Sodium in PDB 8y5w: Human NAS1 Intermediate State 2

The binding sites of Sodium atom in the Human NAS1 Intermediate State 2 (pdb code 8y5w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Human NAS1 Intermediate State 2, PDB code: 8y5w:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Human NAS1 Intermediate State 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human NAS1 Intermediate State 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:21.6 occ:1.00 OD1 A:ASN490 2.4 20.2 1.0 O A:THR485 2.4 21.7 1.0 O A:ALA532 2.4 24.3 1.0 O A:ALA488 2.5 22.8 1.0 OG1 A:THR485 2.6 21.7 1.0 N A:ASN490 3.2 20.2 1.0 CG A:ASN490 3.3 20.2 1.0 C A:ALA532 3.3 24.3 1.0 C A:THR485 3.4 21.7 1.0 CB A:ALA526 3.5 19.2 1.0 C A:SER489 3.5 21.2 1.0 C A:ALA488 3.6 22.8 1.0 CB A:THR485 3.7 21.7 1.0 CA A:THR485 3.7 21.7 1.0 CA A:ASN490 3.8 20.2 1.0 CA A:SER489 3.8 21.2 1.0 CA A:ALA532 4.0 24.3 1.0 ND2 A:ASN490 4.1 20.2 1.0 CB A:ASN490 4.1 20.2 1.0 O A:SER489 4.1 21.2 1.0 N A:SER489 4.2 21.2 1.0 CB A:ALA532 4.3 24.3 1.0 N A:ASN533 4.3 20.1 1.0 CB A:ASN533 4.4 20.1 1.0 CG2 A:THR485 4.4 21.7 1.0 O A:THR523 4.5 16.8 1.0 CA A:ASN533 4.6 20.1 1.0 N A:GLU486 4.6 24.1 1.0 OG1 A:THR493 4.7 20.1 1.0 CA A:ALA526 4.9 19.2 1.0 CA A:ALA488 4.9 22.8 1.0 N A:ALA488 4.9 22.8 1.0

Sodium binding site 2 out of 4 in the Human NAS1 Intermediate State 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human NAS1 Intermediate State 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:9.9 occ:1.00 O A:GLY258 2.4 12.4 1.0 O A:LEU138 2.4 9.7 1.0 OD1 A:ASN140 2.4 11.6 1.0 O A:SER135 2.4 10.7 1.0 OG A:SER135 2.5 10.7 1.0 N A:ASN140 3.0 11.6 1.0 C A:SER139 3.1 10.5 1.0 C A:GLY258 3.3 12.4 1.0 C A:SER135 3.3 10.7 1.0 CG A:ASN140 3.4 11.6 1.0 C A:LEU138 3.5 9.7 1.0 CA A:SER139 3.5 10.5 1.0 CB A:SER135 3.5 10.7 1.0 CA A:SER135 3.5 10.7 1.0 CA A:ASN140 3.6 11.6 1.0 CA A:GLY252 3.7 11.9 1.0 O A:SER139 3.7 10.5 1.0 CA A:GLY258 3.9 12.4 1.0 N A:SER139 4.0 10.5 1.0 CB A:ASN140 4.0 11.6 1.0 N A:THR259 4.2 13.5 1.0 ND2 A:ASN140 4.3 11.6 1.0 N A:GLY252 4.3 11.9 1.0 O2 A:SO4601 4.4 13.4 1.0 CA A:THR259 4.5 13.5 1.0 OG1 A:THR143 4.5 11.6 1.0 O A:SER248 4.5 11.7 1.0 N A:MET136 4.6 10.9 1.0 CB A:THR259 4.7 13.5 1.0 CA A:LEU138 4.8 9.7 1.0 CB A:SER139 4.9 10.5 1.0 C A:GLY252 4.9 11.9 1.0 N A:LEU138 4.9 9.7 1.0 N A:SER135 5.0 10.7 1.0 C A:ASN140 5.0 11.6 1.0

Sodium binding site 3 out of 4 in the Human NAS1 Intermediate State 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human NAS1 Intermediate State 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na901 b:18.5 occ:1.00 O B:GLY258 2.4 24.3 1.0 O B:SER135 2.4 17.1 1.0 OG B:SER135 2.5 17.1 1.0 OD1 B:ASN140 2.5 18.2 1.0 C B:SER139 2.8 17.9 1.0 N B:ASN140 2.9 18.2 1.0 O B:SER139 3.0 17.9 1.0 CG B:ASN140 3.1 18.2 1.0 C B:GLY258 3.2 24.3 1.0 CA B:SER139 3.4 17.9 1.0 C B:SER135 3.4 17.1 1.0 CA B:ASN140 3.5 18.2 1.0 CB B:SER135 3.6 17.1 1.0 CA B:GLY252 3.8 25.0 1.0 CA B:SER135 3.8 17.1 1.0 N B:GLY252 3.8 25.0 1.0 ND2 B:ASN140 3.8 18.2 1.0 CA B:GLY258 3.8 24.3 1.0 CB B:ASN140 3.8 18.2 1.0 O B:GLY251 3.9 23.2 1.0 C B:GLY251 3.9 23.2 1.0 N B:SER139 3.9 17.9 1.0 N B:THR259 4.2 23.4 1.0 O4 B:SO4903 4.3 23.6 1.0 CA B:THR259 4.6 23.4 1.0 N B:MET136 4.6 18.3 1.0 CB B:THR259 4.7 23.4 1.0 CB B:SER139 4.8 17.9 1.0 CA B:GLY251 4.8 23.2 1.0 OG B:SER139 4.9 17.9 1.0 C B:ASN140 4.9 18.2 1.0 C B:LEU138 5.0 17.3 1.0

Sodium binding site 4 out of 4 in the Human NAS1 Intermediate State 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human NAS1 Intermediate State 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:13.8 occ:1.00 O B:ALA488 2.5 17.9 1.0 O B:THR485 2.5 19.1 1.0 CB B:ALA532 2.9 19.2 1.0 OD1 B:ASN490 3.0 18.4 1.0 C B:ALA532 3.3 19.2 1.0 O B:ALA532 3.3 19.2 1.0 OG1 B:THR485 3.5 19.1 1.0 CA B:ALA532 3.5 19.2 1.0 CB B:ALA526 3.5 17.2 1.0 C B:ALA488 3.6 17.9 1.0 N B:ASN490 3.6 18.4 1.0 N B:ASN533 3.7 18.3 1.0 C B:THR485 3.7 19.1 1.0 CG B:ASN490 3.7 18.4 1.0 CA B:SER489 3.8 18.2 1.0 C B:SER489 3.9 18.2 1.0 N B:SER489 4.1 18.2 1.0 CA B:ASN533 4.2 18.3 1.0 ND2 B:ASN490 4.3 18.4 1.0 CA B:THR485 4.4 19.1 1.0 CA B:ASN490 4.4 18.4 1.0 CB B:THR485 4.5 19.1 1.0 CB B:ASN533 4.7 18.3 1.0 CB B:ASN490 4.7 18.4 1.0 O B:SER489 4.7 18.2 1.0 N B:GLU486 4.8 20.2 1.0 N B:ALA488 4.8 17.9 1.0 CA B:ALA488 4.8 17.9 1.0 OD1 B:ASN533 4.9 18.3 1.0 N B:ALA532 4.9 19.2 1.0 CA B:GLU486 5.0 20.2 1.0

X.Chen, Y.Zhang, J.Yin, C.Liu, M.Xie, Y.Wang, M.Chen, R.Zhang, X.Yuan, D.Li, X.Chen, X.Gao, G.Cai, S.Zhang, B.Zhou, M.Yang. Structural Basis For the Reaction Cycle and Transport Mechanism of Human Na + -Sulfate Cotransporter NAS1 (SLC13A1). Sci Adv V. 10 O6778 2024.
ISSN: ESSN 2375-2548
PubMed: 39576865
DOI: 10.1126/SCIADV.ADO6778