Sodium in PDB 5jdg: Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 2.5 Mm Na+ and 0.1MM CA2+

The structure of Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 2.5 Mm Na+ and 0.1MM CA2+, PDB code: 5jdg was solved by J.Liao, Y.X.Jiang, J.D.Faraldo-Gomez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.16 / 2.41
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.477, 72.470, 96.297, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 26.3

The structure of Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 2.5 Mm Na+ and 0.1MM CA2+ also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 2.5 Mm Na+ and 0.1MM CA2+ (pdb code 5jdg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 2.5 Mm Na+ and 0.1MM CA2+, PDB code: 5jdg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 2.5 Mm Na+ and 0.1MM CA2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 2.5 Mm Na+ and 0.1MM CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:41.7 occ:0.70 OG A:SER236 2.3 36.0 1.0 OE2 A:GLU213 2.4 49.1 1.0 OG1 A:THR50 2.4 36.2 1.0 OG A:SER51 2.5 46.1 1.0 O A:ALA47 2.5 40.3 1.0 CB A:SER236 2.9 38.1 1.0 N A:SER51 3.2 44.3 1.0 CD A:GLU213 3.2 39.8 1.0 CG A:GLU213 3.4 36.4 1.0 CB A:SER51 3.4 39.9 1.0 C A:ALA47 3.4 37.4 1.0 CB A:THR50 3.4 33.8 1.0 C A:THR50 3.5 41.2 1.0 CA A:SER236 3.6 36.7 1.0 CA A:SER51 3.6 46.3 1.0 CA A:ALA47 3.6 35.7 1.0 CA A:THR50 3.9 39.9 1.0 O A:THR50 4.1 44.0 1.0 O A:HOH506 4.1 36.0 1.0 N A:THR50 4.3 45.3 1.0 OE1 A:GLU213 4.3 40.2 1.0 OD1 A:ASN232 4.3 49.2 1.0 CB A:ALA47 4.4 40.9 1.0 NA A:NA402 4.4 45.6 0.8 O A:MET46 4.4 45.5 1.0 N A:SER236 4.5 29.7 1.0 O A:ASN232 4.6 37.1 1.0 N A:ILE48 4.6 45.8 1.0 C A:SER236 4.7 35.9 1.0 CG2 A:THR50 4.7 38.2 1.0 N A:ALA47 4.8 42.4 1.0 CB A:GLU213 4.9 36.7 1.0 O A:SER236 4.9 35.2 1.0

Sodium binding site 2 out of 2 in the Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 2.5 Mm Na+ and 0.1MM CA2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 2.5 Mm Na+ and 0.1MM CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:45.6 occ:0.84 OE1 A:GLU54 2.3 47.2 1.0 O A:THR209 2.3 48.9 1.0 O A:THR50 2.3 44.0 1.0 OE2 A:GLU213 2.4 49.1 1.0 OE1 A:GLU213 2.4 40.2 1.0 OE2 A:GLU54 2.5 43.4 1.0 CD A:GLU213 2.7 39.8 1.0 CD A:GLU54 2.7 48.4 1.0 O A:HOH506 3.3 36.0 1.0 C A:THR50 3.3 41.2 1.0 C A:THR209 3.5 51.9 1.0 CA A:SER51 3.7 46.3 1.0 N A:SER51 3.9 44.3 1.0 CG A:GLU213 4.2 36.4 1.0 CG A:GLU54 4.2 46.0 1.0 CA A:SER210 4.2 53.6 1.0 N A:SER210 4.3 54.6 1.0 OG A:SER51 4.4 46.1 1.0 NA A:NA401 4.4 41.7 0.7 CA A:THR209 4.4 50.7 1.0 CD A:PRO53 4.5 43.0 1.0 CA A:THR50 4.5 39.9 1.0 CG A:PRO212 4.5 50.6 1.0 C A:SER51 4.5 45.4 1.0 CB A:THR209 4.5 46.0 1.0 CB A:PRO212 4.5 43.5 1.0 CB A:THR50 4.5 33.8 1.0 CD A:PRO212 4.6 34.8 1.0 CB A:SER51 4.6 39.9 1.0 CG A:PRO53 4.7 45.7 1.0 N A:GLU213 4.8 39.5 1.0 CB A:PRO53 4.8 40.6 1.0 N A:GLU54 4.9 42.2 1.0 C A:SER210 4.9 47.3 1.0 CB A:GLU54 4.9 45.6 1.0 OG1 A:THR50 4.9 36.2 1.0 CB A:GLU213 5.0 36.7 1.0

J.Liao, F.Marinelli, C.Lee, Y.Huang, J.D.Faraldo-Gomez, Y.Jiang. Mechanism of Extracellular Ion Exchange and Binding-Site Occlusion in A Sodium/Calcium Exchanger. Nat.Struct.Mol.Biol. V. 23 590 2016.
ISSN: ESSN 1545-9985
PubMed: 27183196
DOI: 10.1038/NSMB.3230