Sodium in PDB 5jdn: Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 10 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 10 Mm Na+ and 10MM SR2+, PDB code: 5jdn 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)	40.14 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.670, 72.463, 96.428, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.9

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 10MM SR2+ also contains other interesting chemical elements:

Strontium

(Sr)

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 10 Mm Na+ and 10MM SR2+ (pdb code 5jdn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was 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 10MM SR2+, PDB code: 5jdn:

Sodium binding site 1 out of 1 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 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 10 Mm Na+ and 10MM SR2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:36.6 occ:0.71 OE2 A:GLU213 2.3 43.8 1.0 OG A:SER236 2.3 30.7 1.0 OG1 A:THR50 2.4 34.7 1.0 OG A:SER51 2.5 38.7 1.0 O A:ALA47 2.5 34.5 1.0 CB A:SER236 3.0 28.8 1.0 N A:SER51 3.1 34.9 1.0 CD A:GLU213 3.2 45.8 1.0 C A:THR50 3.3 38.0 1.0 CB A:SER51 3.3 33.7 1.0 CB A:THR50 3.4 34.2 1.0 C A:ALA47 3.4 35.2 1.0 CA A:SER51 3.5 40.8 1.0 CA A:SER236 3.6 35.2 1.0 CG A:GLU213 3.7 32.8 1.0 CA A:ALA47 3.7 31.1 1.0 O A:THR50 3.8 38.6 1.0 CA A:THR50 3.8 40.2 1.0 O A:HOH504 4.0 42.5 1.0 N A:THR50 4.2 41.9 1.0 SR A:SR402 4.2 38.2 0.4 OE1 A:GLU213 4.2 39.6 1.0 OD1 A:ASN232 4.3 46.5 1.0 O A:MET46 4.3 36.0 1.0 CB A:ALA47 4.5 33.0 1.0 N A:SER236 4.5 31.0 1.0 C A:SER236 4.6 31.1 1.0 N A:ILE48 4.7 33.5 1.0 CG2 A:THR50 4.7 36.5 1.0 O A:SER236 4.8 29.7 1.0 O A:ASN232 4.8 31.6 1.0 N A:ALA47 4.9 27.6 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