Sodium in PDB 6l85: The Sodium-Dependent Phosphate Transporter

The structure of The Sodium-Dependent Phosphate Transporter, PDB code: 6l85 was solved by J.-Y.Tsai, Y.-J.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.40 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	121.178, 112.650, 110.792, 90.00, 119.36, 90.00
R / Rfree (%)	18.8 / 22.4

The binding sites of Sodium atom in the The Sodium-Dependent Phosphate Transporter (pdb code 6l85). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the The Sodium-Dependent Phosphate Transporter, PDB code: 6l85:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the The Sodium-Dependent Phosphate Transporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Sodium-Dependent Phosphate Transporter within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:46.2 occ:1.00 NZ A:LYS314 2.0 50.5 1.0 O A:VAL104 2.3 50.1 1.0 OD1 A:ASP22 2.3 45.6 1.0 OG1 A:THR347 2.4 40.8 1.0 OD1 A:ASN21 2.5 49.0 1.0 CE A:LYS314 3.1 64.4 1.0 C A:VAL104 3.5 46.5 1.0 CG A:ASP22 3.6 44.5 1.0 CB A:THR347 3.6 43.5 1.0 N A:VAL104 3.6 52.8 1.0 CG A:ASN21 3.7 50.4 1.0 O A:ASN21 3.7 50.1 1.0 CG2 A:THR347 3.8 46.3 1.0 O4 A:PO4501 4.0 33.5 1.0 O1 A:PO4501 4.1 39.5 1.0 OD2 A:ASP22 4.2 44.1 1.0 C A:ASN21 4.2 47.5 1.0 CA A:VAL104 4.2 48.2 1.0 ND2 A:ASN25 4.3 37.2 1.0 CB A:ASN21 4.4 43.2 1.0 C A:PRO103 4.5 58.7 1.0 N A:SER105 4.5 43.0 1.0 CA A:PRO103 4.5 64.6 1.0 CD A:LYS314 4.5 74.7 1.0 CA A:ASP22 4.5 45.4 1.0 OD1 A:ASN25 4.6 47.5 1.0 CB A:ASP22 4.7 42.9 1.0 CA A:SER105 4.7 40.6 1.0 CB A:PRO103 4.7 68.4 1.0 ND2 A:ASN21 4.7 46.0 1.0 N A:ASP22 4.7 48.3 1.0 P A:PO4501 4.7 53.4 1.0 CA A:THR347 4.8 39.9 1.0 CG2 A:VAL104 4.8 48.1 1.0 CG A:ASN25 4.9 41.8 1.0 CA A:ASN21 5.0 44.8 1.0

Sodium binding site 2 out of 6 in the The Sodium-Dependent Phosphate Transporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Sodium-Dependent Phosphate Transporter within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:36.0 occ:1.00 OD1 A:ASN257 2.2 35.0 1.0 OD1 A:ASP258 2.2 32.6 1.0 O A:ILE344 2.3 41.4 1.0 O A:HOH616 2.4 30.1 1.0 OG1 A:THR107 2.5 37.1 1.0 CG A:ASN257 3.3 34.4 1.0 CG A:ASP258 3.4 39.6 1.0 C A:ILE344 3.4 37.3 1.0 N A:ILE344 3.4 35.7 1.0 CG2 A:THR107 3.5 30.1 1.0 CB A:THR107 3.5 38.3 1.0 O A:ASN257 3.7 32.7 1.0 C A:ASN257 3.9 32.7 1.0 CB A:ASN257 4.0 34.2 1.0 CA A:ILE344 4.1 36.0 1.0 C A:PRO343 4.1 43.4 1.0 OD2 A:ASP258 4.1 39.4 1.0 CA A:ASP258 4.1 31.2 1.0 CA A:PRO343 4.2 33.4 1.0 ND2 A:ASN261 4.2 30.1 1.0 N A:ASP258 4.3 31.7 1.0 O3 A:PO4501 4.3 44.0 1.0 CB A:ASP258 4.4 35.1 1.0 O2 A:PO4501 4.4 33.3 1.0 ND2 A:ASN257 4.4 33.6 1.0 OD1 A:ASN261 4.5 33.0 1.0 N A:SER345 4.5 43.5 1.0 CB A:PRO343 4.6 32.4 1.0 CA A:ASN257 4.6 30.2 1.0 CA A:THR107 4.7 35.7 1.0 CG A:ASN261 4.8 35.2 1.0 CA A:SER345 4.8 38.2 1.0 CG2 A:THR346 4.8 36.3 1.0 CG1 A:ILE344 4.9 38.6 1.0 P A:PO4501 5.0 53.4 1.0 O A:PRO343 5.0 37.2 1.0

Sodium binding site 3 out of 6 in the The Sodium-Dependent Phosphate Transporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Sodium-Dependent Phosphate Transporter within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:51.0 occ:1.00 OD2 A:ASP327 2.2 49.4 1.0 OG1 A:THR29 2.4 46.3 1.0 OG A:SER247 2.4 44.5 1.0 OE1 A:GLN243 2.4 48.7 1.0 O A:GLN243 2.5 45.0 1.0 CB A:THR29 3.2 47.8 1.0 CG A:ASP327 3.3 49.4 1.0 N A:ALA30 3.4 47.9 1.0 C A:GLN243 3.5 44.1 1.0 CB A:SER247 3.5 42.0 1.0 CD A:GLN243 3.5 50.6 1.0 OD1 A:ASP327 3.7 52.3 1.0 CB A:ALA30 3.8 47.8 1.0 CB A:GLN243 3.8 47.2 1.0 N A:SER247 3.8 37.2 1.0 C A:THR29 3.9 53.5 1.0 CA A:ALA30 3.9 48.7 1.0 CA A:SER247 4.0 40.7 1.0 CG A:GLN243 4.0 46.0 1.0 CG2 A:THR246 4.1 33.2 1.0 CA A:GLN243 4.1 42.4 1.0 CA A:THR29 4.1 48.5 1.0 CG2 A:THR29 4.4 46.7 1.0 O A:SER26 4.5 43.0 1.0 N A:ILE244 4.5 40.5 1.0 CB A:ASP327 4.5 40.2 1.0 O A:GLY323 4.6 41.0 1.0 O A:THR29 4.7 52.7 1.0 NE2 A:GLN243 4.7 48.6 1.0 N A:THR29 4.7 50.3 1.0 C A:THR246 4.8 38.4 1.0 C A:GLY323 4.8 44.0 1.0 CA A:ILE244 4.9 43.5 1.0

Sodium binding site 4 out of 6 in the The Sodium-Dependent Phosphate Transporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Sodium-Dependent Phosphate Transporter within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:38.8 occ:1.00 O B:VAL104 2.3 47.2 1.0 OD1 B:ASP22 2.3 38.3 1.0 O B:HOH612 2.4 37.3 1.0 OG1 B:THR347 2.4 34.0 1.0 OD1 B:ASN21 2.6 38.4 1.0 C B:VAL104 3.3 46.0 1.0 CG B:ASP22 3.4 38.9 1.0 N B:VAL104 3.6 41.2 1.0 CB B:THR347 3.6 39.6 1.0 CG B:ASN21 3.7 41.2 1.0 CG2 B:THR347 3.8 42.6 1.0 O B:ASN21 3.9 35.0 1.0 O1 B:PO4501 3.9 37.2 1.0 O4 B:PO4501 4.0 33.2 1.0 ND2 B:ASN25 4.0 37.8 1.0 OD2 B:ASP22 4.1 37.8 1.0 CA B:VAL104 4.1 46.6 1.0 OD1 B:ASN25 4.1 36.9 1.0 C B:PRO103 4.2 45.7 1.0 C B:ASN21 4.2 38.0 1.0 CB B:ASN21 4.2 39.4 1.0 N B:SER105 4.3 43.2 1.0 CA B:PRO103 4.3 45.7 1.0 CA B:ASP22 4.3 33.8 1.0 CB B:ASP22 4.4 37.2 1.0 CG B:ASN25 4.5 39.6 1.0 CB B:PRO103 4.5 45.9 1.0 N B:ASP22 4.6 37.1 1.0 CA B:SER105 4.6 39.8 1.0 P B:PO4501 4.6 34.3 1.0 CA B:THR347 4.7 35.8 1.0 ND2 B:ASN21 4.9 37.7 1.0 CA B:ASN21 4.9 36.3 1.0 N B:THR347 5.0 33.1 1.0 CG2 B:THR106 5.0 34.8 1.0 N B:THR106 5.0 38.8 1.0

Sodium binding site 5 out of 6 in the The Sodium-Dependent Phosphate Transporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Sodium-Dependent Phosphate Transporter within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:34.1 occ:1.00 O B:ILE344 2.2 41.6 1.0 O B:HOH615 2.3 30.3 1.0 OD1 B:ASP258 2.3 32.6 1.0 OD1 B:ASN257 2.3 33.0 1.0 OG1 B:THR107 2.5 33.9 1.0 N B:ILE344 3.3 39.3 1.0 C B:ILE344 3.3 40.3 1.0 CG B:ASP258 3.4 31.1 1.0 CG B:ASN257 3.4 31.0 1.0 CB B:THR107 3.5 33.0 1.0 CG2 B:THR107 3.6 31.5 1.0 O B:ASN257 3.6 30.9 1.0 C B:ASN257 3.9 31.3 1.0 CA B:ILE344 3.9 39.2 1.0 CB B:ASN257 4.0 31.0 1.0 C B:PRO343 4.1 38.3 1.0 CA B:ASP258 4.1 30.1 1.0 OD2 B:ASP258 4.1 35.4 1.0 ND2 B:ASN261 4.1 30.1 1.0 O3 B:PO4501 4.2 35.8 1.0 N B:ASP258 4.2 30.1 1.0 CA B:PRO343 4.2 30.1 1.0 OD1 B:ASN261 4.3 36.4 1.0 CB B:ASP258 4.3 30.1 1.0 O2 B:PO4501 4.4 38.5 1.0 N B:SER345 4.5 36.2 1.0 ND2 B:ASN257 4.5 30.1 1.0 CA B:ASN257 4.6 30.1 1.0 CG B:ASN261 4.6 30.1 1.0 CB B:ILE344 4.7 45.1 1.0 CB B:PRO343 4.7 30.5 1.0 CA B:THR107 4.7 33.5 1.0 CA B:SER345 4.8 39.0 1.0 CG2 B:THR346 5.0 34.6 1.0 P B:PO4501 5.0 34.3 1.0

Sodium binding site 6 out of 6 in the The Sodium-Dependent Phosphate Transporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Sodium-Dependent Phosphate Transporter within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:51.4 occ:1.00 OD2 B:ASP327 2.2 52.0 1.0 OG B:SER247 2.4 47.8 1.0 O B:GLN243 2.4 40.8 1.0 OE1 B:GLN243 2.4 58.7 1.0 OG1 B:THR29 2.6 48.2 1.0 C B:GLN243 3.3 41.1 1.0 CB B:SER247 3.4 41.4 1.0 CD B:GLN243 3.4 53.2 1.0 CG B:ASP327 3.4 45.1 1.0 N B:ALA30 3.5 42.6 1.0 CB B:THR29 3.6 43.1 1.0 CB B:GLN243 3.6 40.9 1.0 CG B:GLN243 3.7 44.6 1.0 CG2 B:THR246 3.7 40.3 1.0 CB B:ALA30 3.8 41.7 1.0 N B:SER247 3.8 36.1 1.0 CA B:GLN243 3.9 44.0 1.0 CA B:SER247 3.9 40.1 1.0 CA B:ALA30 4.0 48.0 1.0 OD1 B:ASP327 4.1 56.4 1.0 C B:THR29 4.1 47.7 1.0 N B:ILE244 4.4 43.7 1.0 CA B:THR29 4.4 43.8 1.0 CB B:ASP327 4.5 39.9 1.0 O B:SER26 4.5 37.5 1.0 C B:THR246 4.6 37.0 1.0 NE2 B:GLN243 4.6 51.9 1.0 O B:GLY323 4.6 43.3 1.0 CG2 B:THR29 4.7 45.2 1.0 CA B:ILE244 4.8 40.5 1.0 C B:GLY323 4.9 41.0 1.0 O B:THR29 4.9 45.3 1.0

J.-Y.Tsai, C.-H.Chu, M.-G.Lin, Y.-H.Chou, R.-Y.Hong, C.-Y.Yen, C.-D.Hsiao, Y.-J.Sun. Structure of the Sodium-Dependent Phosphate Transporter Reveals Insights Into Human Solute Carrier SLC20. Sci Adv V. 6 B4024 2020.
ISSN: ESSN 2375-2548
PubMed: 32821837
DOI: 10.1126/SCIADV.ABB4024