Atomistry » Sodium » PDB 9b1u-9end » 9d67
Atomistry »
  Sodium »
    PDB 9b1u-9end »
      9d67 »

Sodium in PDB 9d67: Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound D- Aspartate in An Intermediate Outward Facing State

Other elements in 9d67:

The structure of Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound D- 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 D- Aspartate in An Intermediate Outward Facing State (pdb code 9d67). 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 D- Aspartate in An Intermediate Outward Facing State, PDB code: 9d67:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 9d67

Go back to Sodium Binding Sites List in 9d67
Sodium binding site 1 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound D- 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 D- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:62.6
occ:1.00
 O A:ASN366 2.6 71.1 1.0
OD2 A:ASP455 2.7 70.5 1.0
O A:GLY362 2.7 63.8 1.0
CA A:ALA363 3.4 56.9 1.0
O A:ALA363 3.4 54.5 1.0
CG A:ASP455 3.5 69.6 1.0
O A:ASN451 3.5 66.9 1.0
C A:ALA363 3.5 55.8 1.0
OD1 A:ASP455 3.5 69.0 1.0
C A:GLY362 3.7 64.8 1.0
C A:ASN366 3.7 66.4 1.0
N A:ALA363 3.9 61.1 1.0
C A:ASN451 4.0 64.3 1.0
CB A:SER333 4.0 54.0 1.0
OG A:SER333 4.1 60.6 1.0
CB A:ASN451 4.2 62.0 1.0
CG A:MET367 4.3 60.4 1.0
CA A:MET367 4.4 62.3 1.0
N A:THR364 4.4 62.1 1.0
N A:MET367 4.5 61.5 1.0
CB A:ALA363 4.6 57.1 1.0
N A:VAL452 4.6 68.0 1.0
CA A:ASN451 4.6 62.7 1.0
CA A:ASN366 4.7 63.3 1.0
CB A:ASP455 4.8 69.0 1.0
CA A:VAL452 4.8 62.9 1.0
CB A:ASN366 4.9 66.7 1.0
CG A:ASN451 4.9 58.8 1.0
CE A:MET367 4.9 54.6 1.0
CB A:MET367 4.9 56.9 1.0
N A:ASN366 5.0 59.1 1.0
CA A:GLY362 5.0 61.1 1.0
OD1 A:ASN451 5.0 65.6 1.0

Sodium binding site 2 out of 9 in 9d67

Go back to Sodium Binding Sites List in 9d67
Sodium binding site 2 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound D- 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 D- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:69.9
occ:1.00
 O A:THR364 2.1 58.2 1.0
O A:ALA408 2.2 57.2 1.0
O A:SER405 2.3 59.1 1.0
O A:ILE406 2.8 52.2 1.0
SD A:MET367 2.9 40.3 1.0
C A:ILE406 3.2 56.9 1.0
C A:ALA408 3.3 59.3 1.0
CG A:MET367 3.3 60.4 1.0
C A:THR364 3.3 57.2 1.0
C A:SER405 3.4 55.8 1.0
N A:ALA408 3.5 57.1 1.0
CE A:MET367 3.5 54.6 1.0
CA A:ILE406 3.7 61.2 1.0
CA A:ALA408 3.8 59.3 1.0
N A:ILE406 4.0 61.2 1.0
N A:GLY407 4.0 59.0 1.0
O A:ILE365 4.1 63.9 1.0
CA A:THR364 4.2 61.1 1.0
C A:GLY407 4.2 61.5 1.0
N A:ILE365 4.3 57.6 1.0
CB A:MET367 4.3 56.9 1.0
CB A:ALA408 4.3 57.9 1.0
CA A:ILE365 4.3 56.5 1.0
N A:ALA409 4.4 58.6 1.0
OG1 A:THR364 4.4 65.4 1.0
C A:ILE365 4.5 54.3 1.0
CA A:GLY407 4.5 60.9 1.0
CA A:SER405 4.7 57.4 1.0
CA A:ALA409 4.8 57.6 1.0
O A:ALA404 4.9 65.9 1.0
CB A:THR364 5.0 62.5 1.0
O A:ALA409 5.0 54.5 1.0
C A:ALA409 5.0 57.4 1.0

Sodium binding site 3 out of 9 in 9d67

Go back to Sodium Binding Sites List in 9d67
Sodium binding site 3 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound D- 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 D- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:71.5
occ:1.00
 OG1 A:THR102 2.2 68.0 1.0
OD1 A:ASP368 2.2 71.1 1.0
OG1 A:THR101 2.2 69.4 1.0
OD1 A:ASN366 2.3 70.4 1.0
O A:TYR98 2.3 74.5 1.0
N A:THR102 2.4 68.6 1.0
CB A:THR102 3.0 66.9 1.0
CA A:THR102 3.0 64.6 1.0
C A:THR101 3.2 69.9 1.0
CG A:ASP368 3.3 68.7 1.0
C A:TYR98 3.3 72.9 1.0
CB A:THR101 3.3 67.7 1.0
CG A:ASN366 3.5 64.5 1.0
CA A:THR101 3.6 69.9 1.0
CA A:TYR98 3.8 68.0 1.0
OD2 A:ASP368 3.8 70.7 1.0
N A:THR101 4.0 71.8 1.0
O A:THR101 4.0 69.6 1.0
ND2 A:ASN366 4.1 65.7 1.0
O A:TYR97 4.2 74.7 1.0
CG2 A:THR102 4.4 67.8 1.0
CB A:ASP368 4.4 61.1 1.0
C A:THR102 4.5 64.7 1.0
N A:PHE99 4.5 73.3 1.0
CG2 A:THR101 4.6 67.8 1.0
CB A:ASN366 4.6 66.7 1.0
CB A:TYR98 4.7 66.1 1.0
CA A:ASN366 4.7 63.3 1.0
CA A:ASP368 4.7 58.9 1.0
C A:PHE99 4.8 68.9 1.0
O A:PHE99 4.8 69.8 1.0
N A:TYR98 4.9 70.3 1.0
N A:ASP368 4.9 64.6 1.0
CA A:PHE99 4.9 69.2 1.0
C A:ALA100 5.0 70.6 1.0
C A:TYR97 5.0 74.1 1.0

Sodium binding site 4 out of 9 in 9d67

Go back to Sodium Binding Sites List in 9d67
Sodium binding site 4 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound D- 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 D- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:71.5
occ:1.00
 OG1 B:THR102 2.2 68.0 1.0
OD1 B:ASP368 2.2 71.1 1.0
OG1 B:THR101 2.2 69.4 1.0
OD1 B:ASN366 2.3 70.4 1.0
O B:TYR98 2.3 74.5 1.0
N B:THR102 2.4 68.6 1.0
CB B:THR102 3.0 66.9 1.0
CA B:THR102 3.0 64.6 1.0
C B:THR101 3.2 69.9 1.0
CG B:ASP368 3.3 68.7 1.0
C B:TYR98 3.3 72.9 1.0
CB B:THR101 3.3 67.7 1.0
CG B:ASN366 3.5 64.5 1.0
CA B:THR101 3.6 69.9 1.0
CA B:TYR98 3.8 68.0 1.0
OD2 B:ASP368 3.8 70.7 1.0
N B:THR101 4.0 71.8 1.0
O B:THR101 4.0 69.6 1.0
ND2 B:ASN366 4.1 65.7 1.0
O B:TYR97 4.2 74.7 1.0
CG2 B:THR102 4.4 67.8 1.0
CB B:ASP368 4.4 61.1 1.0
C B:THR102 4.5 64.7 1.0
N B:PHE99 4.5 73.3 1.0
CG2 B:THR101 4.6 67.8 1.0
CB B:ASN366 4.6 66.7 1.0
CB B:TYR98 4.7 66.1 1.0
CA B:ASN366 4.7 63.3 1.0
CA B:ASP368 4.7 58.9 1.0
C B:PHE99 4.8 68.9 1.0
O B:PHE99 4.8 69.8 1.0
N B:TYR98 4.9 70.3 1.0
N B:ASP368 4.9 64.6 1.0
CA B:PHE99 4.9 69.2 1.0
C B:ALA100 5.0 70.6 1.0
C B:TYR97 5.0 74.1 1.0

Sodium binding site 5 out of 9 in 9d67

Go back to Sodium Binding Sites List in 9d67
Sodium binding site 5 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound D- 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 D- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na603

b:69.9
occ:1.00
 O B:THR364 2.1 58.2 1.0
O B:ALA408 2.2 57.2 1.0
O B:SER405 2.3 59.1 1.0
O B:ILE406 2.8 52.2 1.0
SD B:MET367 2.9 40.3 1.0
C B:ILE406 3.2 56.9 1.0
C B:ALA408 3.3 59.3 1.0
CG B:MET367 3.3 60.4 1.0
C B:THR364 3.3 57.2 1.0
C B:SER405 3.4 55.8 1.0
N B:ALA408 3.5 57.1 1.0
CE B:MET367 3.5 54.6 1.0
CA B:ILE406 3.7 61.2 1.0
CA B:ALA408 3.8 59.3 1.0
N B:ILE406 4.0 61.2 1.0
N B:GLY407 4.0 59.0 1.0
O B:ILE365 4.1 63.9 1.0
CA B:THR364 4.2 61.1 1.0
C B:GLY407 4.2 61.5 1.0
N B:ILE365 4.3 57.6 1.0
CB B:MET367 4.3 56.9 1.0
CB B:ALA408 4.3 57.9 1.0
CA B:ILE365 4.3 56.5 1.0
N B:ALA409 4.4 58.6 1.0
OG1 B:THR364 4.4 65.4 1.0
C B:ILE365 4.5 54.3 1.0
CA B:GLY407 4.6 60.9 1.0
CA B:SER405 4.7 57.4 1.0
CA B:ALA409 4.8 57.6 1.0
O B:ALA404 4.9 65.9 1.0
CB B:THR364 5.0 62.5 1.0
O B:ALA409 5.0 54.5 1.0
C B:ALA409 5.0 57.4 1.0

Sodium binding site 6 out of 9 in 9d67

Go back to Sodium Binding Sites List in 9d67
Sodium binding site 6 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound D- 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 D- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na604

b:62.6
occ:1.00
 O B:ASN366 2.6 71.1 1.0
OD2 B:ASP455 2.7 70.5 1.0
O B:GLY362 2.7 63.8 1.0
CA B:ALA363 3.4 56.9 1.0
O B:ALA363 3.4 54.5 1.0
CG B:ASP455 3.5 69.6 1.0
O B:ASN451 3.5 66.9 1.0
C B:ALA363 3.5 55.8 1.0
OD1 B:ASP455 3.5 69.0 1.0
C B:GLY362 3.7 64.8 1.0
C B:ASN366 3.7 66.4 1.0
N B:ALA363 3.9 61.1 1.0
C B:ASN451 4.0 64.3 1.0
CB B:SER333 4.0 54.0 1.0
OG B:SER333 4.1 60.6 1.0
CB B:ASN451 4.2 62.0 1.0
CG B:MET367 4.3 60.4 1.0
CA B:MET367 4.4 62.3 1.0
N B:THR364 4.4 62.1 1.0
N B:MET367 4.5 61.5 1.0
CB B:ALA363 4.6 57.1 1.0
N B:VAL452 4.6 68.0 1.0
CA B:ASN451 4.6 62.7 1.0
CA B:ASN366 4.7 63.3 1.0
CB B:ASP455 4.8 69.0 1.0
CA B:VAL452 4.8 62.9 1.0
CB B:ASN366 4.9 66.7 1.0
CG B:ASN451 4.9 58.8 1.0
CE B:MET367 4.9 54.6 1.0
CB B:MET367 4.9 56.9 1.0
N B:ASN366 5.0 59.1 1.0
CA B:GLY362 5.0 61.1 1.0
OD1 B:ASN451 5.0 65.6 1.0

Sodium binding site 7 out of 9 in 9d67

Go back to Sodium Binding Sites List in 9d67
Sodium binding site 7 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound D- 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 D- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na601

b:62.6
occ:1.00
 O C:ASN366 2.6 71.1 1.0
OD2 C:ASP455 2.7 70.5 1.0
O C:GLY362 2.7 63.8 1.0
CA C:ALA363 3.4 56.9 1.0
O C:ALA363 3.4 54.5 1.0
CG C:ASP455 3.5 69.6 1.0
O C:ASN451 3.5 66.9 1.0
C C:ALA363 3.5 55.8 1.0
OD1 C:ASP455 3.5 69.0 1.0
C C:GLY362 3.7 64.8 1.0
C C:ASN366 3.7 66.4 1.0
N C:ALA363 3.9 61.1 1.0
C C:ASN451 4.0 64.3 1.0
CB C:SER333 4.0 54.0 1.0
OG C:SER333 4.1 60.6 1.0
CB C:ASN451 4.2 62.0 1.0
CG C:MET367 4.3 60.4 1.0
CA C:MET367 4.4 62.3 1.0
N C:THR364 4.4 62.1 1.0
N C:MET367 4.5 61.5 1.0
CB C:ALA363 4.6 57.1 1.0
N C:VAL452 4.6 68.0 1.0
CA C:ASN451 4.6 62.7 1.0
CA C:ASN366 4.7 63.3 1.0
CB C:ASP455 4.8 69.0 1.0
CA C:VAL452 4.8 62.9 1.0
CB C:ASN366 4.9 66.7 1.0
CG C:ASN451 4.9 58.8 1.0
CE C:MET367 4.9 54.6 1.0
CB C:MET367 4.9 56.9 1.0
N C:ASN366 5.0 59.1 1.0
CA C:GLY362 5.0 61.1 1.0
OD1 C:ASN451 5.0 65.6 1.0

Sodium binding site 8 out of 9 in 9d67

Go back to Sodium Binding Sites List in 9d67
Sodium binding site 8 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound D- 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 D- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na602

b:69.9
occ:1.00
 O C:THR364 2.1 58.2 1.0
O C:ALA408 2.2 57.2 1.0
O C:SER405 2.3 59.1 1.0
O C:ILE406 2.8 52.2 1.0
SD C:MET367 2.9 40.3 1.0
C C:ILE406 3.2 56.9 1.0
C C:ALA408 3.3 59.3 1.0
CG C:MET367 3.3 60.4 1.0
C C:THR364 3.3 57.2 1.0
C C:SER405 3.4 55.8 1.0
N C:ALA408 3.5 57.1 1.0
CE C:MET367 3.5 54.6 1.0
CA C:ILE406 3.7 61.2 1.0
CA C:ALA408 3.8 59.3 1.0
N C:ILE406 4.0 61.2 1.0
N C:GLY407 4.0 59.0 1.0
O C:ILE365 4.1 63.9 1.0
CA C:THR364 4.2 61.1 1.0
C C:GLY407 4.2 61.5 1.0
N C:ILE365 4.3 57.6 1.0
CB C:MET367 4.3 56.9 1.0
CB C:ALA408 4.3 57.9 1.0
CA C:ILE365 4.3 56.5 1.0
N C:ALA409 4.4 58.6 1.0
OG1 C:THR364 4.4 65.4 1.0
C C:ILE365 4.5 54.3 1.0
CA C:GLY407 4.5 60.9 1.0
CA C:SER405 4.7 57.4 1.0
CA C:ALA409 4.8 57.6 1.0
O C:ALA404 4.9 65.9 1.0
CB C:THR364 5.0 62.5 1.0
O C:ALA409 5.0 54.5 1.0
C C:ALA409 5.0 57.4 1.0

Sodium binding site 9 out of 9 in 9d67

Go back to Sodium Binding Sites List in 9d67
Sodium binding site 9 out of 9 in the Human Excitatory Amino Acid Transporter 3 (EAAT3) with Bound D- 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 D- Aspartate in An Intermediate Outward Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na603

b:71.5
occ:1.00
 OG1 C:THR102 2.2 68.0 1.0
OD1 C:ASP368 2.2 71.1 1.0
OG1 C:THR101 2.2 69.4 1.0
OD1 C:ASN366 2.3 70.4 1.0
O C:TYR98 2.3 74.5 1.0
N C:THR102 2.4 68.6 1.0
CB C:THR102 3.0 66.9 1.0
CA C:THR102 3.0 64.6 1.0
C C:THR101 3.2 69.9 1.0
CG C:ASP368 3.3 68.7 1.0
C C:TYR98 3.3 72.9 1.0
CB C:THR101 3.3 67.7 1.0
CG C:ASN366 3.5 64.5 1.0
CA C:THR101 3.6 69.9 1.0
CA C:TYR98 3.8 68.0 1.0
OD2 C:ASP368 3.8 70.7 1.0
N C:THR101 4.0 71.8 1.0
O C:THR101 4.0 69.6 1.0
ND2 C:ASN366 4.1 65.7 1.0
O C:TYR97 4.2 74.7 1.0
CG2 C:THR102 4.3 67.8 1.0
CB C:ASP368 4.4 61.1 1.0
C C:THR102 4.5 64.7 1.0
N C:PHE99 4.5 73.3 1.0
CG2 C:THR101 4.6 67.8 1.0
CB C:ASN366 4.6 66.7 1.0
CB C:TYR98 4.7 66.1 1.0
CA C:ASN366 4.7 63.3 1.0
CA C:ASP368 4.7 58.9 1.0
C C:PHE99 4.8 68.9 1.0
O C:PHE99 4.8 69.8 1.0
N C:TYR98 4.9 70.3 1.0
N C:ASP368 4.9 64.6 1.0
CA C:PHE99 4.9 69.2 1.0
C C:ALA100 5.0 70.6 1.0
C C:TYR97 5.0 74.1 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

Last articles

Zn in 9EMG
Zn in 9EDL
Zn in 9BZ0
Zn in 9CKF
Zn in 9CKC
Zn in 9CKG
Zn in 9D89
Zn in 9CXI
Zn in 9CXJ
Zn in 9CXG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy