Sodium in PDB 6x15: Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions

Other elements in 6x15:

The structure of Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions also contains other interesting chemical elements:

Mercury (Hg) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions (pdb code 6x15). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions, PDB code: 6x15:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 6x15

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Sodium binding site 1 out of 9 in the Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:37.7
occ:1.00
 O A:HOH602 2.5 36.8 1.0
OD2 A:ASP405 2.5 37.8 1.0
O A:ASN310 2.5 34.4 1.0
O A:ASN401 2.5 33.1 1.0
O A:GLY306 2.9 35.9 1.0
CG A:ASP405 3.1 37.8 1.0
OD1 A:ASP405 3.1 37.8 1.0
C A:ASN401 3.2 33.1 1.0
C A:ASN310 3.7 34.4 1.0
CB A:ASN401 3.8 33.1 1.0
CA A:ASN401 3.9 33.1 1.0
C A:GLY306 3.9 35.9 1.0
N A:VAL402 4.1 35.9 1.0
ND2 A:ASN310 4.1 34.4 1.0
CA A:ALA307 4.2 36.0 1.0
CA A:VAL402 4.4 35.9 1.0
CB A:ASP405 4.4 37.8 1.0
CG A:MET311 4.5 32.6 1.0
N A:ALA307 4.5 36.0 1.0
C A:ALA307 4.5 36.0 1.0
CB A:ASN310 4.5 34.4 1.0
CA A:ASN310 4.6 34.4 1.0
OG A:SER278 4.6 35.8 1.0
N A:MET311 4.6 32.6 1.0
O A:ALA307 4.6 36.0 1.0
CA A:MET311 4.7 32.6 1.0
CG A:ASN401 4.7 33.1 1.0
N A:ASN310 4.8 34.4 1.0
CG A:ASN310 4.8 34.4 1.0
O A:HOH603 4.9 37.7 1.0
CB A:SER278 4.9 35.8 1.0
N A:ASP405 4.9 37.8 1.0
CA A:GLY306 5.0 35.9 1.0

Sodium binding site 2 out of 9 in 6x15

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Sodium binding site 2 out of 9 in the Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:33.3
occ:1.00
 O A:SER349 2.5 32.1 1.0
O A:THR308 2.5 35.0 1.0
O A:THR352 2.5 33.3 1.0
SD A:MET311 2.9 32.6 1.0
CE A:MET311 3.0 32.6 1.0
O A:ILE350 3.1 31.4 1.0
C A:THR352 3.4 33.3 1.0
C A:THR308 3.4 35.0 1.0
N A:THR352 3.5 33.3 1.0
C A:ILE350 3.6 31.4 1.0
C A:SER349 3.7 32.1 1.0
CA A:THR352 3.7 33.3 1.0
CG A:MET311 3.7 32.6 1.0
CB A:THR352 3.7 33.3 1.0
CA A:ILE350 4.0 31.4 1.0
CA A:THR308 4.1 35.0 1.0
N A:ILE309 4.3 34.0 1.0
N A:ILE350 4.3 31.4 1.0
C A:GLY351 4.3 32.0 1.0
OG1 A:THR352 4.4 33.3 1.0
N A:GLY351 4.4 32.0 1.0
CB A:MET311 4.5 32.6 1.0
N A:ALA353 4.5 33.7 1.0
CA A:ILE309 4.6 34.0 1.0
O A:ILE309 4.6 34.0 1.0
C A:ILE309 4.7 34.0 1.0
CA A:SER349 4.7 32.1 1.0
O A:ALA353 4.7 33.7 1.0
CA A:GLY351 4.8 32.0 1.0
C A:ALA353 4.9 33.7 1.0
CG2 A:THR352 4.9 33.3 1.0
CB A:THR308 4.9 35.0 1.0

Sodium binding site 3 out of 9 in 6x15

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Sodium binding site 3 out of 9 in the Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:35.1
occ:1.00
 O A:TYR89 2.5 35.7 1.0
OD2 A:ASP312 2.5 33.5 1.0
OG A:SER93 2.5 34.3 1.0
OD1 A:ASN310 2.5 34.4 1.0
OG1 A:THR92 2.6 35.0 1.0
N A:SER93 2.7 34.3 1.0
CA A:SER93 3.2 34.3 1.0
C A:THR92 3.3 35.0 1.0
CB A:SER93 3.3 34.3 1.0
CB A:THR92 3.4 35.0 1.0
CG A:ASP312 3.4 33.5 1.0
C A:TYR89 3.5 35.7 1.0
CG A:ASN310 3.6 34.4 1.0
OD1 A:ASP312 3.8 33.5 1.0
CA A:THR92 3.8 35.0 1.0
CA A:TYR89 3.9 35.7 1.0
O A:THR92 4.0 35.0 1.0
N A:THR92 4.2 35.0 1.0
O A:HOH601 4.3 32.5 1.0
CA A:ASN310 4.4 34.4 1.0
CB A:ASN310 4.4 34.4 1.0
ND2 A:ASN310 4.5 34.4 1.0
CB A:ASP312 4.6 33.5 1.0
N A:MET311 4.6 32.6 1.0
N A:ASP312 4.6 33.5 1.0
O A:TYR88 4.6 38.1 1.0
CB A:TYR89 4.6 35.7 1.0
CA A:ASP312 4.7 33.5 1.0
C A:SER93 4.7 34.3 1.0
N A:LEU90 4.7 36.0 1.0
CG2 A:THR92 4.8 35.0 1.0
C A:ASN310 4.8 34.4 1.0
C A:MET311 4.9 32.6 1.0

Sodium binding site 4 out of 9 in 6x15

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Sodium binding site 4 out of 9 in the Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:37.7
occ:1.00
 O B:HOH602 2.5 36.8 1.0
OD2 B:ASP405 2.5 37.8 1.0
O B:ASN310 2.5 34.4 1.0
O B:ASN401 2.5 33.1 1.0
O B:GLY306 2.9 35.9 1.0
CG B:ASP405 3.1 37.8 1.0
OD1 B:ASP405 3.1 37.8 1.0
C B:ASN401 3.2 33.1 1.0
C B:ASN310 3.7 34.4 1.0
CB B:ASN401 3.8 33.1 1.0
CA B:ASN401 3.9 33.1 1.0
C B:GLY306 3.9 35.9 1.0
N B:VAL402 4.1 35.9 1.0
ND2 B:ASN310 4.1 34.4 1.0
CA B:ALA307 4.2 36.0 1.0
CA B:VAL402 4.4 35.9 1.0
CB B:ASP405 4.4 37.8 1.0
CG B:MET311 4.5 32.6 1.0
N B:ALA307 4.5 36.0 1.0
C B:ALA307 4.5 36.0 1.0
CB B:ASN310 4.5 34.4 1.0
CA B:ASN310 4.6 34.4 1.0
OG B:SER278 4.6 35.8 1.0
N B:MET311 4.6 32.6 1.0
O B:ALA307 4.6 36.0 1.0
CA B:MET311 4.7 32.6 1.0
CG B:ASN401 4.7 33.1 1.0
N B:ASN310 4.8 34.4 1.0
CG B:ASN310 4.8 34.4 1.0
O B:HOH603 4.9 37.7 1.0
CB B:SER278 4.9 35.8 1.0
N B:ASP405 4.9 37.8 1.0
CA B:GLY306 5.0 35.9 1.0

Sodium binding site 5 out of 9 in 6x15

Go back to Sodium Binding Sites List in 6x15
Sodium binding site 5 out of 9 in the Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:33.3
occ:1.00
 O B:SER349 2.5 32.1 1.0
O B:THR308 2.5 35.0 1.0
O B:THR352 2.5 33.3 1.0
SD B:MET311 2.9 32.6 1.0
CE B:MET311 3.0 32.6 1.0
O B:ILE350 3.1 31.4 1.0
C B:THR352 3.4 33.3 1.0
C B:THR308 3.4 35.0 1.0
N B:THR352 3.5 33.3 1.0
C B:ILE350 3.6 31.4 1.0
C B:SER349 3.7 32.1 1.0
CA B:THR352 3.7 33.3 1.0
CG B:MET311 3.7 32.6 1.0
CB B:THR352 3.7 33.3 1.0
CA B:ILE350 4.0 31.4 1.0
CA B:THR308 4.1 35.0 1.0
N B:ILE309 4.3 34.0 1.0
N B:ILE350 4.3 31.4 1.0
C B:GLY351 4.3 32.0 1.0
OG1 B:THR352 4.4 33.3 1.0
N B:GLY351 4.4 32.0 1.0
CB B:MET311 4.5 32.6 1.0
N B:ALA353 4.5 33.7 1.0
CA B:ILE309 4.6 34.0 1.0
O B:ILE309 4.6 34.0 1.0
C B:ILE309 4.7 34.0 1.0
CA B:SER349 4.7 32.1 1.0
O B:ALA353 4.7 33.7 1.0
CA B:GLY351 4.8 32.0 1.0
C B:ALA353 4.9 33.7 1.0
CG2 B:THR352 4.9 33.3 1.0
CB B:THR308 4.9 35.0 1.0

Sodium binding site 6 out of 9 in 6x15

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Sodium binding site 6 out of 9 in the Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na504

b:35.1
occ:1.00
 O B:TYR89 2.5 35.7 1.0
OD2 B:ASP312 2.5 33.5 1.0
OG B:SER93 2.5 34.3 1.0
OD1 B:ASN310 2.5 34.4 1.0
OG1 B:THR92 2.6 35.0 1.0
N B:SER93 2.7 34.3 1.0
CA B:SER93 3.2 34.3 1.0
C B:THR92 3.3 35.0 1.0
CB B:SER93 3.3 34.3 1.0
CB B:THR92 3.4 35.0 1.0
CG B:ASP312 3.4 33.5 1.0
C B:TYR89 3.5 35.7 1.0
CG B:ASN310 3.6 34.4 1.0
OD1 B:ASP312 3.8 33.5 1.0
CA B:THR92 3.8 35.0 1.0
CA B:TYR89 3.9 35.7 1.0
O B:THR92 4.0 35.0 1.0
N B:THR92 4.2 35.0 1.0
O B:HOH601 4.3 32.5 1.0
CA B:ASN310 4.4 34.4 1.0
CB B:ASN310 4.4 34.4 1.0
ND2 B:ASN310 4.5 34.4 1.0
CB B:ASP312 4.6 33.5 1.0
N B:MET311 4.6 32.6 1.0
N B:ASP312 4.6 33.5 1.0
O B:TYR88 4.6 38.1 1.0
CB B:TYR89 4.6 35.7 1.0
CA B:ASP312 4.7 33.5 1.0
C B:SER93 4.7 34.3 1.0
N B:LEU90 4.7 36.0 1.0
CG2 B:THR92 4.8 35.0 1.0
C B:ASN310 4.8 34.4 1.0
C B:MET311 4.9 32.6 1.0

Sodium binding site 7 out of 9 in 6x15

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Sodium binding site 7 out of 9 in the Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:37.7
occ:1.00
 O C:HOH602 2.5 36.8 1.0
OD2 C:ASP405 2.5 37.8 1.0
O C:ASN310 2.5 34.4 1.0
O C:ASN401 2.5 33.1 1.0
O C:GLY306 2.9 35.9 1.0
CG C:ASP405 3.1 37.8 1.0
OD1 C:ASP405 3.1 37.8 1.0
C C:ASN401 3.2 33.1 1.0
C C:ASN310 3.7 34.4 1.0
CB C:ASN401 3.8 33.1 1.0
CA C:ASN401 3.9 33.1 1.0
C C:GLY306 3.9 35.9 1.0
N C:VAL402 4.1 35.9 1.0
ND2 C:ASN310 4.1 34.4 1.0
CA C:ALA307 4.2 36.0 1.0
CA C:VAL402 4.4 35.9 1.0
CB C:ASP405 4.4 37.8 1.0
CG C:MET311 4.5 32.6 1.0
N C:ALA307 4.5 36.0 1.0
C C:ALA307 4.5 36.0 1.0
CB C:ASN310 4.5 34.4 1.0
CA C:ASN310 4.6 34.4 1.0
OG C:SER278 4.6 35.8 1.0
N C:MET311 4.6 32.6 1.0
O C:ALA307 4.6 36.0 1.0
CA C:MET311 4.7 32.6 1.0
CG C:ASN401 4.7 33.1 1.0
N C:ASN310 4.8 34.4 1.0
CG C:ASN310 4.8 34.4 1.0
O C:HOH603 4.9 37.7 1.0
CB C:SER278 4.9 35.8 1.0
N C:ASP405 4.9 37.8 1.0
CA C:GLY306 5.0 35.9 1.0

Sodium binding site 8 out of 9 in 6x15

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Sodium binding site 8 out of 9 in the Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:33.3
occ:1.00
 O C:SER349 2.5 32.1 1.0
O C:THR308 2.5 35.0 1.0
O C:THR352 2.5 33.3 1.0
SD C:MET311 2.9 32.6 1.0
CE C:MET311 3.0 32.6 1.0
O C:ILE350 3.1 31.4 1.0
C C:THR352 3.4 33.3 1.0
C C:THR308 3.4 35.0 1.0
N C:THR352 3.5 33.3 1.0
C C:ILE350 3.6 31.4 1.0
C C:SER349 3.7 32.1 1.0
CG C:MET311 3.7 32.6 1.0
CA C:THR352 3.7 33.3 1.0
CB C:THR352 3.7 33.3 1.0
CA C:ILE350 4.0 31.4 1.0
CA C:THR308 4.1 35.0 1.0
N C:ILE309 4.3 34.0 1.0
N C:ILE350 4.3 31.4 1.0
C C:GLY351 4.3 32.0 1.0
OG1 C:THR352 4.4 33.3 1.0
N C:GLY351 4.4 32.0 1.0
CB C:MET311 4.5 32.6 1.0
N C:ALA353 4.5 33.7 1.0
CA C:ILE309 4.6 34.0 1.0
O C:ILE309 4.6 34.0 1.0
C C:ILE309 4.7 34.0 1.0
CA C:SER349 4.7 32.1 1.0
O C:ALA353 4.7 33.7 1.0
CA C:GLY351 4.8 32.0 1.0
C C:ALA353 4.9 33.7 1.0
CG2 C:THR352 4.9 33.3 1.0
CB C:THR308 4.9 35.0 1.0

Sodium binding site 9 out of 9 in 6x15

Go back to Sodium Binding Sites List in 6x15
Sodium binding site 9 out of 9 in the Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Inward-Facing State of the Glutamate Transporter Homologue Gltph in Complex with L-Aspartate and Sodium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na504

b:35.1
occ:1.00
 O C:TYR89 2.5 35.7 1.0
OD2 C:ASP312 2.5 33.5 1.0
OG C:SER93 2.5 34.3 1.0
OD1 C:ASN310 2.5 34.4 1.0
OG1 C:THR92 2.6 35.0 1.0
N C:SER93 2.7 34.3 1.0
CA C:SER93 3.2 34.3 1.0
C C:THR92 3.2 35.0 1.0
CB C:SER93 3.3 34.3 1.0
CB C:THR92 3.4 35.0 1.0
CG C:ASP312 3.4 33.5 1.0
C C:TYR89 3.5 35.7 1.0
CG C:ASN310 3.6 34.4 1.0
OD1 C:ASP312 3.8 33.5 1.0
CA C:THR92 3.8 35.0 1.0
CA C:TYR89 3.9 35.7 1.0
O C:THR92 4.0 35.0 1.0
N C:THR92 4.2 35.0 1.0
O C:HOH601 4.3 32.5 1.0
CA C:ASN310 4.4 34.4 1.0
CB C:ASN310 4.4 34.4 1.0
ND2 C:ASN310 4.5 34.4 1.0
CB C:ASP312 4.6 33.5 1.0
N C:MET311 4.6 32.6 1.0
N C:ASP312 4.6 33.5 1.0
O C:TYR88 4.6 38.1 1.0
CB C:TYR89 4.6 35.7 1.0
CA C:ASP312 4.7 33.5 1.0
C C:SER93 4.7 34.3 1.0
N C:LEU90 4.7 36.0 1.0
CG2 C:THR92 4.8 35.0 1.0
C C:ASN310 4.8 34.4 1.0
C C:MET311 4.9 32.6 1.0

Reference:

X.Wang, O.Boudker. Large Domain Movements Through the Lipid Bilayer Mediate Substrate Release and Inhibition of Glutamate Transporters. Elife V. 9 2020.
ISSN: ESSN 2050-084X
PubMed: 33155546
DOI: 10.7554/ELIFE.58417
Page generated: Tue Dec 15 15:52:33 2020

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