Sodium in PDB 7rcp: Gltph Mutant (S279E/D405N) in Complex with Aspartate and Sodium Ions

The binding sites of Sodium atom in the Gltph Mutant (S279E/D405N) in Complex with Aspartate and Sodium Ions (pdb code 7rcp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Gltph Mutant (S279E/D405N) in Complex with Aspartate and Sodium Ions, PDB code: 7rcp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Gltph Mutant (S279E/D405N) in Complex with Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Gltph Mutant (S279E/D405N) in Complex with Aspartate and Sodium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:26.9 occ:1.00 O A:THR308 2.2 26.5 1.0 O A:SER349 2.2 28.8 1.0 O A:THR352 2.2 28.5 1.0 O A:ILE350 2.5 28.0 1.0 H A:THR352 2.7 28.5 1.0 C A:ILE350 2.9 28.0 1.0 N A:THR352 3.0 28.5 1.0 HB A:THR352 3.1 28.5 1.0 C A:THR352 3.2 28.5 1.0 HA A:ILE350 3.2 28.0 1.0 SD A:MET311 3.3 26.4 1.0 C A:SER349 3.3 28.8 1.0 HA A:ILE309 3.4 25.4 1.0 HE1 A:MET311 3.4 26.4 1.0 HE3 A:MET311 3.4 26.4 1.0 C A:THR308 3.4 26.5 1.0 CA A:THR352 3.4 28.5 1.0 CA A:ILE350 3.5 28.0 1.0 CE A:MET311 3.6 26.4 1.0 C A:GLY351 3.7 28.3 1.0 N A:GLY351 3.7 28.3 1.0 HG3 A:MET311 3.8 26.4 1.0 CB A:THR352 3.8 28.5 1.0 HG23 A:THR308 3.9 26.5 1.0 N A:ILE350 3.9 28.0 1.0 CA A:GLY351 4.1 28.3 1.0 CA A:ILE309 4.1 25.4 1.0 CG A:MET311 4.2 26.4 1.0 HA A:THR308 4.2 26.5 1.0 N A:ILE309 4.2 25.4 1.0 HA2 A:GLY351 4.3 28.3 1.0 H A:GLY351 4.3 28.3 1.0 HB2 A:MET311 4.3 26.4 1.0 HA A:THR352 4.4 28.5 1.0 N A:ALA353 4.4 26.8 1.0 CA A:THR308 4.4 26.5 1.0 HA A:SER349 4.4 28.8 1.0 O A:GLY351 4.5 28.3 1.0 C A:ILE309 4.5 25.4 1.0 HG22 A:THR352 4.5 28.5 1.0 CA A:SER349 4.5 28.8 1.0 HG1 A:THR352 4.5 28.5 1.0 HE2 A:MET311 4.6 26.4 1.0 HA A:ALA353 4.6 26.8 1.0 O A:ALA348 4.7 31.6 1.0 CG2 A:THR308 4.7 26.5 1.0 HG22 A:THR308 4.7 26.5 1.0 H A:ILE350 4.7 28.0 1.0 OG1 A:THR352 4.8 28.5 1.0 CG2 A:THR352 4.8 28.5 1.0 O A:ILE309 4.8 25.4 1.0 HG23 A:ILE350 4.8 28.0 1.0 CB A:MET311 4.9 26.4 1.0 HG2 A:MET311 5.0 26.4 1.0 CA A:ALA353 5.0 26.8 1.0 CB A:ILE350 5.0 28.0 1.0

Sodium binding site 2 out of 6 in the Gltph Mutant (S279E/D405N) in Complex with Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Gltph Mutant (S279E/D405N) in Complex with Aspartate and Sodium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:28.8 occ:1.00 OD1 A:ASP312 2.2 27.9 1.0 OD1 A:ASN310 2.2 24.8 1.0 O A:TYR89 2.3 25.9 1.0 OG1 A:THR92 2.4 27.7 1.0 H A:SER93 2.5 28.1 1.0 OG A:SER93 2.7 28.1 1.0 N A:SER93 2.8 28.1 1.0 HA A:TYR89 2.9 25.9 1.0 HG A:SER93 3.0 28.1 1.0 C A:TYR89 3.2 25.9 1.0 HB2 A:SER93 3.2 28.1 1.0 CB A:SER93 3.3 28.1 1.0 CG A:ASP312 3.3 27.9 1.0 CA A:SER93 3.4 28.1 1.0 CB A:THR92 3.4 27.7 1.0 HA A:SER93 3.4 28.1 1.0 CG A:ASN310 3.5 24.8 1.0 HB A:THR92 3.5 27.7 1.0 C A:THR92 3.5 27.7 1.0 CA A:TYR89 3.5 25.9 1.0 O A:HOH602 3.7 28.1 1.0 OD2 A:ASP312 3.7 27.9 1.0 CA A:THR92 3.9 27.7 1.0 HB3 A:TYR89 3.9 25.9 1.0 H A:THR92 3.9 27.7 1.0 HA A:ASN310 4.0 24.8 1.0 HD22 A:ASN310 4.0 24.8 1.0 N A:THR92 4.2 27.7 1.0 ND2 A:ASN310 4.2 24.8 1.0 HB3 A:SER93 4.2 28.1 1.0 CB A:TYR89 4.3 25.9 1.0 H A:MET311 4.3 26.4 1.0 O A:TYR88 4.3 26.5 1.0 HA A:ASP312 4.3 27.9 1.0 O A:THR92 4.4 27.7 1.0 HD1 A:TYR89 4.4 25.9 1.0 N A:LEU90 4.5 27.9 1.0 O A:HOH603 4.5 24.5 1.0 CB A:ASN310 4.5 24.8 1.0 CB A:ASP312 4.6 27.9 1.0 H A:ASP312 4.6 27.9 1.0 N A:ASP312 4.6 27.9 1.0 CA A:ASN310 4.6 24.8 1.0 N A:MET311 4.7 26.4 1.0 CG2 A:THR92 4.7 27.7 1.0 N A:TYR89 4.7 25.9 1.0 HA A:LEU90 4.7 27.9 1.0 HB2 A:ASN310 4.7 24.8 1.0 CA A:ASP312 4.8 27.9 1.0 HA A:THR92 4.8 27.7 1.0 O A:HOH613 4.8 24.8 1.0 HG21 A:THR92 4.9 27.7 1.0 C A:SER93 4.9 28.1 1.0 HG23 A:THR92 4.9 27.7 1.0 C A:ASN310 4.9 24.8 1.0 C A:TYR88 5.0 26.5 1.0 CD1 A:TYR89 5.0 25.9 1.0 C A:LEU90 5.0 27.9 1.0 CA A:LEU90 5.0 27.9 1.0 C A:MET311 5.0 26.4 1.0

Sodium binding site 3 out of 6 in the Gltph Mutant (S279E/D405N) in Complex with Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Gltph Mutant (S279E/D405N) in Complex with Aspartate and Sodium Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:27.8 occ:1.00 O B:THR308 2.2 26.9 1.0 O B:SER349 2.2 29.3 1.0 O B:THR352 2.2 28.9 1.0 O B:ILE350 2.5 28.4 1.0 H B:THR352 2.7 28.9 1.0 C B:ILE350 2.9 28.4 1.0 N B:THR352 3.0 28.9 1.0 HE3 B:MET311 3.0 26.6 1.0 HB B:THR352 3.1 28.9 1.0 C B:THR352 3.2 28.9 1.0 HA B:ILE350 3.2 28.4 1.0 SD B:MET311 3.3 26.6 1.0 C B:SER349 3.3 29.3 1.0 HA B:ILE309 3.4 25.8 1.0 C B:THR308 3.4 26.9 1.0 CA B:THR352 3.4 28.9 1.0 CA B:ILE350 3.5 28.4 1.0 CE B:MET311 3.6 26.6 1.0 C B:GLY351 3.7 28.7 1.0 N B:GLY351 3.7 28.7 1.0 CB B:THR352 3.8 28.9 1.0 N B:ILE350 3.9 28.4 1.0 HG23 B:THR308 3.9 26.9 1.0 HG3 B:MET311 3.9 26.6 1.0 HE1 B:MET311 4.0 26.6 1.0 CA B:GLY351 4.1 28.7 1.0 CA B:ILE309 4.1 25.8 1.0 CG B:MET311 4.2 26.6 1.0 HA B:THR308 4.2 26.9 1.0 N B:ILE309 4.2 25.8 1.0 HA2 B:GLY351 4.3 28.7 1.0 H B:GLY351 4.3 28.7 1.0 HB2 B:MET311 4.3 26.6 1.0 HA B:THR352 4.4 28.9 1.0 N B:ALA353 4.4 27.2 1.0 HE2 B:MET311 4.4 26.6 1.0 CA B:THR308 4.4 26.9 1.0 HA B:SER349 4.4 29.3 1.0 O B:GLY351 4.5 28.7 1.0 C B:ILE309 4.5 25.8 1.0 HG22 B:THR352 4.5 28.9 1.0 CA B:SER349 4.5 29.3 1.0 HG1 B:THR352 4.5 28.9 1.0 HG22 B:THR308 4.6 26.9 1.0 HA B:ALA353 4.6 27.2 1.0 O B:ALA348 4.7 31.9 1.0 CG2 B:THR308 4.7 26.9 1.0 H B:ILE350 4.7 28.4 1.0 OG1 B:THR352 4.8 28.9 1.0 CG2 B:THR352 4.8 28.9 1.0 O B:ILE309 4.8 25.8 1.0 HG23 B:ILE350 4.9 28.4 1.0 CB B:MET311 4.9 26.6 1.0 CA B:ALA353 5.0 27.2 1.0 CB B:ILE350 5.0 28.4 1.0 HG2 B:MET311 5.0 26.6 1.0

Sodium binding site 4 out of 6 in the Gltph Mutant (S279E/D405N) in Complex with Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Gltph Mutant (S279E/D405N) in Complex with Aspartate and Sodium Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:28.6 occ:1.00 OD1 B:ASP312 2.2 27.9 1.0 OD1 B:ASN310 2.2 25.2 1.0 O B:TYR89 2.3 26.1 1.0 OG1 B:THR92 2.4 27.8 1.0 H B:SER93 2.5 28.4 1.0 OG B:SER93 2.7 28.4 1.0 N B:SER93 2.8 28.4 1.0 HA B:TYR89 2.9 26.1 1.0 C B:TYR89 3.2 26.1 1.0 HB2 B:SER93 3.2 28.4 1.0 CB B:SER93 3.3 28.4 1.0 CG B:ASP312 3.3 27.9 1.0 CA B:SER93 3.4 28.4 1.0 CB B:THR92 3.4 27.8 1.0 HA B:SER93 3.4 28.4 1.0 CG B:ASN310 3.5 25.2 1.0 HB B:THR92 3.5 27.8 1.0 C B:THR92 3.5 27.8 1.0 CA B:TYR89 3.5 26.1 1.0 O B:HOH603 3.7 27.2 1.0 OD2 B:ASP312 3.7 27.9 1.0 CA B:THR92 3.9 27.8 1.0 HB3 B:TYR89 3.9 26.1 1.0 H B:THR92 3.9 27.8 1.0 HA B:ASN310 4.0 25.2 1.0 HD22 B:ASN310 4.0 25.2 1.0 N B:THR92 4.2 27.8 1.0 ND2 B:ASN310 4.2 25.2 1.0 HB3 B:SER93 4.2 28.4 1.0 CB B:TYR89 4.3 26.1 1.0 H B:MET311 4.3 26.6 1.0 O B:TYR88 4.3 26.5 1.0 HA B:ASP312 4.3 27.9 1.0 O B:THR92 4.4 27.8 1.0 HD1 B:TYR89 4.4 26.1 1.0 N B:LEU90 4.5 28.1 1.0 O B:HOH604 4.5 24.3 1.0 CB B:ASN310 4.5 25.2 1.0 CB B:ASP312 4.6 27.9 1.0 H B:ASP312 4.6 27.9 1.0 N B:ASP312 4.6 27.9 1.0 CA B:ASN310 4.6 25.2 1.0 N B:MET311 4.7 26.6 1.0 CG2 B:THR92 4.7 27.8 1.0 N B:TYR89 4.7 26.1 1.0 HA B:LEU90 4.7 28.1 1.0 HB2 B:ASN310 4.7 25.2 1.0 CA B:ASP312 4.8 27.9 1.0 HA B:THR92 4.8 27.8 1.0 O B:HOH617 4.8 25.0 1.0 C B:SER93 4.9 28.4 1.0 HG23 B:THR92 4.9 27.8 1.0 HG21 B:THR92 4.9 27.8 1.0 C B:ASN310 4.9 25.2 1.0 C B:TYR88 5.0 26.5 1.0 CD1 B:TYR89 5.0 26.1 1.0 C B:LEU90 5.0 28.1 1.0 CA B:LEU90 5.0 28.1 1.0 C B:MET311 5.0 26.6 1.0

Sodium binding site 5 out of 6 in the Gltph Mutant (S279E/D405N) in Complex with Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Gltph Mutant (S279E/D405N) in Complex with Aspartate and Sodium Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:27.7 occ:1.00 O C:THR308 2.2 26.9 1.0 O C:SER349 2.2 28.7 1.0 O C:THR352 2.2 28.6 1.0 O C:ILE350 2.5 28.2 1.0 H C:THR352 2.7 28.6 1.0 C C:ILE350 2.9 28.2 1.0 N C:THR352 3.0 28.6 1.0 HB C:THR352 3.1 28.6 1.0 C C:THR352 3.2 28.6 1.0 HA C:ILE350 3.2 28.2 1.0 SD C:MET311 3.3 26.6 1.0 C C:SER349 3.3 28.7 1.0 HA C:ILE309 3.4 25.8 1.0 HE3 C:MET311 3.4 26.6 1.0 C C:THR308 3.4 26.9 1.0 CA C:THR352 3.4 28.6 1.0 HE1 C:MET311 3.5 26.6 1.0 CA C:ILE350 3.5 28.2 1.0 CE C:MET311 3.6 26.6 1.0 C C:GLY351 3.7 28.9 1.0 N C:GLY351 3.7 28.9 1.0 CB C:THR352 3.8 28.6 1.0 HG3 C:MET311 3.8 26.6 1.0 HG23 C:THR308 3.9 26.9 1.0 N C:ILE350 3.9 28.2 1.0 CA C:GLY351 4.1 28.9 1.0 CA C:ILE309 4.1 25.8 1.0 CG C:MET311 4.2 26.6 1.0 HA C:THR308 4.2 26.9 1.0 N C:ILE309 4.2 25.8 1.0 HA2 C:GLY351 4.3 28.9 1.0 H C:GLY351 4.3 28.9 1.0 HB2 C:MET311 4.3 26.6 1.0 HA C:THR352 4.4 28.6 1.0 N C:ALA353 4.4 27.4 1.0 CA C:THR308 4.4 26.9 1.0 HA C:SER349 4.4 28.7 1.0 O C:GLY351 4.5 28.9 1.0 C C:ILE309 4.5 25.8 1.0 HG22 C:THR352 4.5 28.6 1.0 CA C:SER349 4.5 28.7 1.0 HG1 C:THR352 4.5 28.6 1.0 HE2 C:MET311 4.6 26.6 1.0 HA C:ALA353 4.6 27.4 1.0 O C:ALA348 4.7 31.5 1.0 HG22 C:THR308 4.7 26.9 1.0 CG2 C:THR308 4.7 26.9 1.0 H C:ILE350 4.7 28.2 1.0 OG1 C:THR352 4.8 28.6 1.0 CG2 C:THR352 4.8 28.6 1.0 O C:ILE309 4.8 25.8 1.0 HG23 C:ILE350 4.8 28.2 1.0 CB C:MET311 4.9 26.6 1.0 CA C:ALA353 5.0 27.4 1.0 HG2 C:MET311 5.0 26.6 1.0 CB C:ILE350 5.0 28.2 1.0

Sodium binding site 6 out of 6 in the Gltph Mutant (S279E/D405N) in Complex with Aspartate and Sodium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Gltph Mutant (S279E/D405N) in Complex with Aspartate and Sodium Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:28.2 occ:1.00 OD1 C:ASP312 2.2 27.8 1.0 OD1 C:ASN310 2.2 25.1 1.0 O C:TYR89 2.3 25.9 1.0 OG1 C:THR92 2.4 27.6 1.0 H C:SER93 2.5 28.2 1.0 OG C:SER93 2.7 28.2 1.0 N C:SER93 2.8 28.2 1.0 HA C:TYR89 2.9 25.9 1.0 C C:TYR89 3.2 25.9 1.0 HB2 C:SER93 3.2 28.2 1.0 CB C:SER93 3.3 28.2 1.0 CG C:ASP312 3.3 27.8 1.0 CA C:SER93 3.4 28.2 1.0 CB C:THR92 3.4 27.6 1.0 HA C:SER93 3.4 28.2 1.0 CG C:ASN310 3.5 25.1 1.0 HB C:THR92 3.5 27.6 1.0 C C:THR92 3.5 27.6 1.0 CA C:TYR89 3.5 25.9 1.0 O C:HOH602 3.7 27.6 1.0 OD2 C:ASP312 3.7 27.8 1.0 CA C:THR92 3.9 27.6 1.0 HB3 C:TYR89 3.9 25.9 1.0 H C:THR92 3.9 27.6 1.0 HA C:ASN310 4.0 25.1 1.0 HD22 C:ASN310 4.0 25.1 1.0 N C:THR92 4.2 27.6 1.0 ND2 C:ASN310 4.2 25.1 1.0 HB3 C:SER93 4.2 28.2 1.0 CB C:TYR89 4.3 25.9 1.0 H C:MET311 4.3 26.6 1.0 O C:TYR88 4.3 26.5 1.0 HA C:ASP312 4.3 27.8 1.0 O C:THR92 4.4 27.6 1.0 HD1 C:TYR89 4.4 25.9 1.0 N C:LEU90 4.5 28.1 1.0 O C:HOH603 4.5 24.4 1.0 CB C:ASN310 4.5 25.1 1.0 CB C:ASP312 4.6 27.8 1.0 N C:ASP312 4.6 27.8 1.0 H C:ASP312 4.6 27.8 1.0 CA C:ASN310 4.6 25.1 1.0 N C:MET311 4.7 26.6 1.0 CG2 C:THR92 4.7 27.6 1.0 N C:TYR89 4.7 25.9 1.0 HA C:LEU90 4.7 28.1 1.0 HB2 C:ASN310 4.7 25.1 1.0 CA C:ASP312 4.8 27.8 1.0 HA C:THR92 4.8 27.6 1.0 O C:HOH614 4.8 25.2 1.0 C C:SER93 4.9 28.2 1.0 HG23 C:THR92 4.9 27.6 1.0 HG21 C:THR92 4.9 27.6 1.0 C C:ASN310 4.9 25.1 1.0 C C:TYR88 5.0 26.5 1.0 CD1 C:TYR89 5.0 25.9 1.0 C C:LEU90 5.0 28.1 1.0 CA C:LEU90 5.0 28.1 1.0 C C:MET311 5.0 26.6 1.0

K.D.Reddy, D.Ciftci, A.J.Scopelliti, O.Boudker. The Archaeal Glutamate Transporter Homologue Gltph Shows Heterogeneous Substrate Binding. J.Gen.Physiol. V. 154 2022.
ISSN: ESSN 1540-7748
PubMed: 35452090
DOI: 10.1085/JGP.202213131