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Sodium in PDB 8ctc: Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound Glutamate in An Intermediate Outward Facing State

Other elements in 8ctc:

The structure of Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound Glutamate 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 Glutamate in An Intermediate Outward Facing State (pdb code 8ctc). 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 Glutamate in An Intermediate Outward Facing State, PDB code: 8ctc:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 8ctc

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Sodium binding site 1 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound Glutamate 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 Glutamate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:58.8
occ:1.00
 O A:ASN366 2.6 60.7 1.0
OD2 A:ASP455 2.6 60.7 1.0
O A:GLY362 2.9 57.1 1.0
O A:ALA363 3.3 56.6 1.0
C A:ALA363 3.4 55.6 1.0
O A:ASN451 3.4 61.2 1.0
CA A:ALA363 3.5 56.1 1.0
CG A:ASP455 3.6 61.2 1.0
C A:ASN366 3.7 58.6 1.0
C A:GLY362 3.9 56.6 1.0
CG A:MET367 3.9 54.9 1.0
C A:ASN451 4.0 58.8 1.0
OD1 A:ASP455 4.0 62.1 1.0
CB A:ASN451 4.1 56.1 1.0
OG A:SER333 4.1 57.2 1.0
N A:THR364 4.1 54.7 1.0
N A:ALA363 4.2 56.4 1.0
CB A:SER333 4.3 56.9 1.0
CA A:ASN451 4.5 56.5 1.0
CE A:MET367 4.6 55.5 1.0
N A:MET367 4.6 57.9 1.0
CA A:ASN366 4.6 57.8 1.0
CA A:MET367 4.6 57.7 1.0
N A:ASN366 4.7 54.9 1.0
CA A:THR364 4.7 55.4 1.0
CB A:ALA363 4.7 58.3 1.0
CB A:ASN366 4.8 61.1 1.0
N A:VAL452 4.8 58.7 1.0
CB A:ASP455 4.9 62.8 1.0
CB A:MET367 4.9 55.4 1.0
CG A:ASN451 4.9 56.8 1.0

Sodium binding site 2 out of 9 in 8ctc

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Sodium binding site 2 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound Glutamate 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 Glutamate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:58.3
occ:1.00
 O A:ALA408 2.1 56.9 1.0
O A:THR364 2.2 54.0 1.0
O A:SER405 2.2 59.0 1.0
O A:ILE406 2.7 55.7 1.0
C A:ILE406 3.0 56.1 1.0
N A:ALA408 3.1 56.5 1.0
C A:ALA408 3.1 56.0 1.0
C A:SER405 3.3 57.5 1.0
CA A:ILE406 3.4 55.0 1.0
SD A:MET367 3.4 54.1 1.0
C A:THR364 3.4 54.8 1.0
OG1 A:THR364 3.5 54.8 1.0
CA A:ALA408 3.6 56.8 1.0
N A:GLY407 3.7 57.7 1.0
N A:ILE406 3.8 57.0 1.0
C A:GLY407 4.0 55.3 1.0
CB A:ALA408 4.1 57.7 1.0
CE A:MET367 4.1 55.5 1.0
CA A:THR364 4.2 55.4 1.0
CA A:GLY407 4.3 55.8 1.0
N A:ALA409 4.3 55.5 1.0
CG A:MET367 4.4 54.9 1.0
N A:ILE365 4.4 55.1 1.0
CB A:THR364 4.5 55.4 1.0
CA A:ILE365 4.6 54.2 1.0
CA A:SER405 4.6 57.0 1.0
O A:ALA404 4.8 63.3 1.0
CA A:ALA409 4.8 55.7 1.0
CB A:ILE406 4.8 54.0 1.0
O A:ILE365 4.9 57.0 1.0
O A:GLY407 4.9 54.5 1.0
CB A:MET367 5.0 55.4 1.0
C A:ILE365 5.0 55.3 1.0

Sodium binding site 3 out of 9 in 8ctc

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Sodium binding site 3 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound Glutamate 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 Glutamate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:67.9
occ:1.00
 OG1 A:THR102 1.9 65.2 1.0
OD1 A:ASP368 2.3 63.9 1.0
OD1 A:ASN366 2.4 64.5 1.0
O A:TYR98 2.8 67.0 1.0
OG1 A:THR101 2.8 67.0 1.0
N A:THR102 3.2 64.7 1.0
CB A:THR102 3.2 63.2 1.0
CG A:ASN366 3.4 62.9 1.0
CA A:THR102 3.5 62.4 1.0
CG A:ASP368 3.6 63.5 1.0
C A:TYR98 3.7 67.7 1.0
C A:THR101 3.9 65.1 1.0
CA A:TYR98 4.0 67.2 1.0
CB A:THR101 4.0 65.0 1.0
CA A:ASN366 4.2 57.8 1.0
ND2 A:ASN366 4.2 63.9 1.0
N A:MET367 4.3 57.9 1.0
CG2 A:THR102 4.3 62.0 1.0
OD2 A:ASP368 4.3 66.3 1.0
CB A:ASN366 4.3 61.1 1.0
CA A:THR101 4.4 64.6 1.0
N A:ASP368 4.5 58.9 1.0
C A:ASN366 4.5 58.6 1.0
CB A:ASP368 4.6 61.0 1.0
CB A:TYR98 4.6 66.4 1.0
CA A:ASP368 4.6 59.5 1.0
O A:THR101 4.7 65.4 1.0
C A:MET367 4.7 59.2 1.0
N A:THR101 4.8 64.8 1.0
O A:TYR97 4.9 68.2 1.0
N A:PHE99 4.9 68.4 1.0

Sodium binding site 4 out of 9 in 8ctc

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Sodium binding site 4 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound Glutamate 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 Glutamate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:58.8
occ:1.00
 O B:ASN366 2.6 60.7 1.0
OD2 B:ASP455 2.6 60.7 1.0
O B:GLY362 2.9 57.1 1.0
O B:ALA363 3.2 56.6 1.0
C B:ALA363 3.4 55.6 1.0
O B:ASN451 3.4 61.2 1.0
CA B:ALA363 3.5 56.1 1.0
CG B:ASP455 3.6 61.2 1.0
C B:ASN366 3.7 58.6 1.0
C B:GLY362 3.9 56.6 1.0
CG B:MET367 3.9 54.9 1.0
C B:ASN451 4.0 58.8 1.0
OD1 B:ASP455 4.0 62.1 1.0
CB B:ASN451 4.1 56.1 1.0
OG B:SER333 4.1 57.2 1.0
N B:THR364 4.1 54.7 1.0
N B:ALA363 4.2 56.4 1.0
CB B:SER333 4.3 56.9 1.0
CA B:ASN451 4.5 56.5 1.0
CE B:MET367 4.6 55.5 1.0
N B:MET367 4.6 57.9 1.0
CA B:ASN366 4.6 57.8 1.0
CA B:MET367 4.6 57.7 1.0
N B:ASN366 4.7 54.9 1.0
CA B:THR364 4.7 55.4 1.0
CB B:ALA363 4.7 58.3 1.0
CB B:ASN366 4.8 61.1 1.0
N B:VAL452 4.8 58.7 1.0
CB B:ASP455 4.9 62.8 1.0
CB B:MET367 4.9 55.4 1.0
CG B:ASN451 4.9 56.8 1.0

Sodium binding site 5 out of 9 in 8ctc

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Sodium binding site 5 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound Glutamate 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 Glutamate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:58.3
occ:1.00
 O B:ALA408 2.1 56.9 1.0
O B:THR364 2.2 54.0 1.0
O B:SER405 2.2 59.0 1.0
O B:ILE406 2.7 55.7 1.0
C B:ILE406 3.0 56.1 1.0
N B:ALA408 3.1 56.5 1.0
C B:ALA408 3.1 56.0 1.0
C B:SER405 3.3 57.5 1.0
CA B:ILE406 3.4 55.0 1.0
SD B:MET367 3.4 54.1 1.0
C B:THR364 3.4 54.8 1.0
OG1 B:THR364 3.5 54.8 1.0
CA B:ALA408 3.6 56.8 1.0
N B:GLY407 3.7 57.7 1.0
N B:ILE406 3.8 57.0 1.0
C B:GLY407 4.0 55.3 1.0
CB B:ALA408 4.1 57.7 1.0
CE B:MET367 4.1 55.5 1.0
CA B:THR364 4.2 55.4 1.0
CA B:GLY407 4.3 55.8 1.0
N B:ALA409 4.3 55.5 1.0
CG B:MET367 4.4 54.9 1.0
N B:ILE365 4.4 55.1 1.0
CB B:THR364 4.5 55.4 1.0
CA B:ILE365 4.6 54.2 1.0
CA B:SER405 4.6 57.0 1.0
O B:ALA404 4.8 63.3 1.0
CA B:ALA409 4.8 55.7 1.0
CB B:ILE406 4.8 54.0 1.0
O B:ILE365 4.9 57.0 1.0
O B:GLY407 4.9 54.5 1.0
CB B:MET367 5.0 55.4 1.0
C B:ILE365 5.0 55.3 1.0

Sodium binding site 6 out of 9 in 8ctc

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Sodium binding site 6 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound Glutamate 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 Glutamate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na603

b:67.9
occ:1.00
 OG1 B:THR102 1.9 65.2 1.0
OD1 B:ASP368 2.3 63.9 1.0
OD1 B:ASN366 2.4 64.5 1.0
O B:TYR98 2.8 67.0 1.0
OG1 B:THR101 2.8 67.0 1.0
N B:THR102 3.2 64.7 1.0
CB B:THR102 3.2 63.2 1.0
CG B:ASN366 3.4 62.9 1.0
CA B:THR102 3.5 62.4 1.0
CG B:ASP368 3.6 63.5 1.0
C B:TYR98 3.7 67.7 1.0
C B:THR101 3.9 65.1 1.0
CA B:TYR98 4.0 67.2 1.0
CB B:THR101 4.0 65.0 1.0
CA B:ASN366 4.2 57.8 1.0
ND2 B:ASN366 4.2 63.9 1.0
N B:MET367 4.3 57.9 1.0
CG2 B:THR102 4.3 62.0 1.0
OD2 B:ASP368 4.3 66.3 1.0
CB B:ASN366 4.3 61.1 1.0
CA B:THR101 4.4 64.6 1.0
C B:ASN366 4.5 58.6 1.0
N B:ASP368 4.5 58.9 1.0
CB B:ASP368 4.6 61.0 1.0
CB B:TYR98 4.6 66.4 1.0
CA B:ASP368 4.6 59.5 1.0
O B:THR101 4.7 65.4 1.0
C B:MET367 4.7 59.2 1.0
N B:THR101 4.8 64.8 1.0
O B:TYR97 4.9 68.2 1.0
N B:PHE99 4.9 68.4 1.0

Sodium binding site 7 out of 9 in 8ctc

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Sodium binding site 7 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound Glutamate 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 Glutamate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na601

b:58.8
occ:1.00
 O C:ASN366 2.6 60.7 1.0
OD2 C:ASP455 2.6 60.7 1.0
O C:GLY362 2.9 57.1 1.0
O C:ALA363 3.2 56.6 1.0
C C:ALA363 3.4 55.6 1.0
O C:ASN451 3.4 61.2 1.0
CA C:ALA363 3.5 56.1 1.0
CG C:ASP455 3.6 61.2 1.0
C C:ASN366 3.7 58.6 1.0
C C:GLY362 3.9 56.6 1.0
CG C:MET367 3.9 54.9 1.0
C C:ASN451 4.0 58.8 1.0
OD1 C:ASP455 4.0 62.1 1.0
CB C:ASN451 4.1 56.1 1.0
OG C:SER333 4.1 57.2 1.0
N C:THR364 4.1 54.7 1.0
N C:ALA363 4.2 56.4 1.0
CB C:SER333 4.3 56.9 1.0
CA C:ASN451 4.5 56.5 1.0
CE C:MET367 4.6 55.5 1.0
N C:MET367 4.6 57.9 1.0
CA C:ASN366 4.6 57.8 1.0
CA C:MET367 4.6 57.7 1.0
N C:ASN366 4.7 54.9 1.0
CA C:THR364 4.7 55.4 1.0
CB C:ALA363 4.7 58.3 1.0
CB C:ASN366 4.8 61.1 1.0
N C:VAL452 4.8 58.7 1.0
CB C:ASP455 4.9 62.8 1.0
CB C:MET367 4.9 55.4 1.0
CG C:ASN451 4.9 56.8 1.0

Sodium binding site 8 out of 9 in 8ctc

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Sodium binding site 8 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound Glutamate 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 Glutamate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na602

b:58.3
occ:1.00
 O C:ALA408 2.1 56.9 1.0
O C:THR364 2.2 54.0 1.0
O C:SER405 2.2 59.0 1.0
O C:ILE406 2.7 55.7 1.0
C C:ILE406 3.0 56.1 1.0
N C:ALA408 3.1 56.5 1.0
C C:ALA408 3.1 56.0 1.0
C C:SER405 3.3 57.5 1.0
CA C:ILE406 3.4 55.0 1.0
SD C:MET367 3.4 54.1 1.0
C C:THR364 3.4 54.8 1.0
OG1 C:THR364 3.5 54.8 1.0
CA C:ALA408 3.6 56.8 1.0
N C:GLY407 3.7 57.7 1.0
N C:ILE406 3.8 57.0 1.0
C C:GLY407 4.0 55.3 1.0
CB C:ALA408 4.1 57.7 1.0
CE C:MET367 4.1 55.5 1.0
CA C:THR364 4.2 55.4 1.0
CA C:GLY407 4.3 55.8 1.0
N C:ALA409 4.3 55.5 1.0
CG C:MET367 4.4 54.9 1.0
N C:ILE365 4.4 55.1 1.0
CB C:THR364 4.5 55.4 1.0
CA C:ILE365 4.6 54.2 1.0
CA C:SER405 4.6 57.0 1.0
O C:ALA404 4.8 63.3 1.0
CA C:ALA409 4.8 55.7 1.0
CB C:ILE406 4.8 54.0 1.0
O C:ILE365 4.9 57.0 1.0
O C:GLY407 4.9 54.5 1.0
CB C:MET367 5.0 55.4 1.0
C C:ILE365 5.0 55.3 1.0

Sodium binding site 9 out of 9 in 8ctc

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Sodium binding site 9 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound Glutamate 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 Glutamate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na603

b:67.9
occ:1.00
 OG1 C:THR102 1.9 65.2 1.0
OD1 C:ASP368 2.3 63.9 1.0
OD1 C:ASN366 2.4 64.5 1.0
O C:TYR98 2.8 67.0 1.0
OG1 C:THR101 2.8 67.0 1.0
N C:THR102 3.2 64.7 1.0
CB C:THR102 3.2 63.2 1.0
CG C:ASN366 3.4 62.9 1.0
CA C:THR102 3.5 62.4 1.0
CG C:ASP368 3.6 63.5 1.0
C C:TYR98 3.7 67.7 1.0
C C:THR101 3.9 65.1 1.0
CA C:TYR98 4.0 67.2 1.0
CB C:THR101 4.0 65.0 1.0
CA C:ASN366 4.2 57.8 1.0
ND2 C:ASN366 4.2 63.9 1.0
N C:MET367 4.3 57.9 1.0
CG2 C:THR102 4.3 62.0 1.0
OD2 C:ASP368 4.3 66.3 1.0
CB C:ASN366 4.3 61.1 1.0
CA C:THR101 4.4 64.6 1.0
N C:ASP368 4.5 58.9 1.0
C C:ASN366 4.5 58.6 1.0
CB C:ASP368 4.6 61.0 1.0
CB C:TYR98 4.6 66.4 1.0
CA C:ASP368 4.6 59.5 1.0
O C:THR101 4.7 65.4 1.0
C C:MET367 4.7 59.2 1.0
N C:THR101 4.8 64.8 1.0
O C:TYR97 4.9 68.2 1.0
N C:PHE99 4.9 68.4 1.0

Reference:

B.Qiu, O.Boudker. Symport and Antiport Mechanisms of Human Glutamate Transporters Nat Commun 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-38120-5
Page generated: Wed Oct 9 11:06:09 2024

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