Sodium in PDB 6bmi: Crystal Structure of Gltph R397C in Complex with L-Serine

The structure of Crystal Structure of Gltph R397C in Complex with L-Serine, PDB code: 6bmi was solved by J.Font, A.J.Scopelliti, R.J.Vandenberg, O.Boudker, R.M.Ryan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.90
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	114.750, 114.750, 322.336, 90.00, 90.00, 120.00
R / Rfree (%)	22.7 / 24.8

The binding sites of Sodium atom in the Crystal Structure of Gltph R397C in Complex with L-Serine (pdb code 6bmi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Gltph R397C in Complex with L-Serine, PDB code: 6bmi:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Gltph R397C in Complex with L-Serine


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 Gltph R397C in Complex with L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:99.7 occ:1.00 O A:ASN310 2.6 0.0 1.0 O A:GLY306 2.9 1.0 1.0 OD2 A:ASP405 3.1 0.1 1.0 O A:ASN401 3.4 0.5 1.0 OD1 A:ASP405 3.5 0.9 1.0 C A:ASN401 3.7 0.4 1.0 O A:ALA307 3.7 0.5 1.0 CG A:ASP405 3.7 0.5 1.0 CA A:ALA307 3.7 0.8 1.0 C A:ASN310 3.7 0.7 1.0 C A:ALA307 3.8 0.8 1.0 OG A:SER278 3.8 0.9 1.0 CB A:ASN401 3.9 0.0 1.0 C A:GLY306 3.9 0.3 1.0 CG A:MET311 4.0 0.4 1.0 CB A:SER278 4.0 0.0 1.0 N A:VAL402 4.2 0.1 1.0 CA A:ASN401 4.2 0.7 1.0 N A:ALA307 4.2 0.1 1.0 CA A:VAL402 4.5 0.2 1.0 CG A:ASN401 4.5 0.9 1.0 N A:MET311 4.5 0.1 1.0 CA A:MET311 4.5 0.0 1.0 CA A:ASN310 4.6 0.4 1.0 CE A:MET311 4.6 0.7 1.0 N A:THR308 4.6 0.6 1.0 ND2 A:ASN401 4.7 0.3 1.0 N A:ASN310 4.7 0.8 1.0 CB A:MET311 4.8 0.7 1.0 SD A:MET311 4.8 0.8 1.0 CG2 A:VAL402 4.9 0.5 1.0 CB A:ALA307 4.9 0.8 1.0 CB A:ASN310 5.0 0.0 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Gltph R397C in Complex with L-Serine


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 Gltph R397C in Complex with L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:0.1 occ:1.00 O B:ASN310 2.8 0.8 1.0 OD2 B:ASP405 2.9 0.8 1.0 O B:GLY306 3.0 0.3 1.0 O B:ASN401 3.3 0.3 1.0 OD1 B:ASP405 3.5 0.5 1.0 C B:ASN401 3.6 0.1 1.0 CG B:ASP405 3.6 0.5 1.0 CA B:ALA307 3.7 0.5 1.0 O B:ALA307 3.7 0.2 1.0 OG B:SER278 3.8 0.4 1.0 C B:ALA307 3.8 0.6 1.0 CB B:ASN401 3.8 0.4 1.0 C B:ASN310 3.8 0.8 1.0 C B:GLY306 3.9 0.9 1.0 CB B:SER278 4.0 1.0 1.0 CG B:MET311 4.1 0.5 1.0 N B:VAL402 4.1 1.0 1.0 CA B:ASN401 4.2 0.5 1.0 N B:ALA307 4.2 0.5 1.0 CA B:VAL402 4.4 0.1 1.0 CG B:ASN401 4.5 0.4 1.0 CA B:MET311 4.6 0.8 1.0 N B:MET311 4.7 0.2 1.0 ND2 B:ASN401 4.7 0.3 1.0 N B:THR308 4.7 0.6 1.0 CG2 B:VAL402 4.7 0.5 1.0 CA B:ASN310 4.8 0.6 1.0 CE B:MET311 4.8 0.8 1.0 CB B:ALA307 4.9 0.1 1.0 N B:ASN310 4.9 0.3 1.0 CB B:MET311 4.9 0.2 1.0 SD B:MET311 4.9 0.1 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Gltph R397C in Complex with L-Serine


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 Gltph R397C in Complex with L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:0.4 occ:1.00 O C:ASN310 2.8 0.1 1.0 OD2 C:ASP405 3.0 0.1 1.0 O C:GLY306 3.0 0.4 1.0 O C:ASN401 3.4 0.9 1.0 OD1 C:ASP405 3.6 0.2 1.0 C C:ASN401 3.6 0.1 1.0 CG C:ASP405 3.6 0.7 1.0 OG C:SER278 3.7 0.0 1.0 CA C:ALA307 3.7 0.7 1.0 O C:ALA307 3.7 0.4 1.0 CB C:ASN401 3.8 0.0 1.0 C C:ALA307 3.8 0.9 1.0 C C:ASN310 3.9 0.1 1.0 C C:GLY306 3.9 0.0 1.0 CB C:SER278 4.0 0.8 1.0 CG C:MET311 4.1 0.7 1.0 N C:VAL402 4.1 0.9 1.0 CA C:ASN401 4.2 0.7 1.0 N C:ALA307 4.2 0.2 1.0 CA C:VAL402 4.4 0.4 1.0 CG C:ASN401 4.5 0.3 1.0 CA C:MET311 4.6 0.8 1.0 ND2 C:ASN401 4.6 0.1 1.0 CE C:MET311 4.6 0.7 1.0 N C:MET311 4.7 1.0 1.0 N C:THR308 4.7 0.9 1.0 CG2 C:VAL402 4.7 0.9 1.0 CA C:ASN310 4.8 0.8 1.0 CB C:ALA307 4.9 0.9 1.0 CB C:MET311 4.9 1.0 1.0 SD C:MET311 4.9 0.1 1.0 N C:ASN310 4.9 0.9 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Gltph R397C in Complex with L-Serine


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 Gltph R397C in Complex with L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:0.7 occ:1.00 O C:THR308 2.2 0.4 1.0 O C:THR352 2.4 0.6 1.0 O C:SER349 2.4 0.8 1.0 N C:THR352 3.2 0.1 1.0 C C:THR352 3.4 0.6 1.0 C C:SER349 3.4 0.8 1.0 C C:THR308 3.4 0.0 1.0 C C:ILE350 3.5 0.4 1.0 O C:ILE350 3.5 0.7 1.0 CA C:THR352 3.6 0.5 1.0 N C:GLY351 3.7 0.8 1.0 C C:GLY351 3.8 0.3 1.0 CE C:MET311 3.8 0.7 1.0 CB C:THR352 4.0 0.6 1.0 CA C:ILE350 4.1 0.7 1.0 CA C:GLY351 4.1 0.5 1.0 O C:ILE309 4.1 0.8 1.0 CA C:ILE309 4.1 0.0 1.0 SD C:MET311 4.1 0.1 1.0 N C:ILE350 4.1 0.6 1.0 N C:ILE309 4.2 0.0 1.0 CG C:MET311 4.2 0.7 1.0 CA C:SER349 4.4 0.9 1.0 C C:ILE309 4.4 0.9 1.0 CA C:THR308 4.5 0.5 1.0 CG2 C:THR352 4.5 0.4 1.0 O C:GLY351 4.5 0.3 1.0 N C:ALA353 4.6 0.6 1.0 CG2 C:THR308 4.7 0.6 1.0

A.J.Scopelliti, J.Font, R.J.Vandenberg, O.Boudker, R.M.Ryan. Structural Characterisation Reveals Insights Into Substrate Recognition By the Glutamine Transporter ASCT2/SLC1A5. Nat Commun V. 9 38 2018.
ISSN: ESSN 2041-1723
PubMed: 29295993
DOI: 10.1038/S41467-017-02444-W