Strontium in PDB 5jdl: 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 1MM SR2+

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 1MM SR2+, PDB code: 5jdl 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)	41.05 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.764, 72.622, 95.616, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 27.2

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 1MM SR2+ also contains other interesting chemical elements:

Chlorine

(Cl)

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 2.5 Mm Na+ and 1MM SR2+ (pdb code 5jdl). 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 2.5 Mm Na+ and 1MM SR2+, PDB code: 5jdl:
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 2.5 Mm Na+ and 1MM 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 2.5 Mm Na+ and 1MM SR2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr401 b:74.0 occ:1.00 O23 A:OLC404 2.5 72.7 1.0 O A:HOH502 2.5 66.6 1.0 O A:ILE118 2.5 63.3 1.0 OD2 A:ASP127 2.6 59.7 1.0 O A:GLY122 2.6 69.6 1.0 CB A:ASP121 3.0 65.1 1.0 C A:GLY122 3.4 63.5 1.0 N A:GLY122 3.5 66.8 1.0 CG A:ASP127 3.6 60.6 1.0 C A:ILE118 3.7 60.8 1.0 C22 A:OLC404 3.8 77.0 1.0 CA A:ASP121 3.8 70.9 1.0 C A:ASP121 3.9 69.8 1.0 CG A:ASP121 3.9 88.1 1.0 OD1 A:ASP127 4.0 62.3 1.0 N A:ASP121 4.1 77.8 1.0 CA A:GLY122 4.1 65.2 1.0 C24 A:OLC404 4.3 75.0 1.0 N A:PHE123 4.3 60.8 1.0 OD2 A:ASP121 4.3 94.8 1.0 C21 A:OLC404 4.3 85.9 1.0 CA A:GLY119 4.5 57.6 1.0 CA A:PHE123 4.5 59.7 1.0 N A:GLY119 4.5 59.8 1.0 O20 A:OLC404 4.6 95.9 1.0 N A:SER124 4.6 56.4 1.0 CA A:ILE118 4.7 68.5 1.0 C A:GLY119 4.7 62.1 1.0 CB A:ASP127 4.7 51.5 1.0 OD1 A:ASP121 4.7 97.3 1.0 O A:ASP121 4.8 65.2 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 2.5 Mm Na+ and 1MM 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 2.5 Mm Na+ and 1MM SR2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr402 b:68.4 occ:0.49 OE1 A:GLU54 2.4 64.3 1.0 OE2 A:GLU54 2.4 71.2 1.0 O A:THR50 2.4 67.2 1.0 OE1 A:GLU213 2.5 63.1 1.0 OE2 A:GLU213 2.6 66.3 1.0 O A:THR209 2.7 70.2 1.0 CD A:GLU54 2.7 66.3 1.0 CD A:GLU213 2.9 64.6 1.0 O A:HOH501 3.0 58.0 1.0 C A:THR50 3.3 59.6 1.0 CA A:SER51 3.5 57.2 1.0 C A:THR209 3.7 69.1 1.0 N A:SER51 3.8 60.0 1.0 OG A:SER51 4.0 56.6 1.0 CG A:GLU54 4.2 65.1 1.0 CB A:SER51 4.3 53.7 1.0 CG A:GLU213 4.4 55.6 1.0 C A:SER51 4.4 61.5 1.0 CD A:PRO53 4.5 61.9 1.0 CA A:THR50 4.5 57.5 1.0 CA A:SER210 4.5 64.6 1.0 N A:SER210 4.6 67.1 1.0 CB A:THR50 4.6 57.6 1.0 CG A:PRO53 4.7 65.4 1.0 CA A:THR209 4.7 71.2 1.0 CB A:THR209 4.7 66.6 1.0 CB A:PRO53 4.7 60.9 1.0 N A:GLU54 4.8 61.2 1.0 O A:SER51 4.9 57.5 1.0 CB A:PRO212 4.9 62.0 1.0 CG A:PRO212 4.9 62.7 1.0 CB A:GLU54 4.9 63.8 1.0 CD A:PRO212 5.0 56.1 1.0 OD1 A:ASP240 5.0 54.5 1.0 OG1 A:THR50 5.0 58.0 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