Sodium in PDB 7ahk: Crystal Structure of the Outward-Facing State of the Substrate-Free Na+-Only Bound Glutamate Transporter Homolog Gltph

The structure of Crystal Structure of the Outward-Facing State of the Substrate-Free Na+-Only Bound Glutamate Transporter Homolog Gltph, PDB code: 7ahk was solved by K.Kovalev, C.Alleva, A.Astashkin, J.-P.Machtens, C.Fahlke, V.Gordeliy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	152.011, 152.011, 57.521, 90.00, 90.00, 120.00
R / Rfree (%)	21.1 / 25.3

The binding sites of Sodium atom in the Crystal Structure of the Outward-Facing State of the Substrate-Free Na+-Only Bound Glutamate Transporter Homolog Gltph (pdb code 7ahk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Outward-Facing State of the Substrate-Free Na+-Only Bound Glutamate Transporter Homolog Gltph, PDB code: 7ahk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Outward-Facing State of the Substrate-Free Na+-Only Bound Glutamate Transporter Homolog Gltph


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 Outward-Facing State of the Substrate-Free Na+-Only Bound Glutamate Transporter Homolog Gltph within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:36.0 occ:1.00 O A:ASN310 2.3 46.1 1.0 O A:HOH615 2.3 35.3 1.0 OD2 A:ASP405 2.5 49.2 1.0 O A:GLY306 2.5 45.1 1.0 O A:ASN401 2.5 33.2 1.0 OD1 A:ASP405 2.6 59.9 1.0 CG A:ASP405 2.9 56.3 1.0 C A:GLY306 3.3 37.4 1.0 C A:ASN401 3.3 28.6 1.0 C A:ASN310 3.4 44.1 1.0 CA A:ALA307 3.6 36.9 1.0 N A:ALA307 3.8 35.9 1.0 CA A:ASN401 4.0 29.5 1.0 CB A:ASN401 4.0 27.4 1.0 C A:ALA307 4.1 35.7 1.0 N A:VAL402 4.1 30.9 1.0 CB A:ASN310 4.2 38.7 1.0 O A:ALA307 4.2 46.2 1.0 ND2 A:ASN310 4.3 41.3 1.0 CA A:ASN310 4.3 37.4 1.0 O A:HOH618 4.3 53.6 1.0 CA A:VAL402 4.3 34.8 1.0 CB A:ASP405 4.4 48.4 1.0 CA A:GLY306 4.4 39.1 1.0 OG A:SER278 4.4 48.7 1.0 N A:MET311 4.4 48.0 1.0 CG A:MET311 4.5 54.4 1.0 CA A:MET311 4.5 51.3 1.0 N A:ASN310 4.5 38.6 1.0 CG A:ASN310 4.7 39.4 1.0 CB A:ALA307 4.9 35.3 1.0 CB A:SER278 4.9 51.3 1.0 O A:HOH610 4.9 35.0 1.0 N A:THR308 4.9 40.0 1.0 CG A:ASN401 5.0 28.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Outward-Facing State of the Substrate-Free Na+-Only Bound Glutamate Transporter Homolog Gltph


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 Outward-Facing State of the Substrate-Free Na+-Only Bound Glutamate Transporter Homolog Gltph within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:50.0 occ:1.00 OD1 A:ASN310 2.2 39.5 1.0 OD1 A:ASP312 2.3 48.8 1.0 O A:TYR89 2.3 38.5 1.0 OG1 A:THR92 2.5 34.9 1.0 OG A:SER93 2.5 31.8 1.0 N A:SER93 2.8 41.4 1.0 CB A:SER93 3.2 35.0 1.0 CA A:SER93 3.3 40.0 1.0 C A:TYR89 3.3 37.3 1.0 CG A:ASN310 3.3 39.4 1.0 CG A:ASP312 3.3 51.9 1.0 C A:THR92 3.5 40.3 1.0 O A:HOH612 3.6 36.4 1.0 CB A:THR92 3.6 32.8 1.0 CA A:TYR89 3.7 35.0 1.0 OD2 A:ASP312 3.8 53.8 1.0 CA A:THR92 3.9 36.6 1.0 ND2 A:ASN310 4.0 41.3 1.0 N A:THR92 4.2 37.7 1.0 O A:THR92 4.3 45.8 1.0 CB A:TYR89 4.4 36.3 1.0 O A:TYR88 4.4 32.8 1.0 CB A:ASN310 4.4 38.7 1.0 N A:LEU90 4.5 39.5 1.0 CA A:ASN310 4.6 37.4 1.0 CB A:ASP312 4.6 51.3 1.0 N A:ASP312 4.7 41.1 1.0 CD1 A:TYR89 4.8 38.0 1.0 C A:SER93 4.8 37.0 1.0 N A:MET311 4.8 48.0 1.0 CA A:ASP312 4.8 46.9 1.0 N A:TYR89 4.8 30.9 1.0 C A:ASN310 4.8 44.1 1.0 CG2 A:THR92 4.9 32.0 1.0 O A:HOH618 4.9 53.6 1.0 C A:LEU90 5.0 46.1 1.0 O A:LEU90 5.0 51.3 1.0

C.Alleva, K.Kovalev, R.Astashkin, M.I.Berndt, C.Baeken, T.Balandin, V.Gordeliy, C.Fahlke, J.P.Machtens. Na + -Dependent Gate Dynamics and Electrostatic Attraction Ensure Substrate Coupling in Glutamate Transporters. Sci Adv V. 6 2020.
ISSN: ESSN 2375-2548
PubMed: 33208356
DOI: 10.1126/SCIADV.ABA9854