Sodium in PDB 6v8g: Gltph Mutant - Y204L A345V V366A

The structure of Gltph Mutant - Y204L A345V V366A, PDB code: 6v8g was solved by O.Boudker, G.H.M.Huysmans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.38 / 3.38
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.416, 109.416, 305.227, 90.00, 90.00, 120.00
R / Rfree (%)	23.2 / 25.7

The binding sites of Sodium atom in the Gltph Mutant - Y204L A345V V366A (pdb code 6v8g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Gltph Mutant - Y204L A345V V366A, PDB code: 6v8g:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in the Gltph Mutant - Y204L A345V V366A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Gltph Mutant - Y204L A345V V366A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:89.9 occ:1.00 O A:ASN310 2.7 0.6 1.0 O A:GLY306 2.8 0.7 1.0 O A:ASN401 3.0 0.8 1.0 OD2 A:ASP405 3.1 0.6 1.0 CB A:ASN401 3.4 0.0 1.0 CA A:ALA307 3.4 97.1 1.0 OG A:SER278 3.4 0.8 1.0 C A:ASN401 3.5 0.6 1.0 O A:ALA307 3.6 0.1 1.0 C A:ALA307 3.6 0.3 1.0 OD1 A:ASP405 3.7 0.5 1.0 CB A:SER278 3.7 86.1 1.0 C A:GLY306 3.8 91.6 1.0 CG A:ASP405 3.8 0.5 1.0 CG A:MET311 3.9 83.5 1.0 CA A:ASN401 3.9 0.2 1.0 C A:ASN310 3.9 0.2 1.0 N A:ALA307 4.0 84.2 1.0 N A:VAL402 4.2 0.5 1.0 CE A:MET311 4.3 90.2 1.0 N A:THR308 4.4 0.5 1.0 CG A:ASN401 4.5 95.9 1.0 CB A:ALA307 4.5 0.6 1.0 O A:ASP503 4.6 0.9 1.0 CA A:VAL402 4.6 0.8 1.0 CA A:MET311 4.7 87.0 1.0 N A:MET311 4.7 84.8 1.0 ND2 A:ASN310 4.7 0.4 1.0 CA A:ASN310 4.9 0.2 1.0 CB A:MET311 4.9 92.9 1.0 SD A:MET311 4.9 91.5 1.0 ND2 A:ASN401 4.9 0.8 1.0 N A:ASN310 4.9 0.8 1.0 CG2 A:VAL402 5.0 87.5 1.0

Sodium binding site 2 out of 9 in the Gltph Mutant - Y204L A345V V366A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Gltph Mutant - Y204L A345V V366A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:82.5 occ:1.00 O A:SER349 2.4 0.1 1.0 O A:THR352 2.4 0.2 1.0 O A:THR308 2.4 1.0 1.0 SD A:MET311 2.8 91.5 1.0 O A:ILE350 3.1 0.3 1.0 CE A:MET311 3.1 90.2 1.0 CG A:MET311 3.2 83.5 1.0 C A:THR308 3.3 0.1 1.0 C A:THR352 3.4 0.7 1.0 C A:ILE350 3.5 0.5 1.0 C A:SER349 3.5 0.3 1.0 N A:THR352 3.6 0.1 1.0 CA A:ILE350 3.7 96.8 1.0 CB A:THR352 3.8 96.5 1.0 CA A:THR352 3.8 90.9 1.0 CB A:MET311 4.0 92.9 1.0 CA A:THR308 4.0 0.4 1.0 N A:ILE350 4.1 0.5 1.0 N A:ILE309 4.1 99.8 1.0 CA A:ILE309 4.3 98.2 1.0 N A:GLY351 4.4 0.9 1.0 O A:ILE309 4.4 0.8 1.0 C A:ILE309 4.5 0.7 1.0 C A:GLY351 4.5 0.3 1.0 N A:ALA353 4.6 85.3 1.0 CG2 A:THR352 4.7 87.1 1.0 OG1 A:THR352 4.7 94.6 1.0 CA A:SER349 4.7 0.0 1.0 CA A:GLY351 5.0 0.9 1.0 CB A:THR308 5.0 0.9 1.0

Sodium binding site 3 out of 9 in the Gltph Mutant - Y204L A345V V366A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Gltph Mutant - Y204L A345V V366A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:99.6 occ:1.00 OD1 A:ASN310 2.3 0.2 1.0 O A:TYR89 2.3 0.2 1.0 OG1 A:THR92 2.6 0.4 1.0 OG A:SER93 2.7 0.6 1.0 OD1 A:ASP312 2.7 0.8 1.0 CG A:ASN310 3.1 0.2 1.0 C A:TYR89 3.1 0.2 1.0 CA A:TYR89 3.2 0.9 1.0 N A:SER93 3.4 0.1 1.0 CA A:ASN310 3.6 0.2 1.0 CB A:ASN310 3.6 0.5 1.0 CB A:SER93 3.7 0.5 1.0 CG A:ASP312 3.7 0.8 1.0 CB A:TYR89 3.7 0.5 1.0 CB A:THR92 3.8 0.4 1.0 CA A:SER93 4.0 0.4 1.0 OD2 A:ASP312 4.0 0.0 1.0 C A:THR92 4.1 0.7 1.0 ND2 A:ASN310 4.1 0.4 1.0 CD1 A:TYR89 4.2 0.4 1.0 CG A:TYR89 4.2 0.1 1.0 N A:MET311 4.3 84.8 1.0 C A:ASN310 4.3 0.2 1.0 CA A:THR92 4.3 0.2 1.0 N A:LEU90 4.4 0.5 1.0 O A:TYR88 4.4 0.4 1.0 N A:THR92 4.5 0.7 1.0 N A:TYR89 4.5 0.1 1.0 N A:ASP312 4.8 0.0 1.0 N A:ASN310 4.8 0.8 1.0 O A:ILE309 4.8 0.8 1.0 C A:TYR88 4.9 0.6 1.0 O A:THR92 5.0 0.7 1.0 CG2 A:THR92 5.0 0.4 1.0

Sodium binding site 4 out of 9 in the Gltph Mutant - Y204L A345V V366A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Gltph Mutant - Y204L A345V V366A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:0.7 occ:1.00 O B:ASN310 2.7 0.6 1.0 O B:GLY306 2.8 0.1 1.0 O B:ASN401 3.1 1.0 1.0 OD2 B:ASP405 3.1 0.9 1.0 CA B:ALA307 3.4 98.4 1.0 CB B:ASN401 3.4 0.4 1.0 OG B:SER278 3.4 0.1 1.0 C B:ASN401 3.5 99.5 1.0 O B:ALA307 3.6 0.3 1.0 C B:ALA307 3.6 0.5 1.0 CB B:SER278 3.7 81.6 1.0 OD1 B:ASP405 3.7 0.9 1.0 C B:GLY306 3.7 93.0 1.0 CG B:ASP405 3.8 0.7 1.0 CG B:MET311 3.9 79.5 1.0 C B:ASN310 3.9 0.6 1.0 CA B:ASN401 3.9 0.2 1.0 N B:ALA307 4.0 83.6 1.0 N B:VAL402 4.3 0.5 1.0 CE B:MET311 4.3 85.1 1.0 N B:THR308 4.4 0.3 1.0 CG B:ASN401 4.5 78.5 1.0 CB B:ALA307 4.5 98.3 1.0 O B:ASP503 4.6 0.1 1.0 CA B:MET311 4.7 85.9 1.0 CA B:VAL402 4.7 0.0 1.0 N B:MET311 4.7 95.7 1.0 ND2 B:ASN310 4.8 0.1 1.0 CA B:ASN310 4.8 0.2 1.0 CB B:MET311 4.8 82.4 1.0 SD B:MET311 4.9 83.1 1.0 N B:ASN310 4.9 0.5 1.0 ND2 B:ASN401 4.9 72.1 1.0 CG2 B:VAL402 5.0 84.2 1.0 CB B:ASN310 5.0 0.4 1.0

Sodium binding site 5 out of 9 in the Gltph Mutant - Y204L A345V V366A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Gltph Mutant - Y204L A345V V366A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:75.1 occ:1.00 O B:SER349 2.4 0.9 1.0 O B:THR352 2.4 0.5 1.0 O B:THR308 2.5 0.4 1.0 SD B:MET311 2.8 83.1 1.0 O B:ILE350 3.0 0.5 1.0 CE B:MET311 3.1 85.1 1.0 CG B:MET311 3.3 79.5 1.0 C B:THR308 3.3 0.2 1.0 C B:THR352 3.3 97.1 1.0 C B:ILE350 3.5 0.8 1.0 C B:SER349 3.5 0.8 1.0 N B:THR352 3.6 0.8 1.0 CA B:ILE350 3.7 90.8 1.0 CB B:THR352 3.7 95.3 1.0 CA B:THR352 3.7 92.7 1.0 CB B:MET311 4.0 82.4 1.0 CA B:THR308 4.1 0.8 1.0 N B:ILE350 4.1 0.1 1.0 N B:ILE309 4.2 0.7 1.0 CA B:ILE309 4.4 97.8 1.0 N B:GLY351 4.4 0.7 1.0 C B:GLY351 4.4 0.5 1.0 O B:ILE309 4.5 0.9 1.0 C B:ILE309 4.5 0.9 1.0 N B:ALA353 4.6 76.8 1.0 CG2 B:THR352 4.6 87.2 1.0 OG1 B:THR352 4.7 95.3 1.0 CA B:SER349 4.7 0.1 1.0 CA B:GLY351 4.9 0.7 1.0

Sodium binding site 6 out of 9 in the Gltph Mutant - Y204L A345V V366A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Gltph Mutant - Y204L A345V V366A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:0.4 occ:1.00 OD1 B:ASN310 2.3 1.0 1.0 O B:TYR89 2.4 0.2 1.0 OG B:SER93 2.5 1.0 1.0 OD1 B:ASP312 2.6 0.5 1.0 OG1 B:THR92 2.7 0.1 1.0 CG B:ASN310 3.1 0.5 1.0 C B:TYR89 3.2 0.6 1.0 N B:SER93 3.4 0.5 1.0 CA B:TYR89 3.4 0.3 1.0 CA B:ASN310 3.6 0.2 1.0 CB B:SER93 3.6 0.2 1.0 CG B:ASP312 3.6 0.8 1.0 CB B:ASN310 3.6 0.4 1.0 CB B:THR92 3.8 1.0 1.0 CB B:TYR89 3.9 0.7 1.0 CA B:SER93 3.9 0.8 1.0 OD2 B:ASP312 3.9 0.6 1.0 ND2 B:ASN310 4.0 0.1 1.0 C B:THR92 4.1 0.0 1.0 N B:MET311 4.1 95.7 1.0 C B:ASN310 4.2 0.6 1.0 CD1 B:TYR89 4.3 1.0 1.0 CG B:TYR89 4.4 0.5 1.0 CA B:THR92 4.4 0.4 1.0 N B:LEU90 4.5 0.7 1.0 O B:TYR88 4.6 0.4 1.0 N B:THR92 4.6 1.0 1.0 N B:ASP312 4.6 0.4 1.0 N B:TYR89 4.7 0.8 1.0 O B:ILE309 4.7 0.9 1.0 N B:ASN310 4.8 0.5 1.0 CB B:ASP312 4.9 0.9 1.0 O B:THR92 4.9 0.1 1.0 C B:MET311 5.0 0.3 1.0

Sodium binding site 7 out of 9 in the Gltph Mutant - Y204L A345V V366A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Gltph Mutant - Y204L A345V V366A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:92.2 occ:1.00 O C:ASN310 2.6 0.1 1.0 O C:GLY306 2.8 0.6 1.0 O C:ASN401 3.1 0.4 1.0 OD2 C:ASP405 3.2 0.3 1.0 CA C:ALA307 3.4 93.8 1.0 CB C:ASN401 3.4 0.6 1.0 OG C:SER278 3.5 0.3 1.0 C C:ASN401 3.5 0.8 1.0 O C:ALA307 3.6 0.2 1.0 C C:ALA307 3.6 0.4 1.0 OD1 C:ASP405 3.7 0.6 1.0 CB C:SER278 3.7 96.1 1.0 C C:GLY306 3.7 0.3 1.0 CG C:MET311 3.8 98.0 1.0 C C:ASN310 3.8 0.5 1.0 CG C:ASP405 3.8 0.2 1.0 CA C:ASN401 3.9 0.8 1.0 N C:ALA307 4.0 90.6 1.0 N C:VAL402 4.3 0.7 1.0 CE C:MET311 4.3 0.0 1.0 N C:THR308 4.4 0.6 1.0 CG C:ASN401 4.5 0.7 1.0 CB C:ALA307 4.5 0.0 1.0 OXT C:ASP503 4.6 0.4 1.0 CA C:MET311 4.6 95.0 1.0 N C:MET311 4.6 95.2 1.0 CA C:VAL402 4.7 1.0 1.0 ND2 C:ASN310 4.7 0.9 1.0 CA C:ASN310 4.8 0.5 1.0 CB C:MET311 4.8 99.1 1.0 SD C:MET311 4.8 0.2 1.0 N C:ASN310 4.9 0.8 1.0 ND2 C:ASN401 4.9 0.4 1.0 CB C:ASN310 5.0 0.0 1.0

Sodium binding site 8 out of 9 in the Gltph Mutant - Y204L A345V V366A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Gltph Mutant - Y204L A345V V366A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:86.4 occ:1.00 O C:THR352 2.4 0.4 1.0 O C:SER349 2.4 0.1 1.0 O C:THR308 2.4 0.3 1.0 SD C:MET311 2.8 0.2 1.0 O C:ILE350 3.0 0.8 1.0 CE C:MET311 3.1 0.0 1.0 CG C:MET311 3.2 98.0 1.0 C C:THR308 3.3 0.1 1.0 C C:THR352 3.4 0.2 1.0 C C:ILE350 3.5 0.4 1.0 C C:SER349 3.5 0.1 1.0 N C:THR352 3.6 0.7 1.0 CA C:ILE350 3.7 0.3 1.0 CA C:THR352 3.7 0.5 1.0 CB C:THR352 3.7 0.2 1.0 CB C:MET311 4.0 99.1 1.0 CA C:THR308 4.1 0.3 1.0 N C:ILE350 4.1 1.0 1.0 N C:ILE309 4.1 0.2 1.0 CA C:ILE309 4.3 0.8 1.0 N C:GLY351 4.4 0.4 1.0 C C:GLY351 4.4 0.2 1.0 O C:ILE309 4.5 0.1 1.0 C C:ILE309 4.5 0.1 1.0 N C:ALA353 4.6 86.8 1.0 CG2 C:THR352 4.6 0.2 1.0 OG1 C:THR352 4.7 0.8 1.0 CA C:SER349 4.7 1.0 1.0 CA C:GLY351 4.9 0.3 1.0 CB C:THR308 5.0 0.9 1.0

Sodium binding site 9 out of 9 in the Gltph Mutant - Y204L A345V V366A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Gltph Mutant - Y204L A345V V366A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na504 b:0.5 occ:1.00 OG C:SER93 2.4 0.0 1.0 OD1 C:ASN310 2.4 0.7 1.0 O C:TYR89 2.4 0.5 1.0 OD1 C:ASP312 2.6 0.7 1.0 OG1 C:THR92 2.8 0.0 1.0 CG C:ASN310 3.1 0.4 1.0 C C:TYR89 3.3 0.5 1.0 N C:SER93 3.3 0.1 1.0 CB C:SER93 3.4 0.2 1.0 CA C:TYR89 3.5 0.6 1.0 CA C:ASN310 3.5 0.5 1.0 CG C:ASP312 3.6 0.1 1.0 CB C:ASN310 3.7 0.0 1.0 CA C:SER93 3.8 0.6 1.0 CB C:THR92 3.9 0.5 1.0 CB C:TYR89 3.9 0.9 1.0 OD2 C:ASP312 4.0 0.3 1.0 N C:MET311 4.0 95.2 1.0 C C:THR92 4.1 0.7 1.0 ND2 C:ASN310 4.1 0.9 1.0 C C:ASN310 4.1 0.5 1.0 CD1 C:TYR89 4.4 0.3 1.0 CA C:THR92 4.4 0.3 1.0 CG C:TYR89 4.5 0.3 1.0 N C:ASP312 4.5 0.9 1.0 N C:LEU90 4.6 0.7 1.0 O C:ILE309 4.6 0.1 1.0 N C:THR92 4.7 0.3 1.0 O C:TYR88 4.7 0.4 1.0 N C:ASN310 4.7 0.8 1.0 N C:TYR89 4.8 0.1 1.0 CB C:ASP312 4.9 0.8 1.0 C C:MET311 4.9 0.7 1.0 O C:THR92 4.9 0.9 1.0 CA C:ASP312 5.0 0.8 1.0

G.H.M.Huysmans, D.Ciftci, X.Wang, S.C.Blanchard, O.Boudker. The High-Energy Transition State of the Glutamate Transporter Homologue Gltph. Embo J. 05415 2020.
ISSN: ESSN 1460-2075
PubMed: 33185289
DOI: 10.15252/EMBJ.2020105415