Sodium in PDB 5e9s: Crystal Structure of Substrate-Bound Glutamate Transporter Homologue Glttk

The structure of Crystal Structure of Substrate-Bound Glutamate Transporter Homologue Glttk, PDB code: 5e9s was solved by A.Guskov, D.J.Slotboom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.36 / 2.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.520, 117.520, 310.590, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 24.3

The binding sites of Sodium atom in the Crystal Structure of Substrate-Bound Glutamate Transporter Homologue Glttk (pdb code 5e9s). 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 Substrate-Bound Glutamate Transporter Homologue Glttk, PDB code: 5e9s:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in the Crystal Structure of Substrate-Bound Glutamate Transporter Homologue Glttk


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 Substrate-Bound Glutamate Transporter Homologue Glttk within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:63.0 occ:1.00 O A:ASN313 2.5 71.0 1.0 O A:GLY309 2.6 67.3 1.0 O A:ASN405 2.7 76.2 1.0 OD2 A:ASP409 2.7 92.1 1.0 OD1 A:ASP409 3.1 99.7 1.0 CG A:ASP409 3.2 90.3 1.0 C A:ASN405 3.3 71.8 1.0 CA A:ALA310 3.4 64.3 1.0 C A:GLY309 3.5 69.5 1.0 OG A:SER280 3.6 59.6 1.0 C A:ASN313 3.6 73.8 1.0 O A:ALA310 3.7 76.4 1.0 CB A:ASN405 3.7 66.2 1.0 C A:ALA310 3.7 69.0 1.0 N A:ALA310 3.8 69.8 1.0 CA A:ASN405 3.9 69.2 1.0 N A:VAL406 4.1 70.4 1.0 CG A:MET314 4.1 77.1 1.0 CB A:SER280 4.4 59.8 1.0 CA A:VAL406 4.4 66.9 1.0 ND2 A:ASN313 4.5 94.9 1.0 N A:MET314 4.5 75.3 1.0 CA A:MET314 4.5 80.6 1.0 CA A:ASN313 4.6 71.6 1.0 N A:THR311 4.6 64.7 1.0 CG A:ASN405 4.6 67.7 1.0 N A:ASN313 4.7 62.3 1.0 CB A:ASP409 4.7 76.3 1.0 CA A:GLY309 4.7 67.0 1.0 CB A:ASN313 4.7 78.8 1.0 CB A:ALA310 4.7 61.9 1.0 CB A:MET314 4.9 78.8 1.0

Sodium binding site 2 out of 9 in the Crystal Structure of Substrate-Bound Glutamate Transporter Homologue Glttk


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 Substrate-Bound Glutamate Transporter Homologue Glttk within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:65.9 occ:1.00 O A:THR355 2.2 64.8 1.0 O A:THR311 2.3 76.7 1.0 O A:SER352 2.4 61.8 1.0 O A:ILE353 2.7 68.9 1.0 SD A:MET314 2.8 64.1 1.0 CE A:MET314 3.0 50.5 1.0 C A:THR355 3.2 63.5 1.0 N A:THR355 3.3 57.5 1.0 OG1 A:THR355 3.3 93.4 1.0 C A:ILE353 3.3 65.7 1.0 C A:THR311 3.4 72.6 1.0 C A:SER352 3.5 63.6 1.0 CA A:THR355 3.6 62.9 1.0 CG A:MET314 3.7 77.1 1.0 CA A:ILE353 3.9 59.1 1.0 CB A:THR355 3.9 64.5 1.0 C A:GLY354 4.0 58.7 1.0 N A:GLY354 4.0 65.1 1.0 CA A:THR311 4.2 69.6 1.0 N A:ILE353 4.2 62.4 1.0 CG2 A:THR311 4.3 55.7 1.0 N A:ALA356 4.4 58.6 1.0 CA A:GLY354 4.4 61.0 1.0 N A:ILE312 4.4 65.4 1.0 CA A:ILE312 4.5 65.7 1.0 CG2 A:THR355 4.5 54.5 1.0 CB A:MET314 4.6 78.8 1.0 CA A:SER352 4.6 64.9 1.0 C A:ILE312 4.7 63.3 1.0 O A:GLY354 4.7 69.8 1.0 CA A:ALA356 4.9 53.0 1.0 C A:ALA356 4.9 53.3 1.0 CB A:THR311 4.9 68.4 1.0 O A:ILE312 4.9 80.1 1.0 O A:ALA356 5.0 59.7 1.0

Sodium binding site 3 out of 9 in the Crystal Structure of Substrate-Bound Glutamate Transporter Homologue Glttk


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 Substrate-Bound Glutamate Transporter Homologue Glttk within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:86.3 occ:1.00 O A:TYR91 2.1 81.1 1.0 OD1 A:ASN313 2.2 94.4 1.0 OD1 A:ASP315 2.4 80.4 1.0 OG1 A:THR94 2.4 72.2 1.0 OG A:SER95 2.7 84.0 1.0 N A:SER95 2.7 87.5 1.0 C A:TYR91 3.1 78.8 1.0 CB A:SER95 3.2 77.8 1.0 CG A:ASN313 3.2 89.8 1.0 CA A:SER95 3.3 81.6 1.0 CG A:ASP315 3.3 85.8 1.0 C A:THR94 3.4 87.2 1.0 CA A:TYR91 3.5 79.3 1.0 OD2 A:ASP315 3.6 87.4 1.0 CB A:THR94 3.6 77.0 1.0 CA A:THR94 3.8 82.9 1.0 ND2 A:ASN313 3.9 94.9 1.0 N A:THR94 4.0 84.9 1.0 O A:TYR90 4.0 68.5 1.0 O A:THR94 4.2 88.5 1.0 CB A:ASN313 4.3 78.8 1.0 N A:LEU92 4.4 80.2 1.0 CB A:TYR91 4.4 83.9 1.0 N A:TYR91 4.7 76.4 1.0 CA A:ASN313 4.7 71.6 1.0 CB A:ASP315 4.7 87.3 1.0 CD1 A:TYR91 4.7 76.7 1.0 C A:LEU92 4.8 92.1 1.0 C A:SER95 4.8 83.5 1.0 CA A:LEU92 4.8 85.0 1.0 C A:TYR90 4.8 73.4 1.0 CG2 A:THR94 4.8 79.9 1.0 N A:ASP315 4.8 87.4 1.0 O A:LEU92 4.9 99.4 1.0 CG A:TYR91 4.9 82.1 1.0 C A:ALA93 5.0 87.4 1.0 N A:MET314 5.0 75.3 1.0

Sodium binding site 4 out of 9 in the Crystal Structure of Substrate-Bound Glutamate Transporter Homologue Glttk


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 Substrate-Bound Glutamate Transporter Homologue Glttk within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:68.0 occ:1.00 O B:THR311 2.1 85.6 1.0 O B:SER352 2.3 69.2 1.0 O B:THR355 2.4 66.3 1.0 O B:ILE353 2.5 77.2 1.0 C B:ILE353 2.9 76.2 1.0 SD B:MET314 3.1 70.1 1.0 N B:THR355 3.2 67.1 1.0 C B:THR311 3.2 81.6 1.0 C B:THR355 3.3 68.4 1.0 CE B:MET314 3.4 71.3 1.0 C B:SER352 3.4 73.3 1.0 CA B:ILE353 3.5 74.2 1.0 CA B:THR355 3.7 64.7 1.0 N B:GLY354 3.7 75.4 1.0 N B:ILE353 3.9 78.4 1.0 C B:GLY354 3.9 71.3 1.0 CG B:MET314 3.9 82.2 1.0 CB B:THR355 3.9 65.5 1.0 CA B:ILE312 4.1 70.5 1.0 CA B:THR311 4.1 76.9 1.0 N B:ILE312 4.1 76.6 1.0 CA B:GLY354 4.2 69.5 1.0 CG2 B:THR311 4.2 66.0 1.0 C B:ILE312 4.5 72.6 1.0 N B:ALA356 4.6 65.9 1.0 CA B:SER352 4.7 73.1 1.0 O B:ILE312 4.7 80.9 1.0 CG2 B:THR355 4.8 59.6 1.0 O B:GLY354 4.8 82.5 1.0 CB B:MET314 4.8 84.6 1.0 CB B:THR311 4.8 78.6 1.0 CB B:ILE353 4.9 71.3 1.0 O B:ALA351 5.0 79.2 1.0

Sodium binding site 5 out of 9 in the Crystal Structure of Substrate-Bound Glutamate Transporter Homologue Glttk


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 Substrate-Bound Glutamate Transporter Homologue Glttk within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:61.3 occ:1.00 O B:ASN313 2.5 75.0 1.0 O B:GLY309 2.7 74.5 1.0 OD2 B:ASP409 2.7 85.3 1.0 O B:ASN405 2.8 74.7 1.0 OD1 B:ASP409 3.3 96.2 1.0 C B:ASN405 3.3 74.0 1.0 CG B:ASP409 3.4 89.8 1.0 CA B:ALA310 3.4 70.6 1.0 OG B:SER280 3.5 71.4 1.0 C B:GLY309 3.5 74.2 1.0 O B:ALA310 3.7 84.7 1.0 C B:ASN313 3.7 80.2 1.0 CB B:ASN405 3.7 65.4 1.0 C B:ALA310 3.7 78.0 1.0 N B:ALA310 3.9 72.7 1.0 CA B:ASN405 4.0 71.5 1.0 N B:VAL406 4.0 75.5 1.0 CG B:MET314 4.2 82.2 1.0 CB B:SER280 4.2 61.7 1.0 CA B:VAL406 4.3 82.5 1.0 ND2 B:ASN313 4.6 0.7 1.0 N B:MET314 4.6 83.7 1.0 CA B:ASN313 4.6 78.2 1.0 CB B:ALA310 4.6 67.4 1.0 CG B:ASN405 4.6 71.0 1.0 CA B:MET314 4.7 82.7 1.0 N B:THR311 4.7 76.1 1.0 OD2 B:ASP501 4.7 0.8 1.0 N B:ASN313 4.7 69.9 1.0 CB B:ASN313 4.7 88.0 1.0 CA B:GLY309 4.8 74.1 1.0 CB B:ASP409 4.8 84.9 1.0 CG1 B:VAL406 4.9 73.9 1.0 CE B:MET314 4.9 71.3 1.0

Sodium binding site 6 out of 9 in the Crystal Structure of Substrate-Bound Glutamate Transporter Homologue Glttk


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 Substrate-Bound Glutamate Transporter Homologue Glttk within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:0.9 occ:1.00 OD1 B:ASP315 2.1 0.1 1.0 O B:TYR91 2.2 89.8 1.0 OG1 B:THR94 2.3 86.3 1.0 OD1 B:ASN313 2.4 0.4 1.0 OG B:SER95 2.6 90.5 1.0 N B:SER95 2.6 95.2 1.0 CG B:ASP315 3.1 0.0 1.0 CA B:SER95 3.2 90.0 1.0 CB B:SER95 3.2 87.2 1.0 C B:THR94 3.2 89.6 1.0 OD2 B:ASP315 3.3 0.1 1.0 C B:TYR91 3.3 91.4 1.0 CB B:THR94 3.4 86.0 1.0 CG B:ASN313 3.5 98.3 1.0 CA B:THR94 3.7 84.4 1.0 CA B:TYR91 3.8 89.6 1.0 N B:THR94 4.0 88.6 1.0 O B:THR94 4.1 90.9 1.0 ND2 B:ASN313 4.1 0.7 1.0 O B:TYR90 4.2 0.3 1.0 CB B:ASP315 4.4 0.0 1.0 N B:LEU92 4.5 96.1 1.0 CB B:ASN313 4.6 88.0 1.0 CG2 B:THR94 4.7 91.1 1.0 C B:SER95 4.7 87.7 1.0 CB B:TYR91 4.7 83.6 1.0 N B:ASP315 4.7 98.4 1.0 CA B:LEU92 4.7 95.7 1.0 C B:LEU92 4.7 88.2 1.0 CA B:ASP315 4.8 94.3 1.0 O B:LEU92 4.9 87.8 1.0 C B:ALA93 4.9 93.2 1.0 N B:TYR91 4.9 94.9 1.0 CA B:ASN313 5.0 78.2 1.0 CD1 B:TYR91 5.0 84.2 1.0

Sodium binding site 7 out of 9 in the Crystal Structure of Substrate-Bound Glutamate Transporter Homologue Glttk


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 Substrate-Bound Glutamate Transporter Homologue Glttk within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:75.7 occ:1.00 O C:ASN313 2.4 76.0 1.0 OD2 C:ASP409 2.6 82.9 1.0 O C:GLY309 2.8 78.3 1.0 O C:ASN405 3.0 84.5 1.0 OD1 C:ASP409 3.1 95.6 1.0 CG C:ASP409 3.2 88.7 1.0 C C:ASN405 3.5 80.7 1.0 CA C:ALA310 3.6 73.6 1.0 C C:ASN313 3.6 84.7 1.0 C C:GLY309 3.7 74.5 1.0 O C:ALA310 3.7 87.4 1.0 C C:ALA310 3.8 81.5 1.0 CB C:ASN405 3.8 73.0 1.0 OG C:SER280 3.8 69.4 1.0 CG C:MET314 3.9 75.4 1.0 N C:ALA310 4.0 69.2 1.0 CA C:ASN405 4.1 78.7 1.0 N C:VAL406 4.2 80.5 1.0 CB C:SER280 4.3 67.1 1.0 CA C:MET314 4.4 93.4 1.0 N C:MET314 4.4 91.5 1.0 CA C:VAL406 4.5 79.4 1.0 ND2 C:ASN313 4.6 95.1 1.0 CA C:ASN313 4.6 86.8 1.0 CG C:ASN405 4.6 71.5 1.0 N C:THR311 4.6 79.0 1.0 CB C:ASP409 4.7 82.8 1.0 N C:ASN313 4.7 81.7 1.0 CB C:MET314 4.7 80.1 1.0 CB C:ASN313 4.8 85.0 1.0 CB C:ALA310 4.8 74.0 1.0 CA C:GLY309 4.9 71.8 1.0 CE C:MET314 4.9 59.7 1.0

Sodium binding site 8 out of 9 in the Crystal Structure of Substrate-Bound Glutamate Transporter Homologue Glttk


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 Substrate-Bound Glutamate Transporter Homologue Glttk within 5.0Å range: probe atom residue distance (Å) B Occ C:Na503 b:66.2 occ:1.00 O C:THR311 2.2 80.3 1.0 O C:THR355 2.3 69.0 1.0 O C:SER352 2.4 73.3 1.0 O C:ILE353 2.7 75.4 1.0 C C:ILE353 3.1 70.5 1.0 N C:THR355 3.1 71.8 1.0 C C:THR311 3.2 78.8 1.0 C C:THR355 3.3 69.0 1.0 SD C:MET314 3.3 70.2 1.0 CE C:MET314 3.4 59.7 1.0 C C:SER352 3.6 76.7 1.0 CA C:THR355 3.6 65.8 1.0 CA C:ILE353 3.7 68.1 1.0 C C:GLY354 3.7 74.0 1.0 N C:GLY354 3.8 62.8 1.0 CB C:THR355 3.9 69.4 1.0 CG C:MET314 4.1 75.4 1.0 N C:ILE312 4.1 80.1 1.0 N C:ILE353 4.1 75.4 1.0 CG2 C:THR311 4.1 59.9 1.0 CA C:THR311 4.1 74.5 1.0 CA C:ILE312 4.1 77.0 1.0 CA C:GLY354 4.2 67.0 1.0 O C:GLY354 4.5 79.7 1.0 N C:ALA356 4.5 72.5 1.0 C C:ILE312 4.6 78.6 1.0 O C:ILE312 4.7 83.3 1.0 CB C:THR311 4.8 70.4 1.0 CA C:SER352 4.8 81.8 1.0 OG1 C:THR355 4.9 82.8 1.0 CB C:MET314 5.0 80.1 1.0 CG2 C:THR355 5.0 60.5 1.0

Sodium binding site 9 out of 9 in the Crystal Structure of Substrate-Bound Glutamate Transporter Homologue Glttk


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 Substrate-Bound Glutamate Transporter Homologue Glttk within 5.0Å range: probe atom residue distance (Å) B Occ C:Na504 b:85.3 occ:1.00 O C:TYR91 2.2 96.9 1.0 OD1 C:ASN313 2.3 93.3 1.0 OG1 C:THR94 2.4 90.8 1.0 OD1 C:ASP315 2.4 98.4 1.0 OG C:SER95 2.6 91.7 1.0 N C:SER95 2.6 83.9 1.0 CB C:SER95 3.1 87.3 1.0 CA C:SER95 3.2 82.4 1.0 C C:TYR91 3.2 97.7 1.0 C C:THR94 3.3 86.3 1.0 CG C:ASP315 3.3 0.6 1.0 CG C:ASN313 3.3 90.4 1.0 CA C:TYR91 3.5 91.6 1.0 OD2 C:ASP315 3.5 0.1 1.0 CB C:THR94 3.5 86.7 1.0 CA C:THR94 3.8 83.8 1.0 O C:TYR90 4.0 94.6 1.0 N C:THR94 4.0 82.0 1.0 ND2 C:ASN313 4.1 95.1 1.0 O C:THR94 4.1 89.9 1.0 CB C:TYR91 4.3 91.6 1.0 CB C:ASN313 4.3 85.0 1.0 N C:LEU92 4.4 1.0 1.0 N C:TYR91 4.6 91.5 1.0 C C:SER95 4.6 88.6 1.0 CA C:ASN313 4.7 86.8 1.0 CD1 C:TYR91 4.7 94.3 1.0 CB C:ASP315 4.7 0.0 1.0 C C:TYR90 4.7 96.7 1.0 CG2 C:THR94 4.7 82.2 1.0 N C:ASP315 4.9 0.7 1.0 CG C:TYR91 4.9 91.7 1.0 C C:LEU92 4.9 0.4 1.0 CA C:LEU92 4.9 0.1 1.0 C C:ALA93 5.0 91.7 1.0 N C:MET314 5.0 91.5 1.0

A.Guskov, S.Jensen, I.Faustino, S.J.Marrink, D.J.Slotboom. Coupled Binding Mechanism of Three Sodium Ions and Aspartate in the Glutamate Transporter Homologue Glttk. Nat Commun V. 7 13420 2016.
ISSN: ESSN 2041-1723
PubMed: 27830699
DOI: 10.1038/NCOMMS13420