Strontium 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:

Sodium

(Na)

1 atom

The binding sites of Strontium 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 Strontium atom.
In total 2 binding sites of Strontium 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 10MM SR2+, PDB code: 5jdn:
Jump to Strontium binding site number: 1; 2;

Strontium 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 10MM SR2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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:Sr402 b:38.2 occ:0.41 OE1 A:GLU213 2.3 39.6 1.0 OE2 A:GLU213 2.4 43.8 1.0 OE1 A:GLU54 2.5 40.4 1.0 OE2 A:GLU54 2.5 46.1 1.0 O A:THR209 2.5 37.3 1.0 O A:THR50 2.5 38.6 1.0 CD A:GLU213 2.7 45.8 1.0 CD A:GLU54 2.8 44.4 1.0 O A:HOH504 2.8 42.5 1.0 C A:THR209 3.5 38.5 1.0 C A:THR50 3.5 38.0 1.0 CA A:SER51 4.0 40.8 1.0 CA A:SER210 4.1 42.7 1.0 CG A:GLU213 4.1 32.8 1.0 N A:SER51 4.1 34.9 1.0 NA A:NA401 4.2 36.6 0.7 N A:SER210 4.2 39.0 1.0 CG A:GLU54 4.3 41.5 1.0 OG A:SER51 4.4 38.7 1.0 CB A:THR50 4.6 34.2 1.0 CA A:THR209 4.6 42.1 1.0 CA A:THR50 4.7 40.2 1.0 CB A:THR209 4.7 40.4 1.0 C A:SER210 4.8 40.7 1.0 CD A:PRO212 4.8 33.1 1.0 CB A:GLU213 4.8 34.6 1.0 CB A:SER51 4.8 33.7 1.0 N A:GLU213 4.9 37.3 1.0 OG1 A:THR209 4.9 49.2 1.0 OG1 A:THR50 4.9 34.7 1.0 CD A:PRO53 4.9 40.2 1.0 C A:SER51 4.9 38.9 1.0 OG A:SER210 5.0 51.6 1.0 CG A:PRO212 5.0 41.7 1.0

Strontium 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 10MM SR2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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 10MM SR2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr403 b:39.9 occ:1.00 O A:ILE118 2.4 37.7 1.0 OD1 A:ASP121 2.5 52.7 1.0 O A:GLY122 2.6 38.7 1.0 OD2 A:ASP127 2.6 38.5 1.0 O23 A:OLC404 2.6 61.1 1.0 O25 A:OLC404 2.8 72.4 1.0 C24 A:OLC404 2.9 62.9 1.0 C22 A:OLC404 3.3 70.9 1.0 CG A:ASP127 3.5 42.3 1.0 CG A:ASP121 3.6 48.0 1.0 C A:ILE118 3.6 41.6 1.0 C A:GLY122 3.7 40.5 1.0 O A:HOH502 3.8 52.8 1.0 OD1 A:ASP127 3.8 47.2 1.0 OD2 A:ASP121 4.1 53.8 1.0 CA A:PHE123 4.3 35.0 1.0 N A:PHE123 4.4 37.3 1.0 N A:SER124 4.4 32.8 1.0 C A:ASP121 4.4 42.4 1.0 O A:ASP121 4.5 47.4 1.0 CA A:GLY119 4.5 36.6 1.0 N A:GLY119 4.5 41.0 1.0 C21 A:OLC404 4.6 79.9 1.0 CA A:ILE118 4.6 40.2 1.0 N A:GLY122 4.6 40.4 1.0 CA A:GLY122 4.7 38.8 1.0 N A:ASP121 4.8 44.5 1.0 CB A:ILE118 4.8 39.0 1.0 CB A:ASP121 4.8 43.5 1.0 OG A:SER124 4.8 43.4 1.0 CB A:ASP127 4.9 42.4 1.0 C A:PHE123 4.9 40.0 1.0 CA A:ASP121 4.9 39.1 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