Sodium in PDB 5hxc: Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 20 Mm Na+ and Zero CA2+

The structure of Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 20 Mm Na+ and Zero CA2+, PDB code: 5hxc 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)	37.72 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.754, 72.560, 95.775, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23

The structure of Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 20 Mm Na+ and Zero CA2+ also contains other interesting chemical elements:

Calcium

(Ca)

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 20 Mm Na+ and Zero CA2+ (pdb code 5hxc). 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 20 Mm Na+ and Zero CA2+, PDB code: 5hxc:
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 20 Mm Na+ and Zero 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 20 Mm Na+ and Zero CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:22.4 occ:0.99 OE2 A:GLU213 2.3 26.0 1.0 OG1 A:THR50 2.3 21.2 1.0 OG A:SER236 2.3 20.8 1.0 O A:ALA47 2.3 24.9 1.0 OG A:SER51 2.5 25.4 1.0 N A:SER51 2.9 25.4 1.0 CB A:SER236 3.0 26.9 1.0 CD A:GLU213 3.2 27.6 1.0 CB A:SER51 3.2 25.8 1.0 C A:THR50 3.3 27.8 1.0 C A:ALA47 3.3 27.3 1.0 CB A:THR50 3.4 25.0 1.0 CA A:SER51 3.4 26.5 1.0 CG A:GLU213 3.5 24.3 1.0 CA A:ALA47 3.6 23.5 1.0 CA A:SER236 3.7 24.6 1.0 CA A:THR50 3.8 29.7 1.0 O A:THR50 3.9 23.9 1.0 N A:THR50 4.1 28.4 1.0 O A:HOH503 4.1 21.7 1.0 OE1 A:GLU213 4.2 26.4 1.0 O A:MET46 4.3 28.0 1.0 OD1 A:ASN232 4.4 35.2 1.0 CB A:ALA47 4.4 21.8 1.0 NA A:NA405 4.5 23.0 1.0 N A:ILE48 4.5 26.0 1.0 N A:SER236 4.6 20.5 1.0 CG2 A:THR50 4.7 23.0 1.0 N A:ALA47 4.8 24.7 1.0 C A:SER236 4.8 19.4 1.0 O A:ASN232 4.9 23.8 1.0 O A:SER236 4.9 24.0 1.0 C A:SER51 4.9 28.2 1.0 C A:MET46 5.0 26.7 1.0 O A:ILE48 5.0 25.3 1.0 C A:ILE48 5.0 27.9 1.0 CB A:GLU213 5.0 21.1 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 20 Mm Na+ and Zero 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 20 Mm Na+ and Zero CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:27.8 occ:0.67 OG A:SER77 2.2 26.9 1.0 OE2 A:GLU54 2.2 30.9 1.0 O A:ALA206 2.3 34.0 0.6 OG1 A:THR209 2.4 28.6 0.6 OG1 A:THR209 2.5 30.0 0.4 OG A:SER210 2.6 33.5 0.6 CD A:GLU54 2.9 29.6 1.0 CB A:SER77 3.0 28.1 1.0 N A:SER210 3.1 28.7 0.6 N A:SER210 3.1 28.8 0.4 CB A:SER210 3.2 31.7 0.4 CG A:GLU54 3.2 26.0 1.0 C A:THR209 3.2 28.3 0.6 C A:THR209 3.3 28.4 0.4 C A:ALA206 3.3 37.3 0.6 CB A:SER210 3.3 31.7 0.6 CB A:THR209 3.4 30.7 0.4 CB A:THR209 3.4 30.9 0.6 O A:ALA206 3.4 38.0 0.4 CA A:SER210 3.4 31.9 0.4 CA A:SER210 3.5 32.0 0.6 O A:THR209 3.7 29.6 0.4 O A:THR209 3.7 29.7 0.6 CA A:ALA206 3.7 34.0 0.6 CA A:THR209 3.8 30.5 0.6 CA A:SER77 3.9 27.8 1.0 OG A:SER210 3.9 29.1 0.4 CA A:THR209 3.9 30.5 0.4 OE1 A:GLU54 4.0 33.0 1.0 O A:HOH503 4.1 21.7 1.0 NA A:NA405 4.2 23.0 1.0 OD1 A:ASN73 4.3 43.9 1.0 CB A:ALA206 4.3 19.9 0.6 N A:THR209 4.3 27.0 0.6 N A:PHE207 4.5 31.0 0.6 N A:THR209 4.5 27.2 0.4 O A:ASN73 4.6 25.3 1.0 C A:ALA206 4.6 36.7 0.4 N A:SER77 4.7 26.8 1.0 CG2 A:THR209 4.7 31.9 0.4 CG2 A:THR209 4.7 31.9 0.6 CB A:GLU54 4.8 27.2 1.0 O A:VAL205 4.8 34.3 0.6 O A:PHE207 4.9 36.6 0.6 C A:SER210 5.0 28.5 0.4 CA A:PHE207 5.0 35.2 0.6 C A:SER210 5.0 28.5 0.6

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 20 Mm Na+ and Zero CA2+


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 20 Mm Na+ and Zero CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:23.0 occ:0.97 O A:THR209 2.2 29.7 0.6 O A:THR209 2.2 29.6 0.4 OE1 A:GLU54 2.3 33.0 1.0 OE1 A:GLU213 2.3 26.4 1.0 O A:THR50 2.3 23.9 1.0 OE2 A:GLU54 2.5 30.9 1.0 OE2 A:GLU213 2.6 26.0 1.0 CD A:GLU54 2.7 29.6 1.0 CD A:GLU213 2.8 27.6 1.0 C A:THR209 3.3 28.3 0.6 C A:THR209 3.3 28.4 0.4 C A:THR50 3.4 27.8 1.0 O A:HOH503 3.7 21.7 1.0 CA A:SER51 3.8 26.5 1.0 CA A:SER210 3.9 31.9 0.4 CA A:SER210 3.9 32.0 0.6 N A:SER51 4.0 25.4 1.0 N A:SER210 4.0 28.7 0.6 N A:SER210 4.0 28.8 0.4 NA A:NA404 4.2 27.8 0.7 CG A:GLU54 4.2 26.0 1.0 CG A:GLU213 4.3 24.3 1.0 CD A:PRO53 4.3 28.2 1.0 CA A:THR209 4.4 30.5 0.6 CD A:PRO212 4.4 24.4 1.0 CG A:PRO53 4.4 32.0 1.0 CA A:THR209 4.5 30.5 0.4 NA A:NA403 4.5 22.4 1.0 CA A:THR50 4.5 29.7 1.0 CB A:THR209 4.5 30.9 0.6 CB A:THR50 4.5 25.0 1.0 CG A:PRO212 4.5 30.4 1.0 CB A:PRO53 4.6 32.6 1.0 C A:SER51 4.6 28.2 1.0 OG A:SER51 4.6 25.4 1.0 C A:SER210 4.7 28.5 0.4 C A:SER210 4.7 28.5 0.6 OG A:SER210 4.7 33.5 0.6 CB A:THR209 4.7 30.7 0.4 CB A:PRO212 4.7 21.3 1.0 N A:GLU54 4.7 20.7 1.0 N A:GLU213 4.8 24.9 1.0 CB A:SER51 4.8 25.8 1.0 CB A:SER210 4.9 31.7 0.4 CB A:SER210 4.9 31.7 0.6 OG1 A:THR50 4.9 21.2 1.0 OG1 A:THR209 5.0 28.6 0.6 CB A:GLU54 5.0 27.2 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