Sodium in PDB 7t9g: Structure of Vcindy-Na+

The binding sites of Sodium atom in the Structure of Vcindy-Na+ (pdb code 7t9g). 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 Vcindy-Na+, PDB code: 7t9g:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of Vcindy-Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Vcindy-Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:40.7 occ:1.00 O A:SER146 2.3 41.0 1.0 OD1 A:ASN151 2.3 41.5 1.0 O A:GLY199 2.4 38.7 1.0 HA2 A:GLY199 2.4 38.7 1.0 HA A:SER150 2.5 41.6 1.0 C A:SER150 2.7 41.6 1.0 OG A:SER146 2.9 41.0 1.0 N A:ASN151 2.9 41.5 1.0 CA A:GLY199 3.0 38.7 1.0 CA A:SER150 3.0 41.6 1.0 C A:GLY199 3.1 38.7 1.0 O A:SER150 3.1 41.6 1.0 HA3 A:GLY199 3.1 38.7 1.0 H A:ASN151 3.1 41.5 1.0 HA A:SER146 3.2 41.0 1.0 C A:SER146 3.3 41.0 1.0 HA2 A:GLY193 3.3 39.2 1.0 H A:SER150 3.4 41.6 1.0 HG A:SER146 3.5 41.0 1.0 N A:SER150 3.5 41.6 1.0 CG A:ASN151 3.5 41.5 1.0 CA A:SER146 3.6 41.0 1.0 HA A:ASN151 3.6 41.5 1.0 HA3 A:GLY193 3.6 39.2 1.0 CA A:ASN151 3.8 41.5 1.0 CB A:SER146 3.8 41.0 1.0 CA A:GLY193 3.9 39.2 1.0 CB A:ASN151 4.2 41.5 1.0 N A:GLY199 4.4 38.7 1.0 N A:SER200 4.4 38.3 1.0 HB2 A:SER146 4.4 41.0 1.0 CB A:SER150 4.4 41.6 1.0 N A:GLY193 4.4 39.2 1.0 C A:ILE149 4.4 42.0 1.0 HB3 A:SER146 4.4 41.0 1.0 H A:GLY193 4.5 39.2 1.0 N A:MET147 4.5 39.1 1.0 HB2 A:ASN151 4.5 41.5 1.0 ND2 A:ASN151 4.5 41.5 1.0 HG1 A:THR154 4.6 43.2 1.0 HD22 A:ASN151 4.6 41.5 1.0 H A:GLY199 4.6 38.7 1.0 OG A:SER150 4.7 41.6 1.0 HB2 A:SER150 4.8 41.6 1.0 HA A:SER200 4.8 38.3 1.0 O A:ALA189 4.8 41.2 1.0 C A:MET147 4.8 39.1 1.0 HA A:MET147 4.8 39.1 1.0 O A:ILE149 4.9 42.0 1.0 H A:ILE149 4.9 42.0 1.0 HB2 A:SER200 5.0 38.3 1.0 H A:SER200 5.0 38.3 1.0 N A:SER146 5.0 41.0 1.0 N A:ILE149 5.0 42.0 1.0 HB3 A:ASN151 5.0 41.5 1.0

Sodium binding site 2 out of 4 in the Structure of Vcindy-Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Vcindy-Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:41.2 occ:1.00 O A:ALA420 2.3 43.3 1.0 O A:ALA376 2.3 40.1 1.0 OD1 A:ASN378 2.3 39.1 1.0 O A:THR373 2.4 41.1 1.0 HA A:SER377 2.7 39.2 1.0 H A:ASN378 2.9 39.1 1.0 OG1 A:THR373 3.1 41.1 1.0 N A:ASN378 3.2 39.1 1.0 C A:ALA376 3.3 40.1 1.0 CG A:ASN378 3.4 39.1 1.0 C A:ALA420 3.4 43.3 1.0 CA A:SER377 3.4 39.2 1.0 C A:THR373 3.5 41.1 1.0 HA A:ALA420 3.5 43.3 1.0 C A:SER377 3.6 39.2 1.0 HG1 A:THR373 3.6 41.1 1.0 HB3 A:ALA420 3.7 43.3 1.0 HA A:THR373 3.7 41.1 1.0 N A:SER377 3.8 39.2 1.0 CA A:ALA420 3.9 43.3 1.0 HB3 A:ALA414 4.0 41.9 1.0 CA A:THR373 4.0 41.1 1.0 OG1 A:THR421 4.0 43.8 1.0 HD22 A:ASN378 4.0 39.1 1.0 HA A:ASN378 4.1 39.1 1.0 ND2 A:ASN378 4.1 39.1 1.0 CA A:ASN378 4.1 39.1 1.0 CB A:THR373 4.1 41.1 1.0 HB2 A:ALA414 4.3 41.9 1.0 HA A:THR421 4.3 43.8 1.0 CB A:ALA420 4.3 43.3 1.0 CB A:ASN378 4.3 39.1 1.0 HB1 A:ALA414 4.4 41.9 1.0 CB A:ALA414 4.4 41.9 1.0 HG1 A:THR421 4.4 43.8 1.0 H A:ALA376 4.5 40.1 1.0 N A:THR421 4.5 43.8 1.0 O A:SER377 4.5 39.2 1.0 HA A:GLU374 4.6 43.1 1.0 CA A:ALA376 4.6 40.1 1.0 N A:ALA376 4.6 40.1 1.0 N A:GLU374 4.6 43.1 1.0 H A:SER377 4.6 39.2 1.0 HB A:THR373 4.8 41.1 1.0 CB A:SER377 4.8 39.2 1.0 CA A:THR421 4.8 43.8 1.0 HB2 A:ASN378 4.8 39.1 1.0 HB2 A:SER377 4.9 39.2 1.0 HD21 A:ASN378 4.9 39.1 1.0 HG23 A:THR373 4.9 41.1 1.0 C A:GLU374 4.9 43.1 1.0 HB1 A:ALA420 4.9 43.3 1.0 CA A:GLU374 4.9 43.1 1.0 HB2 A:ALA420 4.9 43.3 1.0 O A:GLU374 5.0 43.1 1.0

Sodium binding site 3 out of 4 in the Structure of Vcindy-Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Vcindy-Na+ within 5.0Å range: probe atom residue distance (Å) B Occ Y:Na501 b:40.8 occ:1.00 O Y:SER146 2.3 41.0 1.0 OD1 Y:ASN151 2.3 41.4 1.0 O Y:GLY199 2.4 38.5 1.0 HA2 Y:GLY199 2.4 38.5 1.0 HA Y:SER150 2.5 41.7 1.0 C Y:SER150 2.7 41.7 1.0 OG Y:SER146 2.9 41.0 1.0 N Y:ASN151 2.9 41.4 1.0 CA Y:GLY199 3.0 38.5 1.0 CA Y:SER150 3.0 41.7 1.0 C Y:GLY199 3.1 38.5 1.0 O Y:SER150 3.1 41.7 1.0 HA3 Y:GLY199 3.1 38.5 1.0 H Y:ASN151 3.1 41.4 1.0 HA Y:SER146 3.2 41.0 1.0 C Y:SER146 3.3 41.0 1.0 HA2 Y:GLY193 3.3 39.1 1.0 H Y:SER150 3.4 41.7 1.0 HG Y:SER146 3.5 41.0 1.0 N Y:SER150 3.5 41.7 1.0 CG Y:ASN151 3.5 41.4 1.0 CA Y:SER146 3.6 41.0 1.0 HA Y:ASN151 3.6 41.4 1.0 HA3 Y:GLY193 3.6 39.1 1.0 CA Y:ASN151 3.8 41.4 1.0 CB Y:SER146 3.8 41.0 1.0 CA Y:GLY193 3.9 39.1 1.0 CB Y:ASN151 4.2 41.4 1.0 N Y:GLY199 4.4 38.5 1.0 N Y:SER200 4.4 38.2 1.0 HB2 Y:SER146 4.4 41.0 1.0 CB Y:SER150 4.4 41.7 1.0 N Y:GLY193 4.4 39.1 1.0 C Y:ILE149 4.4 42.0 1.0 HB3 Y:SER146 4.4 41.0 1.0 H Y:GLY193 4.5 39.1 1.0 N Y:MET147 4.5 39.1 1.0 HB2 Y:ASN151 4.5 41.4 1.0 ND2 Y:ASN151 4.5 41.4 1.0 HG1 Y:THR154 4.6 43.2 1.0 HD22 Y:ASN151 4.6 41.4 1.0 H Y:GLY199 4.6 38.5 1.0 OG Y:SER150 4.7 41.7 1.0 HB2 Y:SER150 4.8 41.7 1.0 HA Y:SER200 4.8 38.2 1.0 O Y:ALA189 4.8 41.1 1.0 C Y:MET147 4.8 39.1 1.0 HA Y:MET147 4.8 39.1 1.0 O Y:ILE149 4.9 42.0 1.0 H Y:ILE149 4.9 42.0 1.0 HB2 Y:SER200 5.0 38.2 1.0 H Y:SER200 5.0 38.2 1.0 N Y:SER146 5.0 41.0 1.0 N Y:ILE149 5.0 42.0 1.0 HB3 Y:ASN151 5.0 41.4 1.0

Sodium binding site 4 out of 4 in the Structure of Vcindy-Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Vcindy-Na+ within 5.0Å range: probe atom residue distance (Å) B Occ Y:Na502 b:41.0 occ:1.00 O Y:ALA420 2.3 43.3 1.0 O Y:ALA376 2.3 39.9 1.0 OD1 Y:ASN378 2.3 39.0 1.0 O Y:THR373 2.4 41.0 1.0 HA Y:SER377 2.7 39.0 1.0 H Y:ASN378 2.9 39.0 1.0 OG1 Y:THR373 3.1 41.0 1.0 N Y:ASN378 3.2 39.0 1.0 C Y:ALA376 3.3 39.9 1.0 CG Y:ASN378 3.4 39.0 1.0 C Y:ALA420 3.4 43.3 1.0 CA Y:SER377 3.4 39.0 1.0 C Y:THR373 3.5 41.0 1.0 HA Y:ALA420 3.5 43.3 1.0 C Y:SER377 3.6 39.0 1.0 HG1 Y:THR373 3.6 41.0 1.0 HB3 Y:ALA420 3.7 43.3 1.0 HA Y:THR373 3.7 41.0 1.0 N Y:SER377 3.8 39.0 1.0 CA Y:ALA420 3.9 43.3 1.0 HB3 Y:ALA414 4.0 41.7 1.0 CA Y:THR373 4.0 41.0 1.0 OG1 Y:THR421 4.0 43.7 1.0 HD22 Y:ASN378 4.0 39.0 1.0 HA Y:ASN378 4.1 39.0 1.0 ND2 Y:ASN378 4.1 39.0 1.0 CA Y:ASN378 4.1 39.0 1.0 CB Y:THR373 4.1 41.0 1.0 HB2 Y:ALA414 4.3 41.7 1.0 HA Y:THR421 4.3 43.7 1.0 CB Y:ALA420 4.3 43.3 1.0 CB Y:ASN378 4.3 39.0 1.0 HB1 Y:ALA414 4.4 41.7 1.0 CB Y:ALA414 4.4 41.7 1.0 HG1 Y:THR421 4.4 43.7 1.0 H Y:ALA376 4.5 39.9 1.0 N Y:THR421 4.5 43.7 1.0 O Y:SER377 4.5 39.0 1.0 HA Y:GLU374 4.6 43.1 1.0 CA Y:ALA376 4.6 39.9 1.0 N Y:GLU374 4.6 43.1 1.0 N Y:ALA376 4.6 39.9 1.0 H Y:SER377 4.6 39.0 1.0 HB Y:THR373 4.8 41.0 1.0 CB Y:SER377 4.8 39.0 1.0 CA Y:THR421 4.8 43.7 1.0 HB2 Y:ASN378 4.8 39.0 1.0 HB2 Y:SER377 4.9 39.0 1.0 HG23 Y:THR373 4.9 41.0 1.0 HD21 Y:ASN378 4.9 39.0 1.0 C Y:GLU374 4.9 43.1 1.0 HB1 Y:ALA420 4.9 43.3 1.0 CA Y:GLU374 4.9 43.1 1.0 HB2 Y:ALA420 4.9 43.3 1.0 O Y:GLU374 5.0 43.1 1.0

D.B.Sauer, J.J.Marden, J.C.Sudar, J.Song, C.Mulligan, D.N.Wang. Structural Basis of Ion - Substrate Coupling in the Na + -Dependent Dicarboxylate Transporter Vcindy. Nat Commun V. 13 2644 2022.
ISSN: ESSN 2041-1723
PubMed: 35551191
DOI: 10.1038/S41467-022-30406-4