Sodium in PDB 5hwy: Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 10 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 10 Mm Na+ and Zero CA2+, PDB code: 5hwy 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)	36.02 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.213, 71.966, 95.633, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.3

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 10 Mm Na+ and Zero CA2+ (pdb code 5hwy). 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 10 Mm Na+ and Zero CA2+, PDB code: 5hwy:
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 10 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 10 Mm Na+ and Zero CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:29.6 occ:0.92 OG1 A:THR50 2.4 26.9 1.0 OE2 A:GLU213 2.4 33.2 1.0 O A:ALA47 2.4 29.8 1.0 OG A:SER51 2.4 32.5 1.0 OG A:SER236 2.5 26.5 1.0 N A:SER51 2.9 28.1 1.0 CB A:SER236 3.2 23.2 1.0 CB A:SER51 3.2 27.0 1.0 C A:THR50 3.2 27.9 1.0 CD A:GLU213 3.2 38.4 1.0 CB A:THR50 3.3 28.2 1.0 CA A:SER51 3.4 27.9 1.0 C A:ALA47 3.4 27.4 1.0 CG A:GLU213 3.4 33.3 1.0 CA A:THR50 3.7 27.0 1.0 CA A:ALA47 3.7 24.7 1.0 O A:HOH501 3.7 34.2 1.0 CA A:SER236 3.8 24.5 1.0 O A:THR50 3.8 27.7 1.0 N A:THR50 4.1 28.4 1.0 OE1 A:GLU213 4.4 39.0 1.0 O A:MET46 4.4 28.0 1.0 NA A:NA403 4.5 33.9 0.9 CB A:ALA47 4.5 23.2 1.0 N A:ILE48 4.6 27.9 1.0 CG2 A:THR50 4.7 27.5 1.0 N A:SER236 4.8 22.5 1.0 C A:SER236 4.8 23.4 1.0 O A:ASN232 4.8 26.3 1.0 OD1 A:ASN232 4.8 28.6 0.6 O A:SER236 4.9 26.9 1.0 C A:SER51 4.9 31.0 1.0 N A:ALA47 4.9 25.5 1.0 CB A:GLU213 4.9 30.2 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 10 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 10 Mm Na+ and Zero CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:33.9 occ:0.87 O A:THR50 2.3 27.7 1.0 O A:THR209 2.3 34.2 1.0 OE1 A:GLU213 2.3 39.0 1.0 OE1 A:GLU54 2.3 41.0 1.0 OE2 A:GLU54 2.4 46.7 1.0 OE2 A:GLU213 2.4 33.2 1.0 CD A:GLU54 2.7 42.1 1.0 CD A:GLU213 2.7 38.4 1.0 C A:THR50 3.4 27.9 1.0 C A:THR209 3.5 32.1 1.0 O A:HOH501 3.5 34.2 1.0 CA A:SER51 3.9 27.9 1.0 N A:SER51 4.0 28.1 1.0 CG A:GLU213 4.2 33.3 1.0 CG A:GLU54 4.2 37.3 1.0 CA A:SER210 4.2 32.5 1.0 N A:SER210 4.3 28.9 1.0 CD A:PRO53 4.4 32.1 1.0 CA A:THR50 4.4 27.0 1.0 CD A:PRO212 4.5 28.7 1.0 NA A:NA402 4.5 29.6 0.9 CA A:THR209 4.5 31.6 1.0 CG A:PRO53 4.5 31.7 1.0 CB A:THR50 4.5 28.2 1.0 CB A:PRO212 4.5 27.9 1.0 CG A:PRO212 4.5 29.9 1.0 CB A:PRO53 4.6 32.3 1.0 C A:SER51 4.6 31.0 1.0 N A:GLU213 4.6 27.2 1.0 C A:SER210 4.7 37.2 1.0 OG A:SER51 4.7 32.5 1.0 O A:HOH503 4.8 37.0 1.0 N A:GLU54 4.8 28.1 1.0 CB A:THR209 4.8 30.5 1.0 CB A:GLU213 4.9 30.2 1.0 CB A:SER51 4.9 27.0 1.0 O A:SER210 5.0 30.7 1.0 CB A:GLU54 5.0 30.7 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