Calcium in PDB 5jdg: 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 0.1MM 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 0.1MM CA2+, PDB code: 5jdg 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)	31.16 / 2.41
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.477, 72.470, 96.297, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 26.3

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 0.1MM CA2+ also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Calcium 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 0.1MM CA2+ (pdb code 5jdg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was 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 0.1MM CA2+, PDB code: 5jdg:

Calcium 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 2.5 Mm Na+ and 0.1MM CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 0.1MM CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca427 b:48.2 occ:1.00 O A:ILE118 2.3 47.2 1.0 O A:GLY122 2.3 46.9 1.0 OD2 A:ASP127 2.4 44.0 1.0 OD1 A:ASP121 2.5 56.8 1.0 O A:HOH525 2.5 52.2 1.0 O25 A:OLC410 2.7 72.0 1.0 C24 A:OLC410 3.3 64.2 1.0 CG A:ASP121 3.3 53.8 1.0 CG A:ASP127 3.5 45.1 1.0 C A:GLY122 3.5 43.3 1.0 C A:ILE118 3.6 52.6 1.0 OD2 A:ASP121 3.7 60.8 1.0 OD1 A:ASP127 3.9 51.4 1.0 C21 A:OLC410 4.0 79.2 1.0 C A:ASP121 4.3 47.7 1.0 CA A:PHE123 4.3 45.5 1.0 N A:GLY122 4.3 45.7 1.0 C22 A:OLC410 4.3 78.7 1.0 N A:PHE123 4.3 38.3 1.0 N A:SER124 4.4 40.9 1.0 O A:ASP121 4.4 48.1 1.0 O A:HOH504 4.4 52.9 1.0 CA A:ILE118 4.5 48.5 1.0 N A:GLY119 4.5 48.0 1.0 CA A:GLY119 4.5 43.3 1.0 CA A:GLY122 4.5 45.2 1.0 CB A:ASP121 4.6 44.4 1.0 N A:ASP121 4.6 47.6 1.0 CB A:ILE118 4.7 50.1 1.0 CA A:ASP121 4.7 49.4 1.0 CB A:ASP127 4.7 45.0 1.0 C A:PHE123 4.8 45.8 1.0 C A:GLY119 4.9 48.2 1.0 OG A:SER124 5.0 49.5 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