Sodium in PDB 7jsj: Structure of the Nact-PF2 Complex

The binding sites of Sodium atom in the Structure of the Nact-PF2 Complex (pdb code 7jsj). 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-PF2 Complex, PDB code: 7jsj:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of the Nact-PF2 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-PF2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:25.5 occ:1.00 O A:GLY226 2.3 24.7 1.0 H A:SER140 2.3 25.3 1.0 H A:ASN141 2.4 25.4 1.0 O A:SER136 2.4 24.6 1.0 OD1 A:ASN141 2.5 25.4 1.0 N A:SER140 2.8 25.3 1.0 N A:ASN141 2.9 25.4 1.0 HA A:SER140 3.0 25.3 1.0 CA A:SER140 3.2 25.3 1.0 C A:GLY226 3.4 24.7 1.0 H A:ILE139 3.4 24.8 1.0 HA2 A:GLY226 3.4 24.7 1.0 CG A:ASN141 3.4 25.4 1.0 HA A:SER136 3.4 24.6 1.0 C A:SER136 3.4 24.6 1.0 C A:SER140 3.5 25.3 1.0 HB2 A:SER136 3.5 24.6 1.0 HA2 A:GLY220 3.7 24.4 1.0 HA A:ASN141 3.7 25.4 1.0 C A:ILE139 3.7 24.8 1.0 CA A:ASN141 3.8 25.4 1.0 N A:ILE139 3.8 24.8 1.0 CA A:SER136 3.9 24.6 1.0 CA A:GLY226 3.9 24.7 1.0 O20 A:X3M602 4.1 25.8 1.0 CB A:SER136 4.2 24.6 1.0 HA3 A:GLY220 4.2 24.4 1.0 CB A:ASN141 4.2 25.4 1.0 ND2 A:ASN141 4.2 25.4 1.0 HD22 A:ASN141 4.2 25.4 1.0 HB A:THR227 4.3 25.0 1.0 CA A:ILE139 4.4 24.8 1.0 CA A:GLY220 4.4 24.4 1.0 HG A:SER136 4.5 24.6 1.0 C A:TRP138 4.5 24.2 1.0 O A:ILE139 4.5 24.8 1.0 N A:THR227 4.5 25.0 1.0 N A:TRP138 4.6 24.2 1.0 HA3 A:GLY226 4.6 24.7 1.0 H A:TRP138 4.6 24.2 1.0 N A:MET137 4.6 24.1 1.0 O A:SER140 4.7 25.3 1.0 CB A:SER140 4.7 25.3 1.0 C A:MET137 4.7 24.1 1.0 HB2 A:ASN141 4.7 25.4 1.0 HA A:THR227 4.8 25.0 1.0 N A:GLY226 4.8 24.7 1.0 H A:GLY226 4.8 24.7 1.0 HA A:MET137 4.8 24.1 1.0 OG A:SER136 4.9 24.6 1.0 HB3 A:SER136 4.9 24.6 1.0 HB3 A:ASN141 4.9 25.4 1.0 HB2 A:SER140 4.9 25.3 1.0 HD21 A:ASN141 5.0 25.4 1.0 CA A:TRP138 5.0 24.2 1.0 CA A:MET137 5.0 24.1 1.0

Sodium binding site 2 out of 4 in the Structure of the Nact-PF2 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-PF2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:25.9 occ:1.00 HG1 A:THR460 2.2 24.3 1.0 O A:ALA507 2.3 25.2 1.0 O A:THR460 2.3 24.3 1.0 OD1 A:ASN465 2.4 24.9 1.0 HB2 A:ALA501 2.6 24.6 1.0 HB1 A:ALA507 2.7 25.2 1.0 OG1 A:THR460 2.8 24.3 1.0 C A:ALA507 3.0 25.2 1.0 O A:THR463 3.0 25.0 1.0 HB A:THR508 3.2 25.6 1.0 CB A:ALA501 3.3 24.6 1.0 HB1 A:ALA501 3.3 24.6 1.0 CG A:ASN465 3.3 24.9 1.0 HA A:ALA507 3.4 25.2 1.0 HA A:SER464 3.4 25.3 1.0 CB A:ALA507 3.5 25.2 1.0 CA A:ALA507 3.5 25.2 1.0 C A:THR460 3.5 24.3 1.0 HB3 A:ALA501 3.6 24.6 1.0 HD22 A:ASN465 3.6 24.9 1.0 ND2 A:ASN465 3.8 24.9 1.0 N A:ASN465 3.9 24.9 1.0 N A:THR508 3.9 25.6 1.0 HB3 A:ALA507 4.0 25.2 1.0 H A:ASN465 4.0 24.9 1.0 C A:SER464 4.0 25.3 1.0 CB A:THR460 4.0 24.3 1.0 CB A:THR508 4.1 25.6 1.0 C A:THR463 4.1 25.0 1.0 CA A:SER464 4.1 25.3 1.0 HA A:GLU461 4.1 25.1 1.0 HA A:ASN465 4.1 24.9 1.0 HA A:THR460 4.1 24.3 1.0 CA A:THR460 4.2 24.3 1.0 HB2 A:ALA507 4.2 25.2 1.0 HA A:THR508 4.2 25.6 1.0 HG21 A:THR460 4.3 24.3 1.0 CA A:THR508 4.3 25.6 1.0 CA A:ASN465 4.4 24.9 1.0 CB A:ASN465 4.4 24.9 1.0 O A:SER464 4.5 25.3 1.0 N A:GLU461 4.6 25.1 1.0 N A:SER464 4.6 25.3 1.0 CA A:ALA501 4.6 24.6 1.0 H A:THR508 4.6 25.6 1.0 HG21 A:THR508 4.6 25.6 1.0 HD21 A:ASN465 4.6 24.9 1.0 HA A:ALA501 4.6 24.6 1.0 CG2 A:THR460 4.7 24.3 1.0 HB A:THR460 4.7 24.3 1.0 CA A:GLU461 4.7 25.1 1.0 O A:ALA498 4.8 24.2 1.0 CG2 A:THR508 4.8 25.6 1.0 HG22 A:THR460 4.9 24.3 1.0 N A:ALA507 4.9 25.2 1.0 HG1 A:THR463 4.9 25.0 1.0 HB2 A:ASN465 5.0 24.9 1.0 HG23 A:THR508 5.0 25.6 1.0 OG1 A:THR508 5.0 25.6 1.0

Sodium binding site 3 out of 4 in the Structure of the Nact-PF2 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-PF2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:24.6 occ:1.00 H B:SER140 2.2 25.2 1.0 O B:GLY226 2.3 24.1 1.0 O B:SER136 2.4 24.0 1.0 H B:ASN141 2.5 25.0 1.0 OD1 B:ASN141 2.6 25.0 1.0 N B:SER140 2.7 25.2 1.0 HA B:SER140 2.9 25.2 1.0 N B:ASN141 3.0 25.0 1.0 CA B:SER140 3.2 25.2 1.0 H B:ILE139 3.3 24.5 1.0 HA2 B:GLY226 3.3 24.1 1.0 C B:GLY226 3.3 24.1 1.0 C B:SER136 3.4 24.0 1.0 HA B:SER136 3.5 24.0 1.0 C B:SER140 3.5 25.2 1.0 CG B:ASN141 3.6 25.0 1.0 HB2 B:SER136 3.6 24.0 1.0 C B:ILE139 3.7 24.5 1.0 N B:ILE139 3.7 24.5 1.0 HA2 B:GLY220 3.8 23.8 1.0 HA B:ASN141 3.8 25.0 1.0 CA B:GLY226 3.9 24.1 1.0 CA B:SER136 3.9 24.0 1.0 CA B:ASN141 3.9 25.0 1.0 O19 B:X3M602 4.2 25.4 1.0 CB B:SER136 4.2 24.0 1.0 CA B:ILE139 4.3 24.5 1.0 HA3 B:GLY220 4.3 23.8 1.0 C B:TRP138 4.4 23.7 1.0 CB B:ASN141 4.4 25.0 1.0 HD22 B:ASN141 4.4 25.0 1.0 ND2 B:ASN141 4.4 25.0 1.0 HB B:THR227 4.4 24.3 1.0 O B:ILE139 4.5 24.5 1.0 N B:TRP138 4.5 23.7 1.0 N B:THR227 4.5 24.3 1.0 H B:TRP138 4.5 23.7 1.0 CA B:GLY220 4.5 23.8 1.0 HG B:SER136 4.6 24.0 1.0 HA3 B:GLY226 4.6 24.1 1.0 N B:MET137 4.6 23.6 1.0 CB B:SER140 4.7 25.2 1.0 C B:MET137 4.7 23.6 1.0 H B:GLY226 4.7 24.1 1.0 O B:SER140 4.7 25.2 1.0 N B:GLY226 4.7 24.1 1.0 HA B:THR227 4.8 24.3 1.0 HA B:MET137 4.8 23.6 1.0 CA B:TRP138 4.8 23.7 1.0 HB2 B:SER140 4.8 25.2 1.0 HA B:TRP138 4.9 23.7 1.0 HB2 B:ASN141 4.9 25.0 1.0 HA B:ILE139 4.9 24.5 1.0 CA B:MET137 5.0 23.6 1.0 OG B:SER136 5.0 24.0 1.0 HB3 B:SER136 5.0 24.0 1.0

Sodium binding site 4 out of 4 in the Structure of the Nact-PF2 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-PF2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na604 b:25.2 occ:1.00 HG1 B:THR460 2.2 23.9 1.0 O B:THR460 2.3 23.9 1.0 O B:ALA507 2.3 25.3 1.0 OD1 B:ASN465 2.4 24.2 1.0 OG1 B:THR460 2.7 23.9 1.0 O B:THR463 2.8 24.4 1.0 HB2 B:ALA501 2.8 24.6 1.0 HB1 B:ALA507 2.9 25.3 1.0 C B:ALA507 3.1 25.3 1.0 HA B:SER464 3.3 24.7 1.0 CG B:ASN465 3.4 24.2 1.0 HB B:THR508 3.4 25.3 1.0 HA B:ALA507 3.4 25.3 1.0 C B:THR460 3.4 23.9 1.0 CB B:ALA501 3.5 24.6 1.0 CA B:ALA507 3.5 25.3 1.0 HB1 B:ALA501 3.5 24.6 1.0 CB B:ALA507 3.6 25.3 1.0 C B:SER464 3.8 24.7 1.0 N B:ASN465 3.8 24.2 1.0 HD22 B:ASN465 3.8 24.2 1.0 C B:THR463 3.8 24.4 1.0 HB3 B:ALA501 3.9 24.6 1.0 H B:ASN465 3.9 24.2 1.0 CA B:SER464 3.9 24.7 1.0 CB B:THR460 3.9 23.9 1.0 ND2 B:ASN465 4.0 24.2 1.0 HA B:THR460 4.0 23.9 1.0 HA B:ASN465 4.0 24.2 1.0 N B:THR508 4.0 25.3 1.0 CA B:THR460 4.1 23.9 1.0 HB3 B:ALA507 4.1 25.3 1.0 HA B:GLU461 4.2 24.9 1.0 CB B:THR508 4.2 25.3 1.0 O B:SER464 4.3 24.7 1.0 HB2 B:ALA507 4.3 25.3 1.0 CA B:ASN465 4.3 24.2 1.0 HA B:THR508 4.3 25.3 1.0 N B:SER464 4.3 24.7 1.0 HG21 B:THR460 4.3 23.9 1.0 CB B:ASN465 4.4 24.2 1.0 CA B:THR508 4.5 25.3 1.0 N B:GLU461 4.5 24.9 1.0 HB B:THR460 4.6 23.9 1.0 CG2 B:THR460 4.7 23.9 1.0 HG1 B:THR463 4.7 24.4 1.0 H B:THR508 4.7 25.3 1.0 HD21 B:ASN465 4.7 24.2 1.0 CA B:GLU461 4.7 24.9 1.0 CA B:ALA501 4.8 24.6 1.0 O B:ALA498 4.8 23.5 1.0 HA B:ALA501 4.8 24.6 1.0 HG21 B:THR508 4.8 25.3 1.0 HB2 B:ASN465 4.9 24.2 1.0 HG22 B:THR460 5.0 23.9 1.0 N B:ALA507 5.0 25.3 1.0 H B:THR463 5.0 24.4 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