Sodium in PDB 8uvc: Structure of NADC3-Akg Complex

The binding sites of Sodium atom in the Structure of NADC3-Akg Complex (pdb code 8uvc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of NADC3-Akg Complex, PDB code: 8uvc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of NADC3-Akg Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of NADC3-Akg Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:59.3 occ:1.00 OD1 A:ASN144 2.4 58.1 1.0 O A:LEU142 2.4 56.1 1.0 O A:GLY252 2.4 55.0 1.0 O A:SER139 2.5 54.1 1.0 OG A:SER139 2.7 54.1 1.0 N A:ASN144 2.9 58.1 1.0 C A:SER143 3.1 59.4 1.0 CA A:SER143 3.2 59.4 1.0 C A:SER139 3.3 54.1 1.0 C A:LEU142 3.4 56.1 1.0 CG A:ASN144 3.4 58.1 1.0 C A:GLY252 3.5 55.0 1.0 CA A:SER139 3.5 54.1 1.0 O1 A:AKG702 3.6 61.4 0.5 CB A:SER139 3.7 54.1 1.0 CA A:ASN144 3.7 58.1 1.0 O4 A:AKG702 3.7 61.4 0.5 N A:SER143 3.8 59.4 1.0 O A:SER143 3.8 59.4 1.0 CA A:GLY246 4.0 52.9 1.0 CB A:ASN144 4.1 58.1 1.0 CA A:GLY252 4.2 55.0 1.0 ND2 A:ASN144 4.4 58.1 1.0 N A:THR253 4.6 55.1 1.0 CB A:SER143 4.6 59.4 1.0 N A:MET140 4.6 54.9 1.0 N A:GLY246 4.7 52.9 1.0 CA A:THR253 4.8 55.1 1.0 CA A:LEU142 4.8 56.1 1.0 C1 A:AKG702 4.9 61.4 0.5 O A:ALA242 4.9 52.3 1.0 C5 A:AKG702 4.9 61.4 0.5 CB A:THR253 4.9 55.1 1.0 N A:LEU142 4.9 56.1 1.0 N A:SER139 4.9 54.1 1.0 OG A:SER147 5.0 59.6 1.0

Sodium binding site 2 out of 2 in the Structure of NADC3-Akg Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of NADC3-Akg Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na701 b:59.3 occ:1.00 OD1 B:ASN144 2.4 58.1 1.0 O B:LEU142 2.4 56.1 1.0 O B:GLY252 2.4 55.0 1.0 O B:SER139 2.5 54.1 1.0 OG B:SER139 2.7 54.1 1.0 N B:ASN144 2.9 58.1 1.0 C B:SER143 3.1 59.4 1.0 CA B:SER143 3.2 59.4 1.0 C B:SER139 3.3 54.1 1.0 C B:LEU142 3.4 56.1 1.0 CG B:ASN144 3.4 58.1 1.0 C B:GLY252 3.5 55.0 1.0 CA B:SER139 3.5 54.1 1.0 O1 B:AKG702 3.6 61.4 0.5 CB B:SER139 3.7 54.1 1.0 CA B:ASN144 3.7 58.1 1.0 O4 B:AKG702 3.7 61.4 0.5 N B:SER143 3.8 59.4 1.0 O B:SER143 3.8 59.4 1.0 CA B:GLY246 4.0 52.9 1.0 CB B:ASN144 4.1 58.1 1.0 CA B:GLY252 4.2 55.0 1.0 ND2 B:ASN144 4.4 58.1 1.0 N B:THR253 4.6 55.1 1.0 CB B:SER143 4.6 59.4 1.0 N B:MET140 4.6 54.9 1.0 N B:GLY246 4.7 52.9 1.0 CA B:THR253 4.8 55.1 1.0 CA B:LEU142 4.8 56.1 1.0 C1 B:AKG702 4.9 61.4 0.5 O B:ALA242 4.9 52.3 1.0 C5 B:AKG702 4.9 61.4 0.5 CB B:THR253 4.9 55.1 1.0 N B:LEU142 4.9 56.1 1.0 N B:SER139 4.9 54.1 1.0 OG B:SER147 5.0 59.6 1.0

Y.Li, J.Song, V.Mikusevic, J.J.Marden, A.Becerril, H.Kuang, B.Wang, W.J.Rice, J.A.Mindell, D.N.Wang. Substrate Translocation and Inhibition in Human Dicarboxylate Transporter NADC3. Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
PubMed: 39622972
DOI: 10.1038/S41594-024-01433-0