Sodium in PDB 6zl4: The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis)

The structure of The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis), PDB code: 6zl4 was solved by V.Arkhipova, D.J.Slotboom, A.Guskov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.23 / 3.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.21, 117.21, 309.41, 90, 90, 120
R / Rfree (%)	25.5 / 28.8

The binding sites of Sodium atom in the The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis) (pdb code 6zl4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis), PDB code: 6zl4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in the The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:132.7 occ:1.00 O A:ASN313 2.6 161.8 1.0 OD2 A:ASP409 2.9 165.5 1.0 O A:GLY309 2.9 158.1 1.0 CB A:ASN405 3.2 145.4 1.0 O A:ASN405 3.3 146.3 1.0 OD1 A:ASP409 3.3 167.9 1.0 C A:ASN405 3.4 150.0 1.0 CG A:ASP409 3.4 160.3 1.0 CA A:ALA310 3.5 143.7 1.0 C A:GLY309 3.7 147.0 1.0 CA A:ASN405 3.7 146.1 1.0 C A:ASN313 3.7 157.6 1.0 OG A:SER280 3.9 134.4 1.0 N A:ALA310 3.9 144.2 1.0 N A:VAL406 3.9 153.2 1.0 O A:ALA310 4.0 158.7 1.0 CB A:SER280 4.0 128.2 1.0 C A:ALA310 4.0 147.2 1.0 CG A:MET314 4.2 136.5 1.0 CG A:ASN405 4.3 143.0 1.0 CA A:VAL406 4.4 132.2 1.0 ND2 A:ASN313 4.5 153.5 1.0 CB A:ALA310 4.5 128.6 1.0 CA A:MET314 4.6 151.4 1.0 N A:MET314 4.6 158.3 1.0 ND2 A:ASN405 4.7 134.2 1.0 CA A:ASN313 4.7 154.1 1.0 CB A:ASP409 4.8 147.9 1.0 CB A:ASN313 4.8 158.2 1.0 N A:ASN313 4.9 148.1 1.0 CA A:GLY309 4.9 151.0 1.0 CG2 A:VAL406 4.9 129.6 1.0

Sodium binding site 2 out of 9 in the The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:164.9 occ:1.00 OD1 A:ASP315 2.3 174.0 1.0 OD1 A:ASN313 2.3 163.7 1.0 O A:TYR91 2.4 166.5 1.0 OG1 A:THR94 2.5 156.2 1.0 N A:SER95 2.7 148.8 1.0 OG A:SER95 2.7 142.7 1.0 CB A:THR94 3.3 153.4 1.0 C A:THR94 3.3 151.9 1.0 CG A:ASP315 3.3 173.7 1.0 C A:TYR91 3.3 143.5 1.0 CA A:SER95 3.3 150.1 1.0 CG A:ASN313 3.4 158.8 1.0 CB A:SER95 3.4 151.3 1.0 OD2 A:ASP315 3.7 175.8 1.0 CA A:TYR91 3.7 142.0 1.0 CA A:THR94 3.7 153.6 1.0 ND2 A:ASN313 4.0 153.5 1.0 O A:THR94 4.1 154.2 1.0 N A:THR94 4.1 153.8 1.0 CB A:TYR91 4.4 140.3 1.0 O A:TYR90 4.4 145.6 1.0 CB A:ASN313 4.5 158.2 1.0 N A:LEU92 4.6 144.6 1.0 CB A:ASP315 4.6 165.7 1.0 N A:ASP315 4.6 154.3 1.0 CG2 A:THR94 4.7 147.2 1.0 CA A:ASN313 4.7 154.1 1.0 CA A:ASP315 4.8 160.5 1.0 C A:SER95 4.8 150.9 1.0 CD1 A:TYR91 4.8 149.6 1.0 N A:MET314 4.9 158.3 1.0 N A:TYR91 4.9 143.0 1.0 C A:ASN313 5.0 157.6 1.0

Sodium binding site 3 out of 9 in the The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na510 b:140.7 occ:1.00 O4 A:QM5501 3.0 157.0 1.0 N A:SER281 3.7 126.1 1.0 N A:SER280 3.8 143.4 1.0 OG A:SER280 3.8 134.4 1.0 OG A:SER279 3.9 161.7 1.0 C11 A:QM5501 4.0 158.8 1.0 CB A:SER281 4.0 126.3 1.0 OG A:SER281 4.1 125.2 1.0 CA A:SER279 4.4 153.9 1.0 C A:SER279 4.4 147.5 1.0 N1 A:QM5501 4.4 161.0 1.0 CA A:SER281 4.5 125.8 1.0 CA A:SER280 4.5 137.4 1.0 CB A:SER279 4.6 161.6 1.0 C A:SER280 4.6 138.4 1.0 CB A:SER280 4.6 128.2 1.0 O5 A:QM5501 4.7 157.2 1.0 O1 A:QM5501 4.7 176.7 1.0 C4 A:QM5501 4.7 189.6 1.0 C5 A:QM5501 4.7 182.1 1.0 CE A:MET314 4.7 137.8 1.0 O A:ALA310 4.8 158.7 1.0 C3 A:QM5501 4.8 191.0 1.0 C10 A:QM5501 4.9 164.7 1.0 C6 A:QM5501 4.9 173.0 1.0

Sodium binding site 4 out of 9 in the The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na508 b:147.5 occ:1.00 O B:ASN313 2.5 153.7 1.0 OD2 B:ASP409 2.8 174.8 1.0 CB B:ASN405 3.1 130.5 1.0 O B:ASN405 3.2 131.8 1.0 O B:GLY309 3.3 127.0 1.0 C B:ASN405 3.3 128.4 1.0 OD1 B:ASP409 3.4 181.4 1.0 CG B:ASP409 3.4 176.6 1.0 CA B:ALA310 3.6 134.7 1.0 CA B:ASN405 3.7 130.3 1.0 C B:ASN313 3.7 156.4 1.0 N B:VAL406 3.9 130.6 1.0 CB B:SER280 3.9 126.5 1.0 OG B:SER280 3.9 131.3 1.0 O B:ALA310 3.9 128.7 1.0 C B:GLY309 4.0 131.7 1.0 CG B:MET314 4.1 134.7 1.0 C B:ALA310 4.1 135.1 1.0 N B:ALA310 4.2 131.8 1.0 CG B:ASN405 4.2 122.8 1.0 CA B:VAL406 4.3 125.8 1.0 CA B:MET314 4.5 146.7 1.0 N B:MET314 4.5 155.8 1.0 ND2 B:ASN313 4.5 181.0 1.0 ND2 B:ASN405 4.6 119.6 1.0 CB B:ALA310 4.7 130.4 1.0 O4 B:QM5501 4.7 185.8 1.0 CA B:ASN313 4.7 158.7 1.0 CB B:ASP409 4.7 168.4 1.0 CG2 B:VAL406 4.8 122.2 1.0 CB B:ASN313 4.9 168.5 1.0 CB B:MET314 4.9 140.9 1.0 N B:ASN313 4.9 146.3 1.0

Sodium binding site 5 out of 9 in the The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na509 b:169.2 occ:1.00 OD1 B:ASP315 2.4 173.1 1.0 OD1 B:ASN313 2.4 186.8 1.0 OG1 B:THR94 2.4 160.9 1.0 O B:TYR91 2.4 134.4 1.0 N B:SER95 2.7 155.3 1.0 OG B:SER95 2.9 162.7 1.0 CB B:THR94 3.1 160.9 1.0 C B:THR94 3.2 155.7 1.0 CG B:ASP315 3.3 171.6 1.0 C B:TYR91 3.4 142.7 1.0 CA B:SER95 3.4 158.9 1.0 CG B:ASN313 3.5 178.7 1.0 CB B:SER95 3.5 162.6 1.0 CA B:THR94 3.6 156.1 1.0 CA B:TYR91 3.6 150.4 1.0 OD2 B:ASP315 3.6 173.7 1.0 N B:THR94 4.0 147.7 1.0 O B:THR94 4.0 155.7 1.0 ND2 B:ASN313 4.2 181.0 1.0 O B:TYR90 4.2 144.3 1.0 CB B:TYR91 4.4 156.4 1.0 CG2 B:THR94 4.5 159.7 1.0 CB B:ASN313 4.6 168.5 1.0 N B:LEU92 4.6 140.9 1.0 CB B:ASP315 4.7 171.7 1.0 CD1 B:TYR91 4.7 155.2 1.0 N B:ASP315 4.7 159.8 1.0 N B:TYR91 4.7 151.8 1.0 CA B:ASN313 4.9 158.7 1.0 C B:SER95 4.9 151.9 1.0 CA B:ASP315 4.9 164.3 1.0 C B:TYR90 4.9 148.6 1.0 CG B:TYR91 5.0 158.7 1.0

Sodium binding site 6 out of 9 in the The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na510 b:150.9 occ:1.00 O5 B:QM5501 3.4 182.1 1.0 OG B:SER279 3.5 133.2 1.0 OG B:SER281 3.7 147.2 1.0 N B:SER281 3.7 129.9 1.0 N B:SER280 3.8 129.2 1.0 C4 B:QM5501 3.8 195.8 1.0 CB B:SER281 3.9 142.5 1.0 CA B:SER279 4.1 136.9 1.0 CB B:SER279 4.1 132.6 1.0 C5 B:QM5501 4.2 189.0 1.0 OG B:SER280 4.3 131.3 1.0 C B:SER279 4.3 133.7 1.0 C3 B:QM5501 4.3 195.3 1.0 CA B:SER281 4.4 135.8 1.0 C11 B:QM5501 4.5 183.8 1.0 C B:SER280 4.7 131.8 1.0 CA B:SER280 4.7 130.9 1.0 N2 B:QM5501 4.7 208.8 1.0 N1 B:QM5501 4.8 179.8 1.0 C6 B:QM5501 4.9 181.7 1.0 CB B:SER280 4.9 126.5 1.0 C2 B:QM5501 5.0 183.3 1.0 N B:GLY282 5.0 135.3 1.0

Sodium binding site 7 out of 9 in the The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na505 b:138.7 occ:1.00 O C:ASN313 2.4 193.6 1.0 OD2 C:ASP409 2.8 179.1 1.0 O C:ASN405 3.0 163.1 1.0 OD1 C:ASP409 3.0 180.5 1.0 CB C:ASN405 3.1 155.0 1.0 CG C:ASP409 3.2 176.9 1.0 C C:ASN405 3.2 151.7 1.0 O C:GLY309 3.2 152.5 1.0 CA C:ASN405 3.6 147.2 1.0 C C:ASN313 3.6 185.7 1.0 CA C:ALA310 3.7 138.4 1.0 N C:VAL406 3.8 155.1 1.0 C C:GLY309 3.9 149.7 1.0 OG C:SER280 4.0 149.4 1.0 ND2 C:ASN313 4.1 182.5 1.0 N C:ALA310 4.2 148.5 1.0 O C:ALA310 4.2 149.6 1.0 CG C:ASN405 4.3 156.3 1.0 CA C:VAL406 4.3 152.7 1.0 CB C:SER280 4.3 146.6 1.0 C C:ALA310 4.3 139.6 1.0 CG C:MET314 4.3 173.3 1.0 CB C:ASP409 4.5 169.8 1.0 CA C:MET314 4.5 175.4 1.0 N C:MET314 4.5 182.0 1.0 CA C:ASN313 4.6 180.2 1.0 CB C:ASN313 4.7 179.4 1.0 ND2 C:ASN405 4.7 141.9 1.0 CB C:ALA310 4.8 136.9 1.0 CG2 C:VAL406 4.9 149.2 1.0 CG C:ASN313 4.9 182.1 1.0 N C:ASN313 4.9 170.3 1.0 N C:ASN405 5.0 147.2 1.0

Sodium binding site 8 out of 9 in the The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na506 b:191.6 occ:1.00 OD1 C:ASP315 2.3 176.2 1.0 O C:TYR91 2.4 179.8 1.0 OD1 C:ASN313 2.4 181.8 1.0 OG C:SER95 2.6 163.6 1.0 OG1 C:THR94 2.7 196.7 1.0 N C:SER95 2.7 167.1 1.0 CA C:SER95 3.2 172.8 1.0 CB C:SER95 3.3 169.3 1.0 C C:THR94 3.3 169.1 1.0 C C:TYR91 3.4 174.0 1.0 CB C:THR94 3.4 187.7 1.0 CG C:ASP315 3.4 177.3 1.0 CG C:ASN313 3.5 182.1 1.0 CA C:TYR91 3.7 166.1 1.0 CA C:THR94 3.8 178.9 1.0 OD2 C:ASP315 3.8 178.9 1.0 O C:THR94 4.1 167.6 1.0 N C:THR94 4.2 177.6 1.0 ND2 C:ASN313 4.3 182.5 1.0 CB C:ASN313 4.4 179.4 1.0 CB C:TYR91 4.4 159.0 1.0 CA C:ASN313 4.5 180.2 1.0 N C:ASP315 4.5 176.5 1.0 O C:TYR90 4.6 174.3 1.0 N C:LEU92 4.6 178.2 1.0 CB C:ASP315 4.7 177.7 1.0 N C:MET314 4.7 182.0 1.0 C C:SER95 4.7 175.9 1.0 CA C:ASP315 4.7 176.0 1.0 CG2 C:THR94 4.8 188.3 1.0 CD1 C:TYR91 4.8 155.5 1.0 C C:ASN313 4.8 185.7 1.0 N C:TYR91 4.9 170.4 1.0

Sodium binding site 9 out of 9 in the The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Structure of Glutamate Transporter Homologue Glttk in Complex with the Photo Switchable Compound (Cis) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na507 b:224.5 occ:1.00 C14 C:QM5501 3.4 225.2 1.0 OG C:SER279 3.6 167.6 1.0 C13 C:QM5501 3.7 222.3 1.0 C15 C:QM5501 3.8 229.1 1.0 CB C:SER279 4.0 165.7 1.0 O6 C:QM5501 4.3 224.9 1.0 C12 C:QM5501 4.4 219.7 1.0 C16 C:QM5501 4.5 229.1 1.0 C17 C:QM5501 4.7 222.4 1.0 OG C:SER281 4.9 132.1 1.0

V.Arkhipova, H.Fu, M.W.H.Hoorens, G.Trinco, L.N.Lameijer, E.Marin, B.L.Feringa, G.J.Poelarends, W.Szymanski, D.J.Slotboom, A.Guskov. Structural Aspects of Photopharmacology: Insight Into the Binding of Photoswitchable and Photocaged Inhibitors to the Glutamate Transporter Homologue. J.Am.Chem.Soc. 2021.
ISSN: ESSN 1520-5126
PubMed: 33449695
DOI: 10.1021/JACS.0C11336