Sodium in PDB 6x3e: HEAAT3-Asymmetric-1O2I

Sodium Binding Sites:

The binding sites of Sodium atom in the HEAAT3-Asymmetric-1O2I (pdb code 6x3e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the HEAAT3-Asymmetric-1O2I, PDB code: 6x3e:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6x3e

Go back to Sodium Binding Sites List in 6x3e
Sodium binding site 1 out of 3 in the HEAAT3-Asymmetric-1O2I


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of HEAAT3-Asymmetric-1O2I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:78.0
occ:1.00
O A:ASN366 2.3 83.7 1.0
OD2 A:ASP455 2.7 83.7 1.0
O A:GLY362 2.7 74.3 1.0
O A:ASN451 3.1 83.0 1.0
OD1 A:ASP455 3.1 83.7 1.0
CG A:ASP455 3.1 83.7 1.0
C A:ASN366 3.5 83.7 1.0
ND2 A:ASN366 3.5 83.7 1.0
C A:GLY362 3.7 74.3 1.0
C A:ASN451 3.8 83.0 1.0
CA A:ALA363 3.8 73.9 1.0
CB A:ASN451 4.0 83.0 1.0
N A:ALA363 4.2 73.9 1.0
O A:ALA363 4.2 73.9 1.0
CA A:ASN451 4.2 83.0 1.0
C A:ALA363 4.2 73.9 1.0
CG A:MET367 4.3 89.4 1.0
CA A:MET367 4.3 89.4 1.0
N A:MET367 4.4 89.4 1.0
CG A:ASN366 4.4 83.7 1.0
CB A:ASP455 4.5 83.7 1.0
CA A:ASN366 4.5 83.7 1.0
OD1 A:ASN451 4.5 83.0 1.0
CB A:ASN366 4.5 83.7 1.0
CG A:ASN451 4.6 83.0 1.0
N A:VAL452 4.7 81.3 1.0
N A:ASN366 4.8 83.7 1.0
OG A:SER333 4.8 70.3 1.0
CA A:GLY362 4.8 74.3 1.0
CB A:MET367 4.9 89.4 1.0
CB A:ALA363 4.9 73.9 1.0
CB A:SER333 5.0 70.3 1.0
N A:ASP455 5.0 83.7 1.0

Sodium binding site 2 out of 3 in 6x3e

Go back to Sodium Binding Sites List in 6x3e
Sodium binding site 2 out of 3 in the HEAAT3-Asymmetric-1O2I


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of HEAAT3-Asymmetric-1O2I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:89.1
occ:1.00
O A:ALA408 2.5 90.8 1.0
O A:THR364 2.6 74.0 1.0
O A:SER405 2.6 94.9 1.0
O A:ILE406 2.6 87.6 1.0
SD A:MET367 2.6 89.4 1.0
C A:ILE406 3.2 87.6 1.0
C A:THR364 3.3 74.0 1.0
C A:ALA408 3.5 90.8 1.0
N A:ALA408 3.6 90.8 1.0
CA A:ILE406 3.6 87.6 1.0
CG A:MET367 3.6 89.4 1.0
C A:SER405 3.6 94.9 1.0
N A:ILE365 4.0 74.5 1.0
CA A:ALA408 4.0 90.8 1.0
N A:GLY407 4.1 88.2 1.0
CA A:ILE365 4.1 74.5 1.0
N A:ILE406 4.1 87.6 1.0
CA A:THR364 4.1 74.0 1.0
O A:ILE365 4.2 74.5 1.0
C A:GLY407 4.2 88.2 1.0
CE A:MET367 4.2 89.4 1.0
C A:ILE365 4.4 74.5 1.0
CB A:ALA408 4.4 90.8 1.0
CB A:MET367 4.5 89.4 1.0
CA A:GLY407 4.5 88.2 1.0
OG1 A:THR364 4.5 74.0 1.0
N A:ALA409 4.7 88.1 1.0
CA A:SER405 4.9 94.9 1.0

Sodium binding site 3 out of 3 in 6x3e

Go back to Sodium Binding Sites List in 6x3e
Sodium binding site 3 out of 3 in the HEAAT3-Asymmetric-1O2I


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of HEAAT3-Asymmetric-1O2I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:93.7
occ:1.00
OD2 A:ASP368 2.1 94.3 1.0
OD1 A:ASN366 2.2 83.7 1.0
OG1 A:THR101 2.4 93.6 1.0
OG1 A:THR102 2.5 95.9 1.0
O A:TYR98 2.8 84.5 1.0
CG A:ASP368 3.1 94.3 1.0
N A:THR102 3.2 95.9 1.0
CG A:ASN366 3.3 83.7 1.0
OD1 A:ASP368 3.4 94.3 1.0
CB A:THR101 3.6 93.6 1.0
C A:TYR98 3.6 84.5 1.0
CB A:THR102 3.6 95.9 1.0
CA A:TYR98 3.8 84.5 1.0
CA A:THR102 3.8 95.9 1.0
CB A:ASN366 3.8 83.7 1.0
C A:THR101 3.8 93.6 1.0
CA A:ASN366 4.0 83.7 1.0
CA A:THR101 4.2 93.6 1.0
CB A:TYR98 4.3 84.5 1.0
ND2 A:ASN366 4.4 83.7 1.0
CB A:ASP368 4.4 94.3 1.0
C A:ASN366 4.5 83.7 1.0
N A:THR101 4.5 93.6 1.0
N A:MET367 4.5 89.4 1.0
N A:ASP368 4.5 94.3 1.0
O A:THR101 4.6 93.6 1.0
O A:TYR97 4.7 87.7 1.0
CA A:ASP368 4.7 94.3 1.0
CD1 A:TYR98 4.8 84.5 1.0
CG2 A:THR101 4.8 93.6 1.0
CG2 A:THR102 4.8 95.9 1.0
CG A:TYR98 4.9 84.5 1.0
N A:PHE99 4.9 89.9 1.0

Reference:

B.Qiu, D.Matthies, E.Fortea, Z.Yu, O.Boudker. Cryo-Em Structures of Excitatory Amino Acid Transporter 3 Visualize Coupled Substrate, Sodium, and Proton Binding and Transport. Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
PubMed: 33658209
DOI: 10.1126/SCIADV.ABF5814
Page generated: Sat Apr 3 17:51:28 2021

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