Sodium in PDB 5jdq: Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 100 Mm Na+ and 10MM SR2+

The structure of Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 100 Mm Na+ and 10MM SR2+, PDB code: 5jdq 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)	36.21 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.876, 72.425, 95.913, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 24.2

The structure of Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 100 Mm Na+ and 10MM SR2+ also contains other interesting chemical elements:

Strontium	(Sr)	1 atom
Chlorine	(Cl)	2 atoms

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 100 Mm Na+ and 10MM SR2+ (pdb code 5jdq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 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 100 Mm Na+ and 10MM SR2+, PDB code: 5jdq:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 100 Mm Na+ and 10MM SR2+


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 100 Mm Na+ and 10MM SR2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:43.1 occ:0.90 OE2 A:GLU213 2.4 48.1 1.0 O A:ALA47 2.4 47.6 1.0 OG1 A:THR50 2.4 47.5 1.0 OG A:SER236 2.4 41.3 1.0 OG A:SER51 2.5 48.0 1.0 CB A:SER236 3.0 44.2 1.0 N A:SER51 3.1 50.8 1.0 CD A:GLU213 3.1 48.7 1.0 C A:THR50 3.3 50.0 1.0 CB A:SER51 3.3 46.1 1.0 C A:ALA47 3.4 45.2 1.0 CG A:GLU213 3.4 45.4 1.0 CB A:THR50 3.4 48.1 1.0 CA A:SER51 3.5 47.9 1.0 CA A:SER236 3.7 46.3 1.0 CA A:ALA47 3.7 44.1 1.0 O A:THR50 3.8 48.2 1.0 CA A:THR50 3.8 50.3 1.0 O A:HOH501 4.0 44.1 1.0 OE1 A:GLU213 4.1 51.3 1.0 N A:THR50 4.2 51.6 1.0 NA A:NA402 4.3 45.7 0.8 O A:MET46 4.4 48.6 1.0 OD1 A:ASN232 4.5 47.6 1.0 CB A:ALA47 4.5 43.3 1.0 N A:ILE48 4.6 46.5 1.0 N A:SER236 4.7 40.4 1.0 C A:SER236 4.7 43.0 1.0 CG2 A:THR50 4.8 47.2 1.0 O A:SER236 4.8 44.6 1.0 O A:ASN232 4.9 39.6 1.0 CB A:GLU213 4.9 43.6 1.0 N A:ALA47 4.9 39.2 1.0

Sodium binding site 2 out of 3 in the Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 100 Mm Na+ and 10MM SR2+


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 100 Mm Na+ and 10MM SR2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:45.7 occ:0.79 O A:THR50 2.3 48.2 1.0 O A:THR209 2.3 55.4 1.0 OE1 A:GLU213 2.3 51.3 1.0 OE1 A:GLU54 2.3 52.6 1.0 OE2 A:GLU54 2.4 48.5 1.0 OE2 A:GLU213 2.4 48.1 1.0 CD A:GLU54 2.7 52.7 1.0 CD A:GLU213 2.7 48.7 1.0 C A:THR50 3.3 50.0 1.0 C A:THR209 3.4 57.0 1.0 O A:HOH501 3.5 44.1 1.0 CA A:SER51 3.8 47.9 1.0 N A:SER51 4.0 50.8 1.0 CA A:SER210 4.1 55.3 1.0 N A:SER210 4.2 55.1 1.0 CG A:GLU54 4.2 52.5 1.0 CG A:GLU213 4.2 45.4 1.0 NA A:NA403 4.3 55.2 0.6 NA A:NA401 4.3 43.1 0.9 CD A:PRO212 4.4 48.2 1.0 CA A:THR209 4.4 56.5 1.0 CD A:PRO53 4.5 52.7 1.0 OG A:SER51 4.5 48.0 1.0 CA A:THR50 4.5 50.3 1.0 CB A:THR209 4.5 59.0 1.0 CB A:THR50 4.5 48.1 1.0 CG A:PRO53 4.6 56.5 1.0 CG A:PRO212 4.6 52.2 1.0 C A:SER51 4.6 51.6 1.0 CB A:PRO53 4.7 54.8 1.0 CB A:SER51 4.7 46.1 1.0 CB A:PRO212 4.8 47.7 1.0 C A:SER210 4.8 53.2 1.0 N A:GLU213 4.8 43.0 1.0 N A:GLU54 4.8 52.9 1.0 OG1 A:THR50 5.0 47.5 1.0 CB A:GLU213 5.0 43.6 1.0 CB A:GLU54 5.0 51.7 1.0 OG1 A:THR209 5.0 59.0 1.0

Sodium binding site 3 out of 3 in the Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 100 Mm Na+ and 10MM SR2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 100 Mm Na+ and 10MM SR2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:55.2 occ:0.60 OE2 A:GLU54 2.3 48.5 1.0 OG A:SER77 2.3 46.8 1.0 OG1 A:THR209 2.4 59.0 1.0 OG A:SER210 2.4 63.6 1.0 O A:ALA206 2.5 56.5 1.0 CB A:SER77 2.9 45.1 1.0 N A:SER210 3.1 55.1 1.0 CD A:GLU54 3.1 52.7 1.0 C A:THR209 3.3 57.0 1.0 CB A:THR209 3.4 59.0 1.0 CG A:GLU54 3.4 52.5 1.0 CA A:SER210 3.4 55.3 1.0 CB A:SER210 3.4 61.9 1.0 C A:ALA206 3.6 64.5 1.0 O A:THR209 3.7 55.4 1.0 CA A:SER77 3.8 46.6 1.0 CA A:THR209 3.9 56.5 1.0 O A:HOH501 3.9 44.1 1.0 CA A:ALA206 4.0 63.4 1.0 OE1 A:GLU54 4.2 52.6 1.0 NA A:NA402 4.3 45.7 0.8 N A:THR209 4.4 53.5 1.0 CB A:ALA206 4.5 51.7 1.0 N A:SER77 4.7 48.4 1.0 CG2 A:THR209 4.7 54.6 1.0 O A:ASN73 4.7 52.4 1.0 N A:PHE207 4.7 61.3 1.0 OD1 A:ASN73 4.8 77.5 1.0 C A:SER77 4.9 45.4 1.0 CB A:GLU54 4.9 51.7 1.0 C A:SER210 4.9 53.2 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