Sodium in PDB 8uvd: Structure of NADC3-PF4A Complex

The binding sites of Sodium atom in the Structure of NADC3-PF4A Complex (pdb code 8uvd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of NADC3-PF4A Complex, PDB code: 8uvd:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of NADC3-PF4A 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-PF4A Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:44.4 occ:1.00 OD1 A:ASN144 2.4 39.7 1.0 O A:SER139 2.4 38.7 1.0 O A:GLY252 2.4 39.8 1.0 O A:LEU142 2.4 39.7 1.0 N A:ASN144 3.2 39.7 1.0 C A:SER139 3.4 38.7 1.0 C A:GLY252 3.4 39.8 1.0 C A:SER143 3.5 40.9 1.0 C A:LEU142 3.5 39.7 1.0 CG A:ASN144 3.5 39.7 1.0 CA A:SER143 3.6 40.9 1.0 CA A:SER139 3.7 38.7 1.0 CB A:SER139 3.8 38.7 1.0 CA A:GLY246 3.8 36.7 1.0 O19 A:XKC703 3.9 42.6 0.5 CA A:GLY252 3.9 39.8 1.0 N A:SER143 4.0 40.9 1.0 CA A:ASN144 4.0 39.7 1.0 O19 A:XKC703 4.1 42.6 0.5 O A:SER143 4.2 40.9 1.0 CB A:ASN144 4.4 39.7 1.0 ND2 A:ASN144 4.4 39.7 1.0 OG A:SER139 4.5 38.7 1.0 N A:THR253 4.5 40.7 1.0 N A:MET140 4.6 42.2 1.0 N A:GLY246 4.6 36.7 1.0 C08 A:XKC703 4.8 42.6 0.5 CA A:LEU142 4.8 39.7 1.0 O20 A:XKC703 4.8 42.6 0.5 N A:LEU142 4.8 39.7 1.0 CA A:THR253 4.9 40.7 1.0 CB A:SER143 4.9 40.9 1.0 C A:GLY246 4.9 36.7 1.0 C A:MET140 4.9 42.2 1.0 O A:GLY246 5.0 36.7 1.0 O A:ALA242 5.0 35.1 1.0 C02 A:XKC703 5.0 42.6 0.5

Sodium binding site 2 out of 4 in the Structure of NADC3-PF4A 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-PF4A Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:39.7 occ:1.00 O A:THR479 2.3 38.8 1.0 OD1 A:ASN484 2.3 38.7 1.0 O A:SER526 2.3 43.4 1.0 O A:ALA482 2.4 41.6 1.0 OG1 A:THR479 2.9 38.8 1.0 C A:SER526 3.3 43.4 1.0 C A:THR479 3.4 38.8 1.0 CG A:ASN484 3.5 38.7 1.0 CB A:ALA520 3.6 39.5 1.0 C A:ALA482 3.6 41.6 1.0 N A:ASN484 3.7 38.7 1.0 CA A:SER526 3.8 43.4 1.0 C A:SER483 4.0 39.6 1.0 CB A:THR479 4.0 38.8 1.0 CA A:THR479 4.0 38.8 1.0 CA A:SER483 4.1 39.6 1.0 CB A:SER526 4.2 43.4 1.0 CA A:ASN484 4.3 38.7 1.0 N A:THR527 4.3 43.8 1.0 ND2 A:ASN484 4.3 38.7 1.0 N A:SER483 4.4 39.6 1.0 CB A:ASN484 4.5 38.7 1.0 CG2 A:THR479 4.5 38.8 1.0 N A:GLU480 4.6 42.4 1.0 N A:ALA482 4.6 41.6 1.0 O A:SER483 4.6 39.6 1.0 CA A:THR527 4.7 43.8 1.0 O A:CYS517 4.7 39.1 1.0 CA A:ALA482 4.8 41.6 1.0 CB A:THR527 4.8 43.8 1.0 CA A:GLU480 4.9 42.4 1.0 CA A:ALA520 4.9 39.5 1.0 C A:GLU480 5.0 42.4 1.0

Sodium binding site 3 out of 4 in the Structure of NADC3-PF4A Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of NADC3-PF4A Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na701 b:44.4 occ:1.00 OD1 B:ASN144 2.4 39.7 1.0 O B:SER139 2.4 38.7 1.0 O B:GLY252 2.4 39.8 1.0 O B:LEU142 2.4 39.7 1.0 N B:ASN144 3.2 39.7 1.0 C B:SER139 3.4 38.7 1.0 C B:GLY252 3.4 39.8 1.0 C B:SER143 3.5 40.9 1.0 C B:LEU142 3.5 39.7 1.0 CG B:ASN144 3.5 39.7 1.0 CA B:SER143 3.6 40.9 1.0 CA B:SER139 3.7 38.7 1.0 CB B:SER139 3.8 38.7 1.0 CA B:GLY246 3.8 36.7 1.0 O19 B:XKC703 3.9 42.6 0.5 CA B:GLY252 3.9 39.8 1.0 N B:SER143 4.0 40.9 1.0 CA B:ASN144 4.0 39.7 1.0 O19 B:XKC703 4.1 42.6 0.5 O B:SER143 4.2 40.9 1.0 CB B:ASN144 4.4 39.7 1.0 ND2 B:ASN144 4.4 39.7 1.0 OG B:SER139 4.5 38.7 1.0 N B:THR253 4.5 40.7 1.0 N B:MET140 4.6 42.2 1.0 N B:GLY246 4.6 36.7 1.0 C08 B:XKC703 4.8 42.6 0.5 CA B:LEU142 4.8 39.7 1.0 O20 B:XKC703 4.8 42.6 0.5 N B:LEU142 4.8 39.7 1.0 CA B:THR253 4.9 40.7 1.0 CB B:SER143 4.9 40.9 1.0 C B:GLY246 4.9 36.7 1.0 C B:MET140 4.9 42.2 1.0 O B:GLY246 5.0 36.7 1.0 O B:ALA242 5.0 35.1 1.0 C02 B:XKC703 5.0 42.6 0.5

Sodium binding site 4 out of 4 in the Structure of NADC3-PF4A Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of NADC3-PF4A Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na702 b:39.7 occ:1.00 OD1 B:ASN484 2.3 38.7 1.0 O B:THR479 2.3 38.8 1.0 O B:SER526 2.3 43.4 1.0 O B:ALA482 2.4 41.6 1.0 OG1 B:THR479 2.9 38.8 1.0 C B:SER526 3.3 43.4 1.0 C B:THR479 3.4 38.8 1.0 CG B:ASN484 3.5 38.7 1.0 CB B:ALA520 3.6 39.5 1.0 C B:ALA482 3.6 41.6 1.0 N B:ASN484 3.7 38.7 1.0 CA B:SER526 3.8 43.4 1.0 C B:SER483 4.0 39.6 1.0 CB B:THR479 4.0 38.8 1.0 CA B:THR479 4.0 38.8 1.0 CA B:SER483 4.1 39.6 1.0 CB B:SER526 4.2 43.4 1.0 CA B:ASN484 4.3 38.7 1.0 N B:THR527 4.3 43.8 1.0 ND2 B:ASN484 4.3 38.7 1.0 N B:SER483 4.4 39.6 1.0 CB B:ASN484 4.5 38.7 1.0 CG2 B:THR479 4.5 38.8 1.0 N B:GLU480 4.6 42.4 1.0 N B:ALA482 4.6 41.6 1.0 O B:SER483 4.6 39.6 1.0 CA B:THR527 4.7 43.8 1.0 O B:CYS517 4.7 39.1 1.0 CA B:ALA482 4.8 41.6 1.0 CB B:THR527 4.8 43.8 1.0 CA B:GLU480 4.9 42.4 1.0 CA B:ALA520 4.9 39.5 1.0 C B:GLU480 5.0 42.4 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