Sodium in PDB 4f35: Crystal Structure of A Bacterial Dicarboxylate/Sodium Symporter

The structure of Crystal Structure of A Bacterial Dicarboxylate/Sodium Symporter, PDB code: 4f35 was solved by R.L.Mancusso, G.G.Gregorio, Q.Liu, D.N.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.38 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	101.330, 100.870, 164.568, 90.00, 101.74, 90.00
R / Rfree (%)	22.8 / 29.1

The binding sites of Sodium atom in the Crystal Structure of A Bacterial Dicarboxylate/Sodium Symporter (pdb code 4f35). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of A Bacterial Dicarboxylate/Sodium Symporter, PDB code: 4f35:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of A Bacterial Dicarboxylate/Sodium Symporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Bacterial Dicarboxylate/Sodium Symporter within 5.0Å range: probe atom residue distance (Å) B Occ D:Na501 b:63.0 occ:1.00 O D:SER146 2.7 87.3 1.0 OD1 D:ASN151 2.9 96.5 1.0 OG D:SER146 2.9 78.2 1.0 C D:GLY199 3.3 82.8 1.0 C D:SER150 3.3 95.4 1.0 O D:SER150 3.3 0.5 1.0 C D:SER146 3.4 83.8 1.0 O D:GLY199 3.5 75.8 1.0 CG D:ASN151 3.6 91.7 1.0 CA D:SER150 3.6 87.2 1.0 CA D:GLY199 3.6 86.6 1.0 N D:SER200 3.6 78.8 1.0 CA D:GLY193 3.7 88.7 1.0 N D:SER150 3.7 83.5 1.0 N D:ASN151 3.8 88.2 1.0 CB D:SER146 3.9 88.2 1.0 CA D:SER146 3.9 91.7 1.0 ND2 D:ASN151 3.9 75.6 1.0 O D:GLY192 4.1 86.4 1.0 O D:GLY193 4.2 90.4 1.0 N D:GLY193 4.3 93.8 1.0 N D:MSE147 4.3 89.4 1.0 C D:GLY193 4.4 83.7 1.0 O D:VAL198 4.4 91.5 1.0 C D:GLY192 4.5 86.7 1.0 CA D:ASN151 4.5 99.0 1.0 CA D:SER200 4.6 91.7 1.0 C D:ILE149 4.6 0.5 1.0 CB D:ASN151 4.7 0.2 1.0 C D:MSE147 4.7 74.5 1.0 CA D:MSE147 4.7 80.8 1.0 N D:GLY199 4.8 89.6 1.0 O D:MSE147 4.8 94.1 1.0 CB D:SER200 5.0 96.8 1.0 O D:ALA189 5.0 0.9 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of A Bacterial Dicarboxylate/Sodium Symporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Bacterial Dicarboxylate/Sodium Symporter within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:71.2 occ:1.00 O B:SER146 2.9 100.0 1.0 N B:ASN151 3.1 1.0 1.0 ND2 B:ASN151 3.1 0.1 1.0 O B:ILE149 3.1 0.8 1.0 CG B:ASN151 3.2 0.5 1.0 OG B:SER146 3.3 0.6 1.0 C B:GLY199 3.5 0.7 1.0 C B:SER150 3.6 0.0 1.0 N B:SER200 3.6 98.5 1.0 OD1 B:ASN151 3.6 0.4 1.0 CA B:ASN151 3.6 0.5 1.0 O B:GLY199 3.6 0.2 1.0 CB B:ASN151 3.8 0.7 1.0 CA B:GLY193 3.8 97.7 1.0 CB B:SER200 3.8 0.8 1.0 CA B:SER150 3.9 0.4 1.0 CA B:SER200 4.0 95.4 1.0 CA B:GLY199 4.0 0.3 1.0 C B:SER146 4.0 0.9 1.0 O B:GLY193 4.1 0.3 1.0 C B:ILE149 4.2 0.6 1.0 N B:GLY199 4.2 0.8 1.0 O B:SER150 4.4 0.6 1.0 OG B:SER200 4.4 0.9 1.0 C B:GLY193 4.5 0.7 1.0 CB B:SER146 4.5 0.1 1.0 N B:SER150 4.5 0.6 1.0 CA B:SER146 4.5 0.1 1.0 O3 B:CIT501 4.7 0.5 1.0 O B:GLY192 4.8 87.2 1.0 N B:GLY193 4.8 0.1 1.0 O B:MSE147 4.9 0.1 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of A Bacterial Dicarboxylate/Sodium Symporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of A Bacterial Dicarboxylate/Sodium Symporter within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:77.7 occ:1.00 N A:ASN151 3.1 99.0 1.0 OD1 A:ASN151 3.1 72.8 1.0 CG A:ASN151 3.2 90.2 1.0 C A:GLY199 3.3 88.1 1.0 C A:SER150 3.4 93.6 1.0 CA A:GLY199 3.4 88.4 1.0 OG A:SER146 3.4 86.4 1.0 N A:SER200 3.5 80.8 1.0 CA A:SER150 3.5 84.8 1.0 N A:GLY199 3.6 88.0 1.0 CA A:SER200 3.7 73.8 1.0 ND2 A:ASN151 3.7 97.4 1.0 CB A:ASN151 3.7 1.0 1.0 CA A:ASN151 3.8 0.1 1.0 CB A:SER200 3.8 90.0 1.0 O A:GLY199 3.8 90.5 1.0 O A:SER146 3.9 92.1 1.0 O A:SER150 4.1 0.1 1.0 N A:SER150 4.2 85.7 1.0 CA A:GLY193 4.2 88.4 1.0 OG A:SER200 4.2 0.3 1.0 O3 A:CIT501 4.5 0.8 1.0 O A:GLY193 4.5 85.7 1.0 CB A:SER146 4.7 95.0 1.0 C A:SER146 4.7 94.1 1.0 CB A:SER150 4.8 80.1 1.0 O4 A:CIT501 4.9 0.9 1.0 C A:GLY193 4.9 83.8 1.0 OG A:SER150 4.9 66.8 1.0 C A:VAL198 4.9 90.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of A Bacterial Dicarboxylate/Sodium Symporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of A Bacterial Dicarboxylate/Sodium Symporter within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:53.9 occ:1.00 O C:SER146 2.8 67.1 1.0 OG C:SER146 2.8 55.0 1.0 ND2 C:ASN151 3.2 92.3 1.0 O C:GLY199 3.4 0.2 1.0 CG C:ASN151 3.4 94.5 1.0 N C:ASN151 3.4 0.0 1.0 OD1 C:ASN151 3.5 90.5 1.0 C C:SER150 3.5 0.3 1.0 CA C:SER150 3.5 0.2 1.0 C C:GLY199 3.6 98.6 1.0 C C:SER146 3.7 66.2 1.0 N C:SER200 3.8 78.9 1.0 CA C:GLY193 3.8 90.5 1.0 N C:SER150 3.9 0.9 1.0 CA C:ASN151 4.1 95.5 1.0 CB C:SER146 4.1 61.8 1.0 O C:SER150 4.2 0.6 1.0 CA C:GLY199 4.3 0.6 1.0 CA C:SER146 4.3 62.0 1.0 N C:GLY199 4.3 0.4 1.0 CB C:ASN151 4.4 0.9 1.0 CA C:SER200 4.4 73.0 1.0 C C:ILE149 4.4 0.2 1.0 O C:GLY192 4.5 77.6 1.0 CB C:SER200 4.5 85.8 1.0 O C:ILE149 4.5 0.1 1.0 O C:GLY193 4.7 90.3 1.0 C C:GLY193 4.7 89.8 1.0 N C:MSE147 4.7 69.1 1.0 N C:GLY193 4.8 80.5 1.0 O C:ALA189 4.9 98.6 1.0 CB C:SER150 4.9 0.3 1.0 O C:MSE147 5.0 68.6 1.0 C C:MSE147 5.0 72.0 1.0

R.Mancusso, G.G.Gregorio, Q.Liu, D.N.Wang. Structure and Mechanism of A Bacterial Sodium-Dependent Dicarboxylate Transporter. Nature V. 491 622 2012.
ISSN: ISSN 0028-0836
PubMed: 23086149
DOI: 10.1038/NATURE11542