Sodium in PDB 8w6c: Cryoem Structure of NADC1 with Citrate

The binding sites of Sodium atom in the Cryoem Structure of NADC1 with Citrate (pdb code 8w6c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Cryoem Structure of NADC1 with Citrate, PDB code: 8w6c:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Cryoem Structure of NADC1 with Citrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryoem Structure of NADC1 with Citrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na801 b:21.0 occ:1.00 O A:SER136 2.5 18.9 1.0 O A:GLY239 2.5 24.7 1.0 OD1 A:ASN141 2.5 20.8 1.0 O A:ILE139 2.5 19.8 1.0 OG A:SER136 3.3 18.9 1.0 C A:GLY239 3.3 24.7 1.0 C A:SER136 3.5 18.9 1.0 CG A:ASN141 3.6 20.8 1.0 N A:ASN141 3.7 20.8 1.0 C A:ILE139 3.7 19.8 1.0 CA A:GLY239 3.7 24.7 1.0 C A:SER140 3.8 21.1 1.0 CA A:GLY233 3.8 20.3 1.0 CA A:SER140 4.0 21.1 1.0 O4 A:CIT804 4.0 29.9 1.0 CA A:SER136 4.0 18.9 1.0 C4 A:CIT804 4.0 29.9 1.0 CB A:SER136 4.2 18.9 1.0 N A:SER140 4.3 21.1 1.0 CA A:ASN141 4.3 20.8 1.0 O A:SER140 4.3 21.1 1.0 ND2 A:ASN141 4.4 20.8 1.0 N A:THR240 4.4 27.5 1.0 C5 A:CIT804 4.5 29.9 1.0 CB A:ASN141 4.5 20.8 1.0 N A:GLY233 4.7 20.3 1.0 N A:MET137 4.7 20.1 1.0 O A:GLY233 4.7 20.3 1.0 N A:ILE139 4.8 19.8 1.0 CA A:THR240 4.8 27.5 1.0 C A:GLY233 4.8 20.3 1.0 CA A:ILE139 4.9 19.8 1.0 C A:MET137 5.0 20.1 1.0

Sodium binding site 2 out of 4 in the Cryoem Structure of NADC1 with Citrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryoem Structure of NADC1 with Citrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:29.9 occ:1.00 O A:ALA518 2.5 21.1 1.0 OD1 A:ASN476 2.5 29.2 1.0 O A:THR471 2.5 27.7 1.0 O A:THR474 2.5 30.5 1.0 OG1 A:THR471 3.1 27.7 1.0 C A:ALA518 3.5 21.1 1.0 CG A:ASN476 3.6 29.2 1.0 C A:THR474 3.6 30.5 1.0 C A:THR471 3.6 27.7 1.0 N A:ASN476 3.9 29.2 1.0 CA A:ALA518 3.9 21.1 1.0 C A:SER475 4.0 31.1 1.0 CA A:SER475 4.1 31.1 1.0 CA A:THR471 4.1 27.7 1.0 CB A:THR471 4.1 27.7 1.0 N A:SER475 4.3 31.1 1.0 ND2 A:ASN476 4.3 29.2 1.0 CA A:ASN476 4.5 29.2 1.0 O A:SER475 4.6 31.1 1.0 CB A:ALA518 4.6 21.1 1.0 CB A:ALA512 4.6 21.6 1.0 N A:THR474 4.6 30.5 1.0 CB A:ASN476 4.6 29.2 1.0 N A:THR519 4.7 22.3 1.0 CA A:THR474 4.7 30.5 1.0 N A:GLU472 4.7 27.0 1.0 CG2 A:THR471 4.8 27.7 1.0 O A:VAL517 4.8 23.6 1.0 O A:THR509 4.8 24.5 1.0 OG1 A:THR519 5.0 22.3 1.0

Sodium binding site 3 out of 4 in the Cryoem Structure of NADC1 with Citrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cryoem Structure of NADC1 with Citrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1102 b:20.7 occ:1.00 O B:SER136 2.5 18.5 1.0 O B:GLY239 2.5 24.6 1.0 OD1 B:ASN141 2.5 20.5 1.0 O B:ILE139 2.5 18.5 1.0 OG B:SER136 3.3 18.5 1.0 C B:GLY239 3.3 24.6 1.0 C B:SER136 3.5 18.5 1.0 CG B:ASN141 3.6 20.5 1.0 N B:ASN141 3.7 20.5 1.0 C B:ILE139 3.7 18.5 1.0 CA B:GLY239 3.7 24.6 1.0 C B:SER140 3.8 20.3 1.0 CA B:GLY233 3.8 20.2 1.0 CA B:SER140 4.0 20.3 1.0 O2 B:CIT1104 4.0 29.9 1.0 CA B:SER136 4.0 18.5 1.0 C2 B:CIT1104 4.0 29.9 1.0 CB B:SER136 4.2 18.5 1.0 N B:SER140 4.3 20.3 1.0 CA B:ASN141 4.3 20.5 1.0 O B:SER140 4.3 20.3 1.0 ND2 B:ASN141 4.4 20.5 1.0 N B:THR240 4.4 27.5 1.0 C1 B:CIT1104 4.5 29.9 1.0 CB B:ASN141 4.5 20.5 1.0 N B:GLY233 4.7 20.2 1.0 N B:MET137 4.7 19.5 1.0 O B:GLY233 4.7 20.2 1.0 N B:ILE139 4.8 18.5 1.0 CA B:THR240 4.8 27.5 1.0 C B:GLY233 4.8 20.2 1.0 CA B:ILE139 4.9 18.5 1.0 C B:MET137 5.0 19.5 1.0

Sodium binding site 4 out of 4 in the Cryoem Structure of NADC1 with Citrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cryoem Structure of NADC1 with Citrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1103 b:29.9 occ:1.00 O B:ALA518 2.5 21.2 1.0 OD1 B:ASN476 2.5 29.2 1.0 O B:THR471 2.5 27.6 1.0 O B:THR474 2.5 30.6 1.0 OG1 B:THR471 3.1 27.6 1.0 C B:ALA518 3.5 21.2 1.0 CG B:ASN476 3.6 29.2 1.0 C B:THR474 3.6 30.6 1.0 C B:THR471 3.6 27.6 1.0 N B:ASN476 3.9 29.2 1.0 CA B:ALA518 3.9 21.2 1.0 C B:SER475 4.0 31.2 1.0 CA B:SER475 4.1 31.2 1.0 CA B:THR471 4.1 27.6 1.0 CB B:THR471 4.1 27.6 1.0 N B:SER475 4.3 31.2 1.0 ND2 B:ASN476 4.3 29.2 1.0 CA B:ASN476 4.5 29.2 1.0 O B:SER475 4.6 31.2 1.0 CB B:ALA518 4.6 21.2 1.0 CB B:ALA512 4.6 21.7 1.0 N B:THR474 4.6 30.6 1.0 CB B:ASN476 4.6 29.2 1.0 N B:THR519 4.7 22.4 1.0 CA B:THR474 4.7 30.6 1.0 N B:GLU472 4.7 27.2 1.0 CG2 B:THR471 4.8 27.6 1.0 O B:VAL517 4.8 23.6 1.0 O B:THR509 4.8 24.4 1.0 OG1 B:THR519 5.0 22.4 1.0

X.Chi, Y.Chen, Y.Li, L.Dai, Y.Zhang, Y.Shen, Y.Chen, T.Shi, H.Yang, Z.Wang, R.Yan. Cryo-Em Structures of the Human NAS1 and NADC1 Transporters Revealed the Elevator Transport and Allosteric Regulation Mechanism. Sci Adv V. 10 L3685 2024.
ISSN: ESSN 2375-2548
PubMed: 38552027
DOI: 10.1126/SCIADV.ADL3685