Sodium in PDB 5xar: Structural Insights Into the Elevator-Like Mechanism of the Sodium/Citrate Symporter Cits

The structure of Structural Insights Into the Elevator-Like Mechanism of the Sodium/Citrate Symporter Cits, PDB code: 5xar was solved by M.S.Jin, J.W.Kim, S.Kim, S.Kim, H.Lee, J.-O.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	93.49 / 3.62
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.367, 163.994, 93.670, 90.00, 93.50, 90.00
R / Rfree (%)	23.5 / 26.7

The binding sites of Sodium atom in the Structural Insights Into the Elevator-Like Mechanism of the Sodium/Citrate Symporter Cits (pdb code 5xar). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structural Insights Into the Elevator-Like Mechanism of the Sodium/Citrate Symporter Cits, PDB code: 5xar:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structural Insights Into the Elevator-Like Mechanism of the Sodium/Citrate Symporter Cits


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Insights Into the Elevator-Like Mechanism of the Sodium/Citrate Symporter Cits within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:0.9 occ:1.00 O A:ILE181 2.1 0.3 1.0 O A:ASN401 2.2 0.8 1.0 O A:MET399 2.3 0.9 1.0 O A:GLY183 2.6 0.8 1.0 C A:ALA400 2.9 0.3 1.0 O A:ALA400 2.9 0.4 1.0 CA A:ALA400 3.2 0.4 1.0 C A:ASN401 3.2 0.2 1.0 C A:ILE181 3.3 0.4 1.0 C A:MET399 3.3 0.1 1.0 N A:ASN401 3.3 0.2 1.0 N A:ALA400 3.6 0.2 1.0 C A:MET182 3.7 0.8 1.0 C A:GLY183 3.7 0.3 1.0 O A:MET182 3.8 0.2 1.0 CA A:ASN401 3.9 0.5 1.0 CA A:MET182 4.0 1.0 1.0 N A:MET182 4.0 0.8 1.0 N A:GLY183 4.1 0.4 1.0 OD1 A:ASN401 4.3 0.5 1.0 O A:HOH601 4.3 0.6 1.0 N A:ARG402 4.3 0.5 1.0 CA A:ILE181 4.4 0.9 1.0 N A:GLY185 4.4 0.7 1.0 CD2 A:LEU216 4.5 0.3 1.0 O A:PRO180 4.5 0.8 1.0 CA A:GLY183 4.5 0.4 1.0 N A:GLY403 4.6 1.0 1.0 CA A:MET399 4.6 0.6 1.0 CB A:ALA400 4.7 0.8 1.0 N A:GLY184 4.7 0.3 1.0 CA A:ARG402 4.7 0.5 1.0 CA A:GLY184 4.7 0.9 1.0 CG2 A:ILE181 4.9 0.9 1.0 CG A:LEU216 5.0 0.2 1.0

Sodium binding site 2 out of 4 in the Structural Insights Into the Elevator-Like Mechanism of the Sodium/Citrate Symporter Cits


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Insights Into the Elevator-Like Mechanism of the Sodium/Citrate Symporter Cits within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:0.3 occ:1.00 O B:ASN401 2.0 0.9 1.0 O B:GLY183 2.3 0.5 1.0 O B:ILE181 2.5 0.7 1.0 C B:ASN401 3.1 0.8 1.0 O B:MET399 3.2 0.7 1.0 O B:ALA400 3.3 0.8 1.0 C B:ALA400 3.5 0.3 1.0 C B:GLY183 3.5 1.0 1.0 N B:GLY185 3.6 0.2 1.0 C B:ILE181 3.6 0.8 1.0 CD2 B:LEU216 3.7 0.8 1.0 N B:ASN401 3.8 0.6 1.0 N B:ARG402 3.9 0.2 1.0 CA B:ALA400 4.1 0.8 1.0 CA B:ASN401 4.1 0.1 1.0 CA B:ARG402 4.1 0.1 1.0 N B:GLY403 4.1 0.5 1.0 C B:MET399 4.1 0.8 1.0 C B:MET182 4.2 0.3 1.0 O B:HOH601 4.2 0.3 1.0 O B:PRO180 4.2 0.5 1.0 N B:GLY183 4.3 0.5 1.0 CA B:GLY184 4.3 0.7 1.0 CG B:LEU216 4.3 0.4 1.0 CA B:GLY185 4.3 0.3 1.0 O B:MET182 4.3 0.3 1.0 N B:GLY184 4.4 0.4 1.0 C B:GLY184 4.4 0.9 1.0 CA B:GLY183 4.5 0.8 1.0 N B:ALA400 4.5 0.1 1.0 N B:MET182 4.5 0.8 1.0 CA B:ILE181 4.5 0.5 1.0 OD1 B:ASN401 4.5 0.9 1.0 CA B:MET182 4.6 0.5 1.0 C B:ARG402 4.6 0.8 1.0 CD1 B:LEU216 4.7 0.3 1.0

Sodium binding site 3 out of 4 in the Structural Insights Into the Elevator-Like Mechanism of the Sodium/Citrate Symporter Cits


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structural Insights Into the Elevator-Like Mechanism of the Sodium/Citrate Symporter Cits within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:0.1 occ:1.00 O C:GLY183 2.1 0.2 1.0 O C:ASN401 2.2 1.0 1.0 O C:ILE181 2.3 0.1 1.0 O C:MET399 2.9 0.8 1.0 O C:ALA400 3.3 0.1 1.0 C C:ASN401 3.4 0.5 1.0 C C:GLY183 3.4 0.4 1.0 C C:ILE181 3.4 0.2 1.0 C C:ALA400 3.5 1.0 1.0 O C:HOH601 3.7 0.3 1.0 N C:GLY185 3.8 0.4 1.0 C C:MET182 3.8 0.8 1.0 N C:ASN401 3.9 0.7 1.0 CA C:ALA400 3.9 0.3 1.0 N C:GLY183 4.0 0.0 1.0 C C:MET399 4.0 0.9 1.0 CD2 C:LEU216 4.0 0.3 1.0 O C:MET182 4.0 0.6 1.0 O C:PRO180 4.1 0.5 1.0 CA C:GLY183 4.2 0.4 1.0 N C:MET182 4.2 0.6 1.0 CA C:ASN401 4.2 0.7 1.0 N C:ARG402 4.2 0.7 1.0 CA C:MET182 4.3 0.3 1.0 CA C:GLY184 4.3 0.1 1.0 N C:GLY403 4.3 0.9 1.0 N C:GLY184 4.3 0.9 1.0 N C:ALA400 4.4 0.1 1.0 CA C:ILE181 4.4 0.1 1.0 CA C:ARG402 4.4 0.2 1.0 CG C:LEU216 4.4 0.4 1.0 CA C:GLY185 4.5 0.2 1.0 C C:GLY184 4.5 0.1 1.0 OD1 C:ASN401 4.6 0.3 1.0 CD1 C:LEU216 4.8 0.1 1.0 C C:ARG402 4.9 0.4 1.0

Sodium binding site 4 out of 4 in the Structural Insights Into the Elevator-Like Mechanism of the Sodium/Citrate Symporter Cits


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structural Insights Into the Elevator-Like Mechanism of the Sodium/Citrate Symporter Cits within 5.0Å range: probe atom residue distance (Å) B Occ D:Na501 b:0.9 occ:1.00 O D:ILE181 2.1 0.9 1.0 O D:GLY183 2.2 0.9 1.0 O D:ASN401 2.4 0.3 1.0 C D:ILE181 3.2 0.1 1.0 O D:MET399 3.2 0.3 1.0 O D:ALA400 3.3 0.0 1.0 C D:GLY183 3.4 1.0 1.0 C D:ASN401 3.5 0.4 1.0 C D:ALA400 3.5 0.3 1.0 CD2 D:LEU216 3.7 0.9 1.0 O D:PRO180 3.8 0.9 1.0 N D:GLY185 3.8 0.1 1.0 C D:MET182 3.9 0.8 1.0 N D:GLY183 3.9 0.9 1.0 CA D:ALA400 4.0 0.5 1.0 N D:ASN401 4.0 1.0 1.0 CA D:ILE181 4.1 0.5 1.0 CG D:LEU216 4.1 0.8 1.0 N D:MET182 4.1 0.2 1.0 O D:MET182 4.1 0.9 1.0 O D:HOH601 4.1 1.0 1.0 C D:MET399 4.2 0.5 1.0 CA D:GLY183 4.2 0.4 1.0 CA D:MET182 4.3 0.3 1.0 N D:ARG402 4.3 0.9 1.0 CA D:ASN401 4.4 0.5 1.0 N D:GLY184 4.4 0.4 1.0 CA D:GLY184 4.5 0.7 1.0 CA D:ARG402 4.5 0.0 1.0 CD1 D:LEU216 4.5 0.4 1.0 CA D:GLY185 4.5 0.7 1.0 N D:GLY403 4.5 0.3 1.0 N D:ALA400 4.6 0.4 1.0 C D:GLY184 4.6 0.2 1.0 C D:PRO180 4.7 0.3 1.0 N D:ILE181 4.9 0.4 1.0 OD1 D:ASN401 4.9 0.1 1.0

J.W.Kim, S.Kim, S.Kim, H.Lee, J.O.Lee, M.S.Jin. Structural Insights Into the Elevator-Like Mechanism of the Sodium/Citrate Symporter Cits Sci Rep V. 7 2548 2017.
ISSN: ESSN 2045-2322
PubMed: 28566738
DOI: 10.1038/S41598-017-02794-X