Sodium in PDB 6ol1: Structure of Vcindy in Complex with Succinate

The structure of Structure of Vcindy in Complex with Succinate, PDB code: 6ol1 was solved by D.B.Sauer, J.J.Marden, D.N.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.48 / 3.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	105.529, 102.540, 171.116, 90.00, 98.81, 90.00
R / Rfree (%)	25.9 / 30

The binding sites of Sodium atom in the Structure of Vcindy in Complex with Succinate (pdb code 6ol1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Structure of Vcindy in Complex with Succinate, PDB code: 6ol1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Structure of Vcindy in Complex with Succinate


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 in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:76.1 occ:1.00 O C:ALA376 2.4 54.8 1.0 OD1 C:ASN378 2.4 76.9 1.0 O C:THR373 2.5 77.3 1.0 O C:ALA420 2.6 70.3 1.0 OG1 C:THR373 2.7 69.0 1.0 N C:ASN378 2.9 77.7 1.0 C C:SER377 3.1 75.0 1.0 CG C:ASN378 3.4 71.6 1.0 CA C:ASN378 3.4 59.1 1.0 CB C:ALA414 3.5 69.8 1.0 C C:THR373 3.5 73.6 1.0 C C:ALA376 3.6 64.2 1.0 O C:SER377 3.6 71.0 1.0 C C:ALA420 3.6 74.3 1.0 CA C:SER377 3.7 55.6 1.0 CB C:THR373 3.8 71.3 1.0 CA C:THR373 3.9 66.6 1.0 CB C:ASN378 4.0 67.9 1.0 N C:SER377 4.1 67.9 1.0 O C:ALA411 4.1 60.5 1.0 OG1 C:THR421 4.2 86.1 1.0 CA C:ALA420 4.3 65.5 1.0 O4 C:SIN503 4.3 74.6 1.0 ND2 C:ASN378 4.5 78.0 1.0 CG2 C:THR373 4.5 66.7 1.0 N C:THR421 4.6 72.4 1.0 CB C:ALA420 4.6 70.0 1.0 N C:GLU374 4.7 72.9 1.0 C C:ASN378 4.8 68.2 1.0 CA C:ALA376 4.8 58.5 1.0 CA C:ALA414 4.8 79.2 1.0 N C:ALA376 4.9 61.5 1.0 OG C:SER381 4.9 62.2 1.0 CA C:THR421 4.9 64.4 1.0

Sodium binding site 2 out of 8 in the Structure of Vcindy in Complex with Succinate


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 in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:81.3 occ:1.00 O C:SER146 2.3 75.7 1.0 O C:GLY199 2.3 78.1 1.0 O C:SER150 2.3 93.9 1.0 C C:SER150 2.7 81.4 1.0 CA C:GLY199 2.7 63.2 1.0 CA C:SER150 2.7 62.8 1.0 N C:SER150 2.8 62.3 1.0 C C:GLY199 2.9 68.7 1.0 C C:SER146 3.2 72.2 1.0 OG C:SER146 3.5 66.7 1.0 OD1 C:ASN151 3.5 70.7 1.0 C C:ILE149 3.6 76.9 1.0 CA C:SER146 3.6 65.7 1.0 N C:ASN151 3.8 69.0 1.0 N C:GLY199 3.9 62.8 1.0 N C:ILE149 4.0 75.0 1.0 O C:ILE149 4.1 96.3 1.0 CB C:SER146 4.1 65.2 1.0 N C:SER200 4.2 52.6 1.0 CB C:SER150 4.2 58.6 1.0 N C:TRP148 4.3 74.3 1.0 N C:MET147 4.3 73.5 1.0 CA C:ILE149 4.4 80.8 1.0 CG C:ASN151 4.4 70.9 1.0 C C:MET147 4.4 80.6 1.0 C C:TRP148 4.4 74.3 1.0 CA C:GLY193 4.5 72.9 1.0 OG1 C:THR154 4.6 65.5 1.0 CA C:MET147 4.7 73.0 1.0 CA C:ASN151 4.7 65.9 1.0 O C:LEU145 4.7 84.8 1.0 O C:MET147 4.8 89.6 1.0 OG C:SER150 4.8 61.5 1.0 CA C:TRP148 4.9 72.5 1.0 C C:VAL198 4.9 91.3 1.0 O2 C:SIN503 4.9 63.9 1.0 N C:SER146 4.9 69.4 1.0 O C:TRP148 4.9 86.6 1.0

Sodium binding site 3 out of 8 in the Structure of Vcindy in Complex with Succinate


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 in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ D:Na501 b:77.0 occ:1.00 OD1 D:ASN378 2.3 61.7 1.0 O D:ALA376 2.4 78.1 1.0 O D:ALA420 2.4 80.3 1.0 O D:THR373 2.5 69.5 1.0 OG1 D:THR373 2.6 57.5 1.0 N D:ASN378 2.7 63.9 1.0 C D:SER377 2.9 71.0 1.0 CA D:ASN378 3.2 72.0 1.0 CG D:ASN378 3.3 59.0 1.0 C D:ALA420 3.3 77.3 1.0 O D:SER377 3.4 87.3 1.0 C D:ALA376 3.5 89.3 1.0 C D:THR373 3.5 71.3 1.0 CA D:SER377 3.6 73.5 1.0 CB D:THR373 3.7 59.1 1.0 CB D:ASN378 3.8 75.8 1.0 CA D:THR373 3.8 75.5 1.0 CB D:ALA414 3.9 64.0 1.0 CA D:ALA420 3.9 62.9 1.0 N D:SER377 4.0 86.7 1.0 OG1 D:THR421 4.2 91.4 1.0 O D:ALA411 4.3 73.9 1.0 CB D:ALA420 4.3 64.7 1.0 N D:THR421 4.4 87.2 1.0 ND2 D:ASN378 4.4 77.2 1.0 CG2 D:THR373 4.4 57.0 1.0 C D:ASN378 4.6 72.8 1.0 N D:GLU374 4.8 70.3 1.0 CA D:ALA376 4.8 88.6 1.0 CA D:THR421 4.8 72.6 1.0 OG D:SER381 4.8 64.5 1.0 N D:ALA376 4.8 76.2 1.0 CB D:SER377 5.0 56.9 1.0

Sodium binding site 4 out of 8 in the Structure of Vcindy in Complex with Succinate


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 in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ D:Na502 b:79.0 occ:1.00 O D:SER146 2.3 56.6 1.0 O D:SER150 2.4 80.6 1.0 N D:SER150 2.4 61.1 1.0 CA D:SER150 2.9 72.9 1.0 C D:SER150 2.9 75.4 1.0 C D:SER146 3.0 63.1 1.0 CA D:GLY199 3.1 64.7 1.0 C D:ILE149 3.1 72.0 1.0 N D:ILE149 3.2 54.9 1.0 O D:GLY199 3.3 75.9 1.0 CA D:SER146 3.5 66.4 1.0 N D:TRP148 3.6 64.9 1.0 C D:TRP148 3.7 62.8 1.0 CA D:ILE149 3.7 74.8 1.0 C D:GLY199 3.7 68.7 1.0 OG D:SER146 3.8 74.9 1.0 C D:MET147 3.9 61.9 1.0 O D:ILE149 3.9 78.3 1.0 OD1 D:ASN151 4.0 72.3 1.0 N D:MET147 4.0 52.2 1.0 N D:GLY199 4.1 61.9 1.0 CA D:TRP148 4.1 61.8 1.0 N D:ASN151 4.2 74.6 1.0 O D:LEU145 4.2 78.2 1.0 CB D:SER146 4.2 71.5 1.0 OG1 D:THR154 4.3 72.1 1.0 O D:TRP148 4.3 63.1 1.0 CA D:MET147 4.4 52.1 1.0 CB D:ILE149 4.4 68.7 1.0 CB D:SER150 4.4 51.0 1.0 O D:MET147 4.4 63.5 1.0 N D:SER146 4.7 67.3 1.0 CA D:GLY193 4.8 63.9 1.0 C D:VAL198 4.8 81.9 1.0 O D:VAL198 4.9 78.5 1.0 C D:LEU145 4.9 67.8 1.0 CG D:ASN151 4.9 70.0 1.0

Sodium binding site 5 out of 8 in the Structure of Vcindy in Complex with Succinate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Vcindy in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:76.5 occ:1.00 O A:THR373 2.4 91.7 1.0 OD1 A:ASN378 2.4 75.2 1.0 O A:ALA376 2.4 59.4 1.0 O A:ALA420 2.5 87.3 1.0 OG1 A:THR373 2.5 74.4 1.0 N A:ASN378 2.9 68.1 1.0 C A:SER377 3.1 73.8 1.0 CA A:ASN378 3.4 73.0 1.0 CG A:ASN378 3.4 70.6 1.0 C A:THR373 3.4 93.7 1.0 C A:ALA420 3.4 88.8 1.0 O A:SER377 3.5 66.7 1.0 C A:ALA376 3.6 70.2 1.0 CB A:THR373 3.6 84.5 1.0 CB A:ALA414 3.6 78.1 1.0 CA A:SER377 3.8 69.1 1.0 CA A:THR373 3.8 81.7 1.0 CB A:ASN378 3.9 70.7 1.0 CA A:ALA420 4.1 89.0 1.0 N A:SER377 4.1 68.7 1.0 OG1 A:THR421 4.1 84.4 1.0 O A:ALA411 4.2 77.6 1.0 CG2 A:THR373 4.2 75.3 1.0 N A:THR421 4.4 90.0 1.0 O1 A:SIN503 4.4 76.6 1.0 ND2 A:ASN378 4.5 68.2 1.0 CB A:ALA420 4.5 84.9 1.0 N A:GLU374 4.6 90.9 1.0 C A:ASN378 4.7 81.7 1.0 CA A:THR421 4.8 76.9 1.0 OG A:SER381 4.8 78.2 1.0 N A:ALA376 4.8 91.9 1.0 CA A:ALA376 4.8 73.9 1.0 CA A:ALA414 4.9 92.8 1.0

Sodium binding site 6 out of 8 in the Structure of Vcindy in Complex with Succinate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Vcindy in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:0.7 occ:1.00 O A:SER146 2.3 93.1 1.0 O A:GLY199 2.3 92.0 1.0 O A:SER150 2.4 0.2 1.0 N A:SER150 2.5 61.5 1.0 CA A:SER150 2.6 71.3 1.0 CA A:GLY199 2.6 69.5 1.0 C A:SER150 2.7 92.5 1.0 C A:GLY199 2.8 72.8 1.0 C A:SER146 3.2 92.4 1.0 C A:ILE149 3.2 95.8 1.0 OG A:SER146 3.5 84.6 1.0 CA A:SER146 3.6 83.3 1.0 N A:ILE149 3.7 82.4 1.0 N A:GLY199 3.7 67.5 1.0 OD1 A:ASN151 3.8 79.0 1.0 O A:ILE149 3.8 0.0 1.0 N A:ASN151 3.9 92.8 1.0 CA A:ILE149 4.1 1.0 1.0 N A:TRP148 4.1 89.2 1.0 C A:TRP148 4.1 77.7 1.0 CB A:SER150 4.1 67.4 1.0 N A:SER200 4.1 57.2 1.0 CB A:SER146 4.2 85.7 1.0 N A:MET147 4.3 91.3 1.0 C A:MET147 4.3 87.3 1.0 CA A:GLY193 4.3 91.3 1.0 O A:TRP148 4.6 77.0 1.0 CA A:TRP148 4.6 88.4 1.0 CA A:MET147 4.7 82.2 1.0 CG A:ASN151 4.7 81.8 1.0 C A:VAL198 4.7 85.6 1.0 O A:LEU145 4.7 95.0 1.0 O A:MET147 4.7 90.8 1.0 OG1 A:THR154 4.8 97.9 1.0 OG A:SER150 4.8 77.6 1.0 CB A:ILE149 4.9 0.3 1.0 CA A:ASN151 4.9 91.0 1.0 O A:VAL198 4.9 0.5 1.0 O3 A:SIN503 4.9 74.0 1.0 N A:GLY193 4.9 83.3 1.0 N A:SER146 4.9 82.0 1.0

Sodium binding site 7 out of 8 in the Structure of Vcindy in Complex with Succinate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Vcindy in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:57.1 occ:1.00 O B:ALA376 2.3 53.8 1.0 O B:ALA420 2.4 67.5 1.0 OD1 B:ASN378 2.4 72.9 1.0 O B:THR373 2.7 67.1 1.0 N B:ASN378 2.7 61.1 1.0 OG1 B:THR373 2.8 59.4 1.0 C B:SER377 2.9 62.5 1.0 CA B:ASN378 3.2 67.1 1.0 CG B:ASN378 3.3 64.8 1.0 C B:ALA420 3.3 61.6 1.0 O B:SER377 3.4 71.6 1.0 C B:ALA376 3.4 68.9 1.0 CA B:SER377 3.5 64.8 1.0 C B:THR373 3.7 71.2 1.0 CB B:ASN378 3.8 71.6 1.0 CB B:ALA414 3.9 57.7 1.0 CB B:THR373 3.9 69.2 1.0 N B:SER377 3.9 55.1 1.0 OG1 B:THR421 4.0 86.7 1.0 CA B:ALA420 4.0 58.0 1.0 CA B:THR373 4.1 77.0 1.0 O B:ALA411 4.2 72.4 1.0 N B:THR421 4.3 69.2 1.0 CB B:ALA420 4.4 48.8 1.0 ND2 B:ASN378 4.5 80.0 1.0 O3 B:SIN503 4.5 85.9 1.0 C B:ASN378 4.6 71.0 1.0 CG2 B:THR373 4.6 59.1 1.0 CA B:THR421 4.6 63.0 1.0 CA B:ALA376 4.7 67.5 1.0 OG B:SER381 4.8 64.9 1.0 N B:ALA376 4.8 61.6 1.0 CB B:THR421 4.9 64.5 1.0 N B:GLU374 4.9 73.5 1.0 CB B:SER377 5.0 56.8 1.0

Sodium binding site 8 out of 8 in the Structure of Vcindy in Complex with Succinate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Vcindy in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:85.8 occ:1.00 O B:SER146 2.3 69.4 1.0 N B:SER150 2.4 81.4 1.0 N B:ILE149 2.5 72.8 1.0 C B:SER146 2.7 79.0 1.0 N B:TRP148 2.8 70.9 1.0 C B:ILE149 2.9 77.2 1.0 O B:SER150 2.9 87.8 1.0 C B:TRP148 3.0 76.5 1.0 CA B:ILE149 3.2 79.5 1.0 CA B:SER150 3.2 72.5 1.0 CA B:SER146 3.3 75.2 1.0 C B:MET147 3.3 68.3 1.0 CA B:TRP148 3.4 70.5 1.0 C B:SER150 3.4 76.3 1.0 CA B:GLY199 3.5 80.1 1.0 N B:MET147 3.5 66.3 1.0 O B:LEU145 3.5 77.0 1.0 O B:TRP148 3.7 74.2 1.0 O B:ILE149 3.7 97.1 1.0 O B:GLY199 3.9 90.3 1.0 CA B:MET147 3.9 66.9 1.0 O B:MET147 3.9 73.8 1.0 CB B:ILE149 4.0 81.8 1.0 C B:GLY199 4.1 82.4 1.0 OG B:SER146 4.2 91.2 1.0 N B:GLY199 4.3 76.3 1.0 N B:SER146 4.3 74.5 1.0 C B:LEU145 4.3 73.3 1.0 CB B:SER146 4.4 82.4 1.0 CB B:SER150 4.6 63.0 1.0 OG1 B:THR154 4.6 63.3 1.0 CB B:TRP148 4.7 60.1 1.0 N B:ASN151 4.7 81.2 1.0 OD1 B:ASN151 4.8 85.7 1.0 CG2 B:ILE149 4.8 78.6 1.0

D.B.Sauer, J.J.Marden, D.N.Wang. Dynamics of Protomer Conformational States Regulate the Transport Cycle of the Homodimeric Dicarboxylate Transporter Vcindy To Be Published.