Sodium in PDB 5hwx: 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 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 2.5 Mm Na+ and Zero CA2+, PDB code: 5hwx 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)	39.92 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.702, 72.278, 95.783, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25.4

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 Zero CA2+ also contains other interesting chemical elements:

Chlorine

(Cl)

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 Zero CA2+ (pdb code 5hwx). 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 Zero CA2+, PDB code: 5hwx:
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 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 2.5 Mm Na+ and Zero CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:42.6 occ:0.74 O A:THR209 2.2 46.2 1.0 OE1 A:GLU213 2.3 45.6 1.0 O A:THR50 2.3 42.0 1.0 OE1 A:GLU54 2.3 46.3 1.0 OE2 A:GLU213 2.5 44.3 1.0 OE2 A:GLU54 2.5 52.2 1.0 CD A:GLU213 2.7 45.0 1.0 CD A:GLU54 2.8 50.5 1.0 C A:THR50 3.3 43.6 1.0 C A:THR209 3.4 52.1 1.0 O A:HOH502 3.6 42.5 0.9 CA A:SER51 3.8 44.1 1.0 N A:SER51 4.0 43.0 1.0 CA A:SER210 4.2 50.0 1.0 N A:SER210 4.2 52.5 1.0 CG A:GLU213 4.2 40.2 1.0 CG A:GLU54 4.3 46.7 1.0 NA A:NA402 4.4 41.5 0.8 CG A:PRO212 4.4 50.1 1.0 CB A:PRO212 4.4 43.6 1.0 CA A:THR209 4.4 52.5 1.0 CD A:PRO53 4.4 45.1 1.0 OG A:SER51 4.4 42.5 1.0 CD A:PRO212 4.5 46.3 1.0 CA A:THR50 4.5 41.9 1.0 CB A:THR50 4.5 42.2 1.0 CB A:THR209 4.6 54.7 1.0 CG A:PRO53 4.6 47.0 1.0 C A:SER51 4.6 44.7 1.0 C A:SER210 4.7 49.8 1.0 N A:GLU213 4.7 40.6 1.0 CB A:SER51 4.8 41.1 1.0 CB A:PRO53 4.8 46.8 1.0 N A:GLU54 4.9 45.4 1.0 CB A:GLU213 4.9 38.5 1.0 OG1 A:THR50 5.0 39.0 1.0 O A:SER210 5.0 44.6 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 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 2.5 Mm Na+ and Zero CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:41.5 occ:0.84 OG A:SER236 2.3 38.0 1.0 OG1 A:THR50 2.4 39.0 1.0 OE2 A:GLU213 2.4 44.3 1.0 O A:ALA47 2.4 42.3 1.0 OG A:SER51 2.6 42.5 1.0 N A:SER51 3.0 43.0 1.0 CB A:SER236 3.1 40.7 1.0 CD A:GLU213 3.1 45.0 1.0 CB A:SER51 3.2 41.1 1.0 C A:THR50 3.3 43.6 1.0 CG A:GLU213 3.4 40.2 1.0 CB A:THR50 3.4 42.2 1.0 C A:ALA47 3.4 42.1 1.0 CA A:SER51 3.4 44.1 1.0 CA A:ALA47 3.7 40.8 1.0 CA A:SER236 3.8 40.4 1.0 CA A:THR50 3.8 41.9 1.0 O A:THR50 3.9 42.0 1.0 O A:HOH502 4.0 42.5 0.9 N A:THR50 4.2 44.9 1.0 OE1 A:GLU213 4.2 45.6 1.0 O A:MET46 4.3 43.2 1.0 OD1 A:ASN232 4.4 48.8 1.0 NA A:NA401 4.4 42.6 0.7 CB A:ALA47 4.5 39.7 1.0 N A:ILE48 4.6 42.0 1.0 CG2 A:THR50 4.7 43.8 1.0 N A:SER236 4.7 36.4 1.0 C A:SER236 4.8 38.7 1.0 N A:ALA47 4.8 39.5 1.0 CB A:GLU213 4.9 38.5 1.0 O A:ASN232 4.9 39.6 1.0 C A:SER51 4.9 44.7 1.0 O A:SER236 4.9 40.9 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