Sodium in PDB 6r7r: Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate

Protein crystallography data

The structure of Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate, PDB code: 6r7r was solved by V.Arkhipova, A.Guskov, D.J.Slotboom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.06 / 2.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.550, 116.550, 314.770, 90.00, 90.00, 120.00
R / Rfree (%) 23.2 / 26.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate (pdb code 6r7r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate, PDB code: 6r7r:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 6r7r

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Sodium binding site 1 out of 9 in the Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:0.7
occ:1.00
O A:ASN405 2.3 0.1 1.0
O A:GLY309 2.5 0.8 1.0
O A:ASN313 2.6 0.1 1.0
OD2 A:ASP409 2.8 0.1 1.0
C A:ASN405 3.0 0.8 1.0
CG A:ASP409 3.3 0.7 1.0
OD1 A:ASP409 3.3 0.4 1.0
CA A:ALA310 3.3 91.6 1.0
C A:GLY309 3.4 0.5 1.0
OG A:SER280 3.4 77.1 1.0
CB A:ASN405 3.6 0.5 1.0
O A:ALA310 3.6 0.8 1.0
C A:ASN313 3.7 0.8 1.0
C A:ALA310 3.7 1.0 1.0
CA A:ASN405 3.7 0.2 1.0
N A:ALA310 3.7 87.6 1.0
N A:VAL406 3.8 0.8 1.0
ND2 A:ASN313 4.2 0.5 1.0
CA A:VAL406 4.2 96.9 1.0
CB A:SER280 4.3 76.1 1.0
CG A:MET314 4.5 87.7 1.0
CB A:ASP409 4.5 0.0 1.0
CB A:ASN313 4.5 0.1 1.0
CB A:ALA310 4.5 97.1 1.0
CA A:ASN313 4.5 0.3 1.0
CA A:GLY309 4.6 0.6 1.0
N A:MET314 4.6 0.8 1.0
CA A:MET314 4.7 91.5 1.0
N A:THR311 4.7 0.8 1.0
CG A:ASN405 4.7 0.7 1.0
N A:ASN313 4.7 0.6 1.0
CG2 A:VAL406 4.9 79.5 1.0
CG A:ASN313 4.9 0.1 1.0

Sodium binding site 2 out of 9 in 6r7r

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Sodium binding site 2 out of 9 in the Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:96.9
occ:1.00
O A:SER352 2.1 0.4 1.0
O A:THR311 2.2 0.3 1.0
O A:THR355 2.3 82.6 1.0
O A:ILE353 2.6 91.9 1.0
C A:ILE353 2.9 97.0 1.0
N A:THR355 3.0 83.5 1.0
SD A:MET314 3.0 89.8 1.0
C A:THR355 3.1 85.6 1.0
C A:SER352 3.2 0.6 1.0
CA A:THR355 3.4 76.4 1.0
C A:THR311 3.4 93.2 1.0
CA A:ILE353 3.5 86.1 1.0
N A:GLY354 3.5 0.9 1.0
C A:GLY354 3.6 81.4 1.0
CB A:THR355 3.6 83.0 1.0
N A:ILE353 3.8 96.7 1.0
CE A:MET314 3.9 94.3 1.0
CA A:GLY354 4.0 84.0 1.0
CA A:ILE312 4.1 89.4 1.0
O A:GLY354 4.2 97.8 1.0
N A:ILE312 4.2 79.0 1.0
CA A:SER352 4.3 0.6 1.0
N A:ALA356 4.3 85.3 1.0
CA A:THR311 4.4 84.2 1.0
OG1 A:THR355 4.4 94.2 1.0
CG A:MET314 4.5 87.7 1.0
CG2 A:THR311 4.5 76.5 1.0
O A:ALA351 4.6 0.6 1.0
C A:ILE312 4.7 94.9 1.0
CG2 A:THR355 4.7 76.1 1.0
CB A:MET314 4.9 93.7 1.0
CB A:ILE353 5.0 87.5 1.0
CA A:ALA356 5.0 81.6 1.0

Sodium binding site 3 out of 9 in 6r7r

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Sodium binding site 3 out of 9 in the Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:0.6
occ:1.00
OD1 A:ASN313 2.2 0.4 1.0
OG1 A:THR94 2.4 0.0 1.0
O A:TYR91 2.4 92.1 1.0
OD1 A:ASP315 2.6 1.0 1.0
N A:SER95 2.8 0.4 1.0
CB A:THR94 3.1 0.8 1.0
OG A:SER95 3.2 0.5 1.0
C A:TYR91 3.3 0.8 1.0
C A:THR94 3.3 0.9 1.0
CG A:ASN313 3.3 0.1 1.0
CG A:ASP315 3.5 1.0 1.0
CA A:TYR91 3.5 0.5 1.0
CA A:THR94 3.6 0.9 1.0
CA A:SER95 3.6 1.0 1.0
OD2 A:ASP315 3.7 0.5 1.0
CB A:SER95 3.7 0.6 1.0
N A:THR94 3.9 0.6 1.0
ND2 A:ASN313 4.1 0.5 1.0
O A:THR94 4.2 0.8 1.0
O A:TYR90 4.2 0.3 1.0
CD1 A:TYR91 4.3 0.6 1.0
CB A:ASN313 4.3 0.1 1.0
CB A:TYR91 4.3 0.3 1.0
CG2 A:THR94 4.5 0.8 1.0
N A:LEU92 4.6 0.5 1.0
CA A:ASN313 4.6 0.3 1.0
N A:TYR91 4.6 0.5 1.0
O A:LEU92 4.7 0.6 1.0
CG A:TYR91 4.8 0.7 1.0
CB A:ASP315 4.8 0.0 1.0
C A:TYR90 4.8 0.2 1.0
C A:LEU92 4.9 0.9 1.0
N A:ASP315 5.0 0.7 1.0
C A:ALA93 5.0 1.0 1.0

Sodium binding site 4 out of 9 in 6r7r

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Sodium binding site 4 out of 9 in the Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:0.6
occ:1.00
O B:SER352 2.2 94.9 1.0
O B:THR311 2.3 0.4 1.0
O B:ILE353 2.3 0.3 1.0
O B:THR355 2.3 0.5 1.0
C B:ILE353 2.7 0.4 1.0
N B:THR355 3.0 84.5 1.0
SD B:MET314 3.1 90.4 1.0
C B:THR355 3.2 89.8 1.0
C B:SER352 3.3 0.9 1.0
CA B:ILE353 3.3 0.3 1.0
C B:THR311 3.4 0.4 1.0
N B:GLY354 3.5 89.6 1.0
C B:GLY354 3.5 94.5 1.0
CA B:THR355 3.5 85.5 1.0
N B:ILE353 3.8 0.8 1.0
CB B:THR355 3.8 84.6 1.0
CA B:GLY354 3.9 88.0 1.0
CE B:MET314 4.0 99.7 1.0
O B:GLY354 4.1 0.5 1.0
CA B:ILE312 4.2 93.4 1.0
N B:ILE312 4.2 0.1 1.0
CG2 B:THR311 4.3 80.6 1.0
CA B:THR311 4.3 0.9 1.0
N B:ALA356 4.3 84.5 1.0
CA B:SER352 4.5 0.9 1.0
OG1 B:THR355 4.6 88.6 1.0
CG B:MET314 4.7 0.7 1.0
O B:ALA351 4.8 0.7 1.0
CB B:ILE353 4.8 96.3 1.0
C B:ILE312 4.8 0.3 1.0
CA B:ALA356 4.9 91.7 1.0
CG2 B:THR355 4.9 89.1 1.0
CB B:THR311 4.9 95.1 1.0

Sodium binding site 5 out of 9 in 6r7r

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Sodium binding site 5 out of 9 in the Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:98.1
occ:1.00
O B:ASN313 2.5 0.5 1.0
O B:GLY309 2.6 0.5 1.0
O B:ASN405 2.7 98.8 1.0
OD2 B:ASP409 3.0 0.6 1.0
CA B:ALA310 3.4 0.6 1.0
C B:ASN405 3.4 96.3 1.0
O B:ALA310 3.4 0.6 1.0
C B:ASN313 3.5 0.3 1.0
C B:GLY309 3.5 0.7 1.0
C B:ALA310 3.6 0.1 1.0
CG B:ASP409 3.6 0.1 1.0
OG B:SER280 3.6 80.9 1.0
OD1 B:ASP409 3.6 0.7 1.0
CB B:ASN405 3.7 0.8 1.0
N B:ALA310 3.8 0.2 1.0
CA B:ASN405 4.0 0.4 1.0
CG B:MET314 4.2 0.7 1.0
N B:VAL406 4.2 96.8 1.0
ND2 B:ASN313 4.3 0.3 1.0
N B:MET314 4.3 0.3 1.0
CB B:SER280 4.3 79.7 1.0
CA B:ASN313 4.4 0.7 1.0
CA B:MET314 4.4 0.9 1.0
N B:THR311 4.5 0.4 1.0
N B:ASN313 4.5 0.3 1.0
CB B:ASN313 4.5 0.8 1.0
CA B:VAL406 4.6 0.3 1.0
CG B:ASN405 4.6 0.0 1.0
CB B:ALA310 4.6 1.0 1.0
CA B:GLY309 4.7 0.9 1.0
CB B:ASP409 4.9 0.5 1.0
CB B:MET314 4.9 0.7 1.0
CG B:ASN313 5.0 0.4 1.0

Sodium binding site 6 out of 9 in 6r7r

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Sodium binding site 6 out of 9 in the Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:0.1
occ:1.00
OD1 B:ASN313 2.2 0.9 1.0
O B:TYR91 2.2 0.9 1.0
OG1 B:THR94 2.6 0.0 1.0
OD1 B:ASP315 2.8 0.8 1.0
OG B:SER95 2.8 0.5 1.0
N B:SER95 3.0 0.8 1.0
C B:TYR91 3.2 0.3 1.0
CG B:ASN313 3.3 0.4 1.0
CA B:TYR91 3.5 0.8 1.0
CB B:SER95 3.5 0.2 1.0
CB B:THR94 3.5 0.1 1.0
CA B:SER95 3.6 0.6 1.0
CG B:ASP315 3.7 0.8 1.0
C B:THR94 3.7 0.9 1.0
OD2 B:ASP315 3.9 0.5 1.0
CA B:THR94 4.0 0.2 1.0
ND2 B:ASN313 4.1 0.3 1.0
CB B:ASN313 4.2 0.8 1.0
N B:THR94 4.2 0.3 1.0
CB B:TYR91 4.2 0.9 1.0
O B:TYR90 4.3 0.1 1.0
CD1 B:TYR91 4.4 0.8 1.0
N B:LEU92 4.4 0.3 1.0
CA B:ASN313 4.4 0.7 1.0
O B:THR94 4.6 0.4 1.0
N B:TYR91 4.7 0.6 1.0
CG B:TYR91 4.7 0.2 1.0
C B:ASN313 4.8 0.3 1.0
CG2 B:THR94 4.9 0.2 1.0
C B:LEU92 4.9 0.9 1.0
CA B:LEU92 4.9 0.8 1.0
O B:LEU92 5.0 0.1 1.0
C B:TYR90 5.0 0.7 1.0
N B:ASP315 5.0 0.8 1.0
N B:MET314 5.0 0.3 1.0

Sodium binding site 7 out of 9 in 6r7r

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Sodium binding site 7 out of 9 in the Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:0.5
occ:1.00
O C:ASN313 2.3 0.1 1.0
OD2 C:ASP409 2.6 0.2 1.0
O C:ASN405 2.7 0.0 1.0
O C:GLY309 2.7 0.5 1.0
OD1 C:ASP409 3.1 0.5 1.0
CG C:ASP409 3.1 0.7 1.0
C C:ASN405 3.3 0.8 1.0
C C:ASN313 3.5 0.7 1.0
CA C:ALA310 3.6 0.2 1.0
C C:GLY309 3.6 0.5 1.0
CB C:ASN405 3.7 0.1 1.0
OG C:SER280 3.7 93.9 1.0
O C:ALA310 3.8 0.3 1.0
C C:ALA310 3.8 0.6 1.0
CA C:ASN405 3.9 0.4 1.0
N C:ALA310 4.0 1.0 1.0
N C:VAL406 4.2 0.3 1.0
ND2 C:ASN313 4.2 0.4 1.0
CG C:MET314 4.2 0.6 1.0
N C:MET314 4.4 0.7 1.0
CA C:MET314 4.4 0.9 1.0
CB C:ASP409 4.4 0.3 1.0
CB C:SER280 4.5 90.0 1.0
CA C:ASN313 4.5 0.3 1.0
CB C:ASN313 4.6 0.9 1.0
CA C:VAL406 4.6 0.4 1.0
CG C:ASN405 4.6 0.3 1.0
N C:ASN313 4.7 0.3 1.0
N C:THR311 4.8 0.9 1.0
CA C:GLY309 4.8 0.1 1.0
CB C:ALA310 4.8 0.3 1.0
CG C:ASN313 4.9 0.8 1.0
CB C:MET314 4.9 1.0 1.0

Sodium binding site 8 out of 9 in 6r7r

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Sodium binding site 8 out of 9 in the Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:0.9
occ:1.00
O C:THR311 2.1 0.9 1.0
O C:THR355 2.3 1.0 1.0
O C:SER352 2.3 0.9 1.0
O C:ILE353 2.6 0.4 1.0
SD C:MET314 3.0 0.3 1.0
C C:ILE353 3.1 95.1 1.0
C C:THR355 3.1 0.4 1.0
N C:THR355 3.2 98.7 1.0
C C:THR311 3.3 0.2 1.0
C C:SER352 3.4 0.7 1.0
CA C:THR355 3.5 0.5 1.0
CA C:ILE353 3.6 94.7 1.0
C C:GLY354 3.6 97.3 1.0
N C:GLY354 3.7 0.3 1.0
CB C:THR355 3.8 0.9 1.0
N C:ILE353 4.0 0.8 1.0
CE C:MET314 4.1 0.9 1.0
CA C:ILE312 4.1 0.6 1.0
CA C:GLY354 4.1 96.6 1.0
N C:ILE312 4.2 98.0 1.0
O C:GLY354 4.3 0.1 1.0
CA C:THR311 4.3 0.6 1.0
N C:ALA356 4.3 90.8 1.0
CG C:MET314 4.4 0.6 1.0
C C:ILE312 4.6 0.0 1.0
OG1 C:THR355 4.6 0.1 1.0
CG2 C:THR311 4.6 81.1 1.0
CA C:SER352 4.7 0.1 1.0
CB C:MET314 4.7 1.0 1.0
O C:ILE312 4.8 0.1 1.0
CA C:ALA356 4.8 89.1 1.0
CG2 C:THR355 4.9 97.9 1.0

Sodium binding site 9 out of 9 in 6r7r

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Sodium binding site 9 out of 9 in the Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of the Glutamate Transporter Homologue Glttk in Complex with D-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:0.4
occ:1.00
OD1 C:ASP315 2.2 0.2 1.0
O C:TYR91 2.3 0.7 1.0
N C:SER95 2.4 0.3 1.0
OG C:SER95 2.5 0.3 1.0
OD1 C:ASN313 2.6 0.8 1.0
CA C:SER95 2.9 0.5 1.0
CB C:SER95 3.0 0.8 1.0
OG1 C:THR94 3.0 0.0 1.0
C C:THR94 3.1 0.7 1.0
CG C:ASP315 3.3 0.7 1.0
C C:TYR91 3.3 0.6 1.0
CG C:ASN313 3.6 0.8 1.0
CB C:THR94 3.6 0.8 1.0
CA C:THR94 3.8 0.4 1.0
OD2 C:ASP315 3.9 0.1 1.0
CA C:TYR91 3.9 0.8 1.0
O C:THR94 3.9 0.4 1.0
N C:THR94 4.2 0.1 1.0
ND2 C:ASN313 4.3 0.4 1.0
N C:ASP315 4.4 0.1 1.0
C C:SER95 4.4 0.3 1.0
CB C:ASP315 4.5 0.7 1.0
CA C:ASP315 4.5 0.1 1.0
N C:LEU92 4.5 0.5 1.0
CB C:ASN313 4.5 0.9 1.0
CB C:TYR91 4.5 0.9 1.0
CA C:ASN313 4.6 0.3 1.0
O C:TYR90 4.7 0.6 1.0
O C:LEU92 4.7 0.0 1.0
N C:MET314 4.8 0.7 1.0
C C:MET314 4.8 0.2 1.0
C C:LEU92 4.8 0.3 1.0
CA C:LEU92 4.9 0.5 1.0
C C:ASN313 4.9 0.7 1.0

Reference:

V.Arkhipova, G.Trinco, T.W.Ettema, S.Jensen, D.J.Slotboom, A.Guskov. Binding and Transport of D-Aspartate By the Glutamate Transporter Homolog Glttk. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 30969168
DOI: 10.7554/ELIFE.45286
Page generated: Tue Dec 15 12:51:56 2020

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