Sodium in PDB 8uvf: Structure of NADC3-Dms Complex in Ci-Ci Conformation

The binding sites of Sodium atom in the Structure of NADC3-Dms Complex in Ci-Ci Conformation (pdb code 8uvf). 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-Dms Complex in Ci-Ci Conformation, PDB code: 8uvf:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of NADC3-Dms Complex in Ci-Ci Conformation


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-Dms Complex in Ci-Ci Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:31.5 occ:1.00 O A:GLY252 2.3 27.4 1.0 OD1 A:ASN144 2.3 30.5 1.0 O A:LEU142 2.3 28.8 1.0 O A:SER139 2.4 29.5 1.0 N A:ASN144 3.2 30.5 1.0 C A:SER139 3.4 29.5 1.0 C A:GLY252 3.4 27.4 1.0 CG A:ASN144 3.4 30.5 1.0 C A:SER143 3.4 31.0 1.0 C A:LEU142 3.5 28.8 1.0 CA A:SER143 3.5 31.0 1.0 CA A:SER139 3.6 29.5 1.0 CB A:SER139 3.8 29.5 1.0 N A:SER143 3.9 31.0 1.0 CA A:ASN144 4.0 30.5 1.0 CA A:GLY252 4.0 27.4 1.0 CA A:GLY246 4.0 27.6 1.0 O A:SER143 4.2 31.0 1.0 CB A:ASN144 4.3 30.5 1.0 ND2 A:ASN144 4.3 30.5 1.0 OG A:SER139 4.4 29.5 1.0 N A:THR253 4.5 26.5 1.0 N A:MET140 4.6 30.6 1.0 CA A:LEU142 4.8 28.8 1.0 N A:GLY246 4.8 27.6 1.0 CA A:THR253 4.8 26.5 1.0 N A:LEU142 4.8 28.8 1.0 CB A:SER143 4.8 31.0 1.0

Sodium binding site 2 out of 4 in the Structure of NADC3-Dms Complex in Ci-Ci Conformation


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-Dms Complex in Ci-Ci Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:30.7 occ:1.00 OD1 A:ASN484 2.3 28.5 1.0 O A:THR479 2.3 31.7 1.0 O A:SER526 2.4 35.9 1.0 O A:ALA482 2.4 32.5 1.0 OG1 A:THR479 2.5 31.7 1.0 C A:THR479 3.4 31.7 1.0 C A:SER526 3.4 35.9 1.0 N A:ASN484 3.4 28.5 1.0 CG A:ASN484 3.5 28.5 1.0 C A:ALA482 3.5 32.5 1.0 CB A:ALA520 3.6 32.4 1.0 CB A:THR479 3.6 31.7 1.0 C A:SER483 3.7 29.6 1.0 CA A:THR479 3.7 31.7 1.0 CA A:SER483 3.8 29.6 1.0 CA A:SER526 4.0 35.9 1.0 CA A:ASN484 4.0 28.5 1.0 N A:SER483 4.1 29.6 1.0 O A:SER483 4.3 29.6 1.0 O A:CYS517 4.4 28.8 1.0 CB A:ASN484 4.4 28.5 1.0 CG2 A:THR479 4.4 31.7 1.0 ND2 A:ASN484 4.4 28.5 1.0 CB A:SER526 4.4 35.9 1.0 N A:THR527 4.5 34.8 1.0 N A:GLU480 4.5 34.4 1.0 N A:ALA482 4.7 32.5 1.0 CA A:ALA482 4.7 32.5 1.0 CA A:THR527 4.8 34.8 1.0 CB A:THR527 4.8 34.8 1.0 CA A:ALA520 4.9 32.4 1.0 CA A:GLU480 5.0 34.4 1.0

Sodium binding site 3 out of 4 in the Structure of NADC3-Dms Complex in Ci-Ci Conformation


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-Dms Complex in Ci-Ci Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Na701 b:31.5 occ:1.00 O B:GLY252 2.3 27.4 1.0 OD1 B:ASN144 2.3 30.5 1.0 O B:LEU142 2.3 28.8 1.0 O B:SER139 2.4 29.5 1.0 N B:ASN144 3.2 30.5 1.0 C B:SER139 3.4 29.5 1.0 C B:GLY252 3.4 27.4 1.0 CG B:ASN144 3.4 30.5 1.0 C B:SER143 3.4 31.0 1.0 C B:LEU142 3.5 28.8 1.0 CA B:SER143 3.5 31.0 1.0 CA B:SER139 3.6 29.5 1.0 CB B:SER139 3.8 29.5 1.0 N B:SER143 3.9 31.0 1.0 CA B:ASN144 4.0 30.5 1.0 CA B:GLY252 4.0 27.4 1.0 CA B:GLY246 4.0 27.6 1.0 O B:SER143 4.2 31.0 1.0 CB B:ASN144 4.3 30.5 1.0 ND2 B:ASN144 4.3 30.5 1.0 OG B:SER139 4.4 29.5 1.0 N B:THR253 4.5 26.5 1.0 N B:MET140 4.6 30.6 1.0 CA B:LEU142 4.8 28.8 1.0 N B:GLY246 4.8 27.6 1.0 CA B:THR253 4.8 26.5 1.0 N B:LEU142 4.8 28.8 1.0 CB B:SER143 4.8 31.0 1.0

Sodium binding site 4 out of 4 in the Structure of NADC3-Dms Complex in Ci-Ci Conformation


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-Dms Complex in Ci-Ci Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Na702 b:30.7 occ:1.00 OD1 B:ASN484 2.3 28.5 1.0 O B:THR479 2.3 31.7 1.0 O B:SER526 2.4 35.9 1.0 O B:ALA482 2.4 32.5 1.0 OG1 B:THR479 2.5 31.7 1.0 C B:THR479 3.4 31.7 1.0 C B:SER526 3.4 35.9 1.0 N B:ASN484 3.4 28.5 1.0 CG B:ASN484 3.5 28.5 1.0 C B:ALA482 3.5 32.5 1.0 CB B:ALA520 3.6 32.4 1.0 CB B:THR479 3.6 31.7 1.0 C B:SER483 3.7 29.6 1.0 CA B:THR479 3.7 31.7 1.0 CA B:SER483 3.8 29.6 1.0 CA B:SER526 4.0 35.9 1.0 CA B:ASN484 4.0 28.5 1.0 N B:SER483 4.1 29.6 1.0 O B:SER483 4.3 29.6 1.0 O B:CYS517 4.4 28.8 1.0 CB B:ASN484 4.4 28.5 1.0 CG2 B:THR479 4.4 31.7 1.0 ND2 B:ASN484 4.4 28.5 1.0 CB B:SER526 4.4 35.9 1.0 N B:THR527 4.5 34.8 1.0 N B:GLU480 4.5 34.4 1.0 N B:ALA482 4.7 32.5 1.0 CA B:ALA482 4.7 32.5 1.0 CA B:THR527 4.8 34.8 1.0 CB B:THR527 4.8 34.8 1.0 CA B:ALA520 4.9 32.4 1.0 CA B:GLU480 5.0 34.4 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