB B:ILE406 4.9 39.7 1.0
O B:GLY407 5.0 53.8 1.0

Sodium binding site 6 out of 9 in 9d66

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Sodium binding site 6 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na605

b:45.2
occ:1.00
 O B:ASN366 2.2 55.0 1.0
O B:ASN451 2.7 52.3 1.0
O B:GLY362 2.8 50.5 1.0
OD2 B:ASP455 2.9 57.8 1.0
C B:ASN366 3.4 53.1 1.0
C B:ASN451 3.5 47.8 1.0
CB B:ASN451 3.6 38.1 1.0
OD1 B:ASP455 3.6 54.7 1.0
CG B:ASP455 3.7 58.5 1.0
CG B:MET367 3.7 40.9 1.0
O B:ALA363 3.7 53.6 1.0
C B:ALA363 3.7 48.3 1.0
CA B:ALA363 3.8 47.3 1.0
C B:GLY362 3.8 46.1 1.0
CA B:ASN451 3.9 44.6 1.0
CA B:MET367 4.0 40.2 1.0
N B:MET367 4.1 49.3 1.0
N B:ALA363 4.3 46.0 1.0
N B:THR364 4.3 47.5 1.0
CB B:MET367 4.4 39.1 1.0
OG B:SER333 4.4 50.1 1.0
CA B:ASN366 4.4 45.6 1.0
CB B:SER333 4.5 44.5 1.0
N B:VAL452 4.5 43.7 1.0
CG B:ASN451 4.5 37.2 1.0
N B:ASN366 4.6 41.7 1.0
CB B:ASN366 4.8 43.3 1.0
CE B:MET367 4.8 46.0 1.0
CA B:THR364 4.8 47.8 1.0
CA B:VAL452 4.9 43.7 1.0

Sodium binding site 7 out of 9 in 9d66

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Sodium binding site 7 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na601

b:61.2
occ:1.00
 OD1 C:ASP368 2.1 56.1 1.0
OG1 C:THR102 2.2 52.9 1.0
OD1 C:ASN366 2.2 50.7 1.0
O C:TYR98 2.4 53.0 1.0
OG1 C:THR101 2.5 51.0 1.0
N C:THR102 2.8 50.1 1.0
CG C:ASP368 3.1 57.2 1.0
CB C:THR102 3.2 48.2 1.0
CA C:THR102 3.3 44.3 1.0
CG C:ASN366 3.3 50.1 1.0
C C:TYR98 3.4 51.3 1.0
OD2 C:ASP368 3.4 61.6 1.0
C C:THR101 3.4 49.6 1.0
CB C:THR101 3.4 49.9 1.0
CA C:TYR98 3.8 51.3 1.0
CA C:THR101 3.9 50.8 1.0
ND2 C:ASN366 4.0 57.7 1.0
N C:THR101 4.2 51.2 1.0
O C:THR101 4.2 53.0 1.0
O C:TYR97 4.4 56.0 1.0
CB C:ASN366 4.4 43.3 1.0
CB C:ASP368 4.4 43.4 1.0
CG2 C:THR102 4.4 47.6 1.0
CA C:ASN366 4.5 45.6 1.0
CB C:TYR98 4.6 49.5 1.0
N C:PHE99 4.6 56.6 1.0
N C:ASP368 4.6 53.2 1.0
CA C:ASP368 4.7 48.7 1.0
CG2 C:THR101 4.8 54.5 1.0
C C:THR102 4.8 48.5 1.0
N C:MET367 4.9 49.3 1.0
C C:ASN366 4.9 53.1 1.0
N C:TYR98 4.9 54.4 1.0

Sodium binding site 8 out of 9 in 9d66

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Sodium binding site 8 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na602

b:49.8
occ:1.00
 O C:THR364 2.1 45.9 1.0
O C:ALA408 2.1 45.4 1.0
O C:SER405 2.4 44.1 1.0
O C:ILE406 2.8 43.8 1.0
SD C:MET367 2.9 40.7 1.0
C C:THR364 3.2 43.5 1.0
C C:ALA408 3.3 45.3 1.0
C C:ILE406 3.3 41.3 1.0
OG1 C:THR364 3.4 47.9 1.0
C C:SER405 3.5 36.5 1.0
CA C:ILE406 3.5 42.2 1.0
CE C:MET367 3.7 46.0 1.0
CG C:MET367 3.7 40.9 1.0
N C:ALA408 3.8 43.6 1.0
CA C:THR364 3.9 47.8 1.0
CA C:ALA408 4.0 40.3 1.0
N C:ILE406 4.0 36.8 1.0
N C:ILE365 4.2 44.3 1.0
CB C:THR364 4.2 50.2 1.0
N C:GLY407 4.3 45.8 1.0
CB C:ALA408 4.3 42.6 1.0
C C:GLY407 4.3 47.8 1.0
N C:ALA409 4.4 45.6 1.0
CA C:ILE365 4.4 41.0 1.0
CB C:MET367 4.6 39.1 1.0
O C:ILE365 4.6 45.6 1.0
C C:ILE365 4.6 40.6 1.0
CA C:ALA409 4.7 42.2 1.0
CA C:SER405 4.8 39.0 1.0
CA C:GLY407 4.8 45.0 1.0
CB C:ILE406 4.9 39.7 1.0
O C:GLY407 5.0 53.8 1.0

Sodium binding site 9 out of 9 in 9d66

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Sodium binding site 9 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound L- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na604

b:45.2
occ:1.00
 O C:ASN366 2.2 55.0 1.0
O C:ASN451 2.7 52.3 1.0
O C:GLY362 2.8 50.5 1.0
OD2 C:ASP455 2.9 57.8 1.0
C C:ASN366 3.4 53.1 1.0
C C:ASN451 3.5 47.8 1.0
CB C:ASN451 3.6 38.1 1.0
OD1 C:ASP455 3.6 54.7 1.0
CG C:ASP455 3.7 58.5 1.0
CG C:MET367 3.7 40.9 1.0
O C:ALA363 3.7 53.6 1.0
C C:ALA363 3.7 48.3 1.0
CA C:ALA363 3.8 47.3 1.0
C C:GLY362 3.8 46.1 1.0
CA C:ASN451 3.9 44.6 1.0
CA C:MET367 4.0 40.2 1.0
N C:MET367 4.1 49.3 1.0
N C:ALA363 4.3 46.0 1.0
N C:THR364 4.3 47.5 1.0
CB C:MET367 4.4 39.1 1.0
OG C:SER333 4.4 50.1 1.0
CA C:ASN366 4.4 45.6 1.0
CB C:SER333 4.5 44.5 1.0
N C:VAL452 4.5 43.7 1.0
CG C:ASN451 4.5 37.2 1.0
N C:ASN366 4.6 41.7 1.0
CB C:ASN366 4.8 43.3 1.0
CE C:MET367 4.8 46.0 1.0
CA C:THR364 4.8 47.8 1.0
CA C:VAL452 4.9 43.7 1.0

Reference:

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
Page generated: Sat Feb 8 23:50:19 2025

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