Sodium in PDB 7jsk: Structure of the Nact-Citrate Complex

The binding sites of Sodium atom in the Structure of the Nact-Citrate Complex (pdb code 7jsk). 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 the Nact-Citrate Complex, PDB code: 7jsk:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of the Nact-Citrate 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 the Nact-Citrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:67.0 occ:1.00 OD1 A:ASN141 1.4 65.7 1.0 O A:SER136 2.1 62.1 1.0 CG A:ASN141 2.5 65.7 1.0 HB2 A:SER136 2.8 62.1 1.0 O A:GLY226 2.8 61.4 1.0 HA2 A:GLY220 2.9 61.9 1.0 HD22 A:ASN141 2.9 65.7 1.0 HA3 A:GLY220 3.0 61.9 1.0 ND2 A:ASN141 3.1 65.7 1.0 C A:SER136 3.1 62.1 1.0 H A:ASN141 3.1 65.7 1.0 HA A:SER136 3.4 62.1 1.0 CA A:GLY220 3.4 61.9 1.0 CA A:SER136 3.6 62.1 1.0 CB A:SER136 3.6 62.1 1.0 N A:ASN141 3.8 65.7 1.0 HA2 A:GLY226 3.8 61.4 1.0 CB A:ASN141 3.8 65.7 1.0 HA A:ASN141 3.9 65.7 1.0 C A:GLY226 3.9 61.4 1.0 HG A:SER136 3.9 62.1 1.0 HD21 A:ASN141 3.9 65.7 1.0 H A:SER140 4.0 65.4 1.0 N A:GLY220 4.0 61.9 1.0 CA A:ASN141 4.1 65.7 1.0 H A:GLY220 4.1 61.9 1.0 OG A:SER136 4.2 62.1 1.0 N A:MET137 4.3 61.1 1.0 H A:ILE139 4.3 63.0 1.0 HB3 A:SER136 4.3 62.1 1.0 HB2 A:ASN141 4.4 65.7 1.0 CA A:GLY226 4.4 61.4 1.0 HA A:MET137 4.4 61.1 1.0 HB3 A:ASN141 4.4 65.7 1.0 HB A:THR227 4.4 63.6 1.0 N A:SER140 4.4 65.4 1.0 HA A:SER140 4.5 65.4 1.0 O A:ALA216 4.5 64.2 1.0 C A:GLY220 4.6 61.9 1.0 CA A:MET137 4.7 61.1 1.0 C A:SER140 4.8 65.4 1.0 HG22 A:THR227 4.8 63.6 1.0 C A:MET137 4.8 61.1 1.0 CA A:SER140 4.8 65.4 1.0 HA3 A:GLY226 4.8 61.4 1.0 O A:GLY220 4.8 61.9 1.0 N A:ILE139 4.9 63.0 1.0 C A:GLY219 4.9 62.5 1.0 N A:TRP138 4.9 60.8 1.0 H A:TRP138 4.9 60.8 1.0 H A:MET137 5.0 61.1 1.0

Sodium binding site 2 out of 4 in the Structure of the Nact-Citrate 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 the Nact-Citrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:65.5 occ:1.00 O A:THR460 2.2 64.3 1.0 HG1 A:THR460 2.2 64.3 1.0 HB3 A:ALA501 2.6 65.4 1.0 HB3 A:ALA507 2.7 68.8 1.0 HG1 A:THR508 2.8 69.2 1.0 OG1 A:THR460 2.8 64.3 1.0 OD1 A:ASN465 2.9 64.3 1.0 O A:ALA507 3.0 68.8 1.0 O A:THR463 3.1 65.0 1.0 C A:THR460 3.3 64.3 1.0 HB2 A:ALA501 3.3 65.4 1.0 CB A:ALA501 3.4 65.4 1.0 OG1 A:THR508 3.4 69.2 1.0 C A:ALA507 3.5 68.8 1.0 HG23 A:THR460 3.6 64.3 1.0 CB A:ALA507 3.6 68.8 1.0 HA A:SER464 3.6 64.8 1.0 HB1 A:ALA501 3.7 65.4 1.0 HA A:ALA507 3.7 68.8 1.0 CG A:ASN465 3.8 64.3 1.0 HA A:GLU461 3.8 67.1 1.0 CB A:THR460 3.8 64.3 1.0 CA A:ALA507 3.9 68.8 1.0 CA A:THR460 4.0 64.3 1.0 N A:ASN465 4.0 64.3 1.0 H A:ASN465 4.0 64.3 1.0 HA A:THR460 4.1 64.3 1.0 C A:THR463 4.1 65.0 1.0 HB1 A:ALA507 4.1 68.8 1.0 HB2 A:ALA507 4.1 68.8 1.0 C A:SER464 4.2 64.8 1.0 CG2 A:THR460 4.2 64.3 1.0 HD22 A:ASN465 4.2 64.3 1.0 HA A:ASN465 4.2 64.3 1.0 CA A:SER464 4.2 64.8 1.0 N A:GLU461 4.3 67.1 1.0 ND2 A:ASN465 4.4 64.3 1.0 N A:THR508 4.4 69.2 1.0 CA A:GLU461 4.5 67.1 1.0 O A:ALA498 4.5 62.7 1.0 CA A:ASN465 4.6 64.3 1.0 N A:SER464 4.6 64.8 1.0 CA A:ALA501 4.6 65.4 1.0 CB A:THR508 4.6 69.2 1.0 HB A:THR460 4.7 64.3 1.0 HA A:ALA501 4.7 65.4 1.0 HG21 A:THR508 4.7 69.2 1.0 HA A:THR508 4.7 69.2 1.0 O A:SER464 4.7 64.8 1.0 CB A:ASN465 4.7 64.3 1.0 HG21 A:THR460 4.8 64.3 1.0 HG22 A:THR460 4.8 64.3 1.0 CA A:THR508 4.9 69.2 1.0 C A:GLU461 5.0 67.1 1.0 O4 A:CIT602 5.0 70.7 1.0

Sodium binding site 3 out of 4 in the Structure of the Nact-Citrate 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 the Nact-Citrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:68.3 occ:1.00 OD1 B:ASN141 1.4 64.6 1.0 O B:SER136 2.1 61.7 1.0 CG B:ASN141 2.5 64.6 1.0 HB2 B:SER136 2.8 61.7 1.0 O B:GLY226 2.8 61.8 1.0 HA2 B:GLY220 2.9 61.2 1.0 HD22 B:ASN141 2.9 64.6 1.0 HA3 B:GLY220 3.0 61.2 1.0 ND2 B:ASN141 3.1 64.6 1.0 C B:SER136 3.1 61.7 1.0 H B:ASN141 3.1 64.6 1.0 CA B:GLY220 3.4 61.2 1.0 HA B:SER136 3.4 61.7 1.0 CA B:SER136 3.6 61.7 1.0 CB B:SER136 3.6 61.7 1.0 HA2 B:GLY226 3.8 61.8 1.0 N B:ASN141 3.8 64.6 1.0 CB B:ASN141 3.8 64.6 1.0 HA B:ASN141 3.9 64.6 1.0 C B:GLY226 3.9 61.8 1.0 H B:SER140 3.9 65.3 1.0 HD21 B:ASN141 4.0 64.6 1.0 HG B:SER136 4.0 61.7 1.0 N B:GLY220 4.0 61.2 1.0 CA B:ASN141 4.1 64.6 1.0 H B:GLY220 4.1 61.2 1.0 OG B:SER136 4.2 61.7 1.0 H B:ILE139 4.3 63.0 1.0 N B:MET137 4.3 61.4 1.0 HB3 B:SER136 4.3 61.7 1.0 CA B:GLY226 4.3 61.8 1.0 HB2 B:ASN141 4.4 64.6 1.0 HA B:MET137 4.4 61.4 1.0 HB3 B:ASN141 4.4 64.6 1.0 HB B:THR227 4.4 63.6 1.0 N B:SER140 4.4 65.3 1.0 HA B:SER140 4.5 65.3 1.0 O B:ALA216 4.5 63.3 1.0 C B:GLY220 4.6 61.2 1.0 CA B:MET137 4.7 61.4 1.0 C B:SER140 4.8 65.3 1.0 HG22 B:THR227 4.8 63.6 1.0 CA B:SER140 4.8 65.3 1.0 C B:MET137 4.8 61.4 1.0 HA3 B:GLY226 4.8 61.8 1.0 O B:GLY220 4.8 61.2 1.0 N B:ILE139 4.9 63.0 1.0 C B:GLY219 4.9 61.5 1.0 N B:TRP138 4.9 61.3 1.0 H B:TRP138 5.0 61.3 1.0

Sodium binding site 4 out of 4 in the Structure of the Nact-Citrate 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 the Nact-Citrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na604 b:66.4 occ:1.00 HG1 B:THR460 2.0 64.8 1.0 O B:THR460 2.2 64.8 1.0 HB3 B:ALA501 2.6 64.9 1.0 HB3 B:ALA507 2.7 68.1 1.0 HG1 B:THR508 2.8 68.3 1.0 OG1 B:THR460 2.8 64.8 1.0 OD1 B:ASN465 2.9 64.8 1.0 O B:ALA507 3.0 68.1 1.0 O B:THR463 3.1 66.3 1.0 C B:THR460 3.3 64.8 1.0 HB2 B:ALA501 3.3 64.9 1.0 CB B:ALA501 3.3 64.9 1.0 OG1 B:THR508 3.4 68.3 1.0 HG23 B:THR460 3.5 64.8 1.0 C B:ALA507 3.5 68.1 1.0 CB B:ALA507 3.6 68.1 1.0 HA B:SER464 3.6 65.7 1.0 HB1 B:ALA501 3.7 64.9 1.0 HA B:ALA507 3.7 68.1 1.0 CG B:ASN465 3.8 64.8 1.0 CB B:THR460 3.8 64.8 1.0 HA B:GLU461 3.8 66.5 1.0 CA B:ALA507 3.9 68.1 1.0 CA B:THR460 4.0 64.8 1.0 N B:ASN465 4.0 64.8 1.0 H B:ASN465 4.0 64.8 1.0 HA B:THR460 4.0 64.8 1.0 HB2 B:ALA507 4.1 68.1 1.0 C B:THR463 4.1 66.3 1.0 C B:SER464 4.2 65.7 1.0 CG2 B:THR460 4.2 64.8 1.0 HB1 B:ALA507 4.2 68.1 1.0 HD22 B:ASN465 4.2 64.8 1.0 HA B:ASN465 4.2 64.8 1.0 CA B:SER464 4.3 65.7 1.0 N B:GLU461 4.3 66.5 1.0 ND2 B:ASN465 4.4 64.8 1.0 N B:THR508 4.4 68.3 1.0 CA B:GLU461 4.5 66.5 1.0 O B:ALA498 4.5 62.7 1.0 CA B:ASN465 4.6 64.8 1.0 CA B:ALA501 4.6 64.9 1.0 N B:SER464 4.6 65.7 1.0 CB B:THR508 4.6 68.3 1.0 HB B:THR460 4.6 64.8 1.0 HA B:ALA501 4.7 64.9 1.0 HG21 B:THR508 4.7 68.3 1.0 HA B:THR508 4.7 68.3 1.0 CB B:ASN465 4.7 64.8 1.0 O B:SER464 4.7 65.7 1.0 HG21 B:THR460 4.8 64.8 1.0 HG22 B:THR460 4.8 64.8 1.0 CA B:THR508 4.9 68.3 1.0 C B:GLU461 5.0 66.5 1.0 O4 B:CIT602 5.0 69.8 1.0

D.B.Sauer, J.Song, B.Wang, J.K.Hilton, N.K.Karpowich, J.A.Mindell, W.J.Rice, D.N.Wang. Structure and Inhibition Mechanism of the Human Citrate Transporter Nact Nature 2021.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-021-03230-X