Calcium in PDB 5hxc: Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 20 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 20 Mm Na+ and Zero CA2+, PDB code: 5hxc 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)	37.72 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.754, 72.560, 95.775, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23

The structure of Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 20 Mm Na+ and Zero CA2+ also contains other interesting chemical elements:

Sodium

(Na)

3 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 20 Mm Na+ and Zero CA2+ (pdb code 5hxc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 20 Mm Na+ and Zero CA2+, PDB code: 5hxc:
Jump to Calcium binding site number: 1; 2;

Calcium 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 20 Mm Na+ and Zero 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 20 Mm Na+ and Zero CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:34.5 occ:0.48 O A:GLY122 2.4 32.6 1.0 O A:ILE118 2.4 31.7 1.0 OD1 A:ASP121 2.4 38.4 0.9 O A:HOH543 2.4 49.8 1.0 O25 A:OLC418 2.5 51.8 1.0 OD2 A:ASP127 2.6 32.9 1.0 CG A:ASP121 3.3 43.9 1.0 C24 A:OLC418 3.4 61.5 1.0 CG A:ASP127 3.5 31.2 1.0 C A:GLY122 3.5 30.9 1.0 C A:ILE118 3.6 34.3 1.0 OD2 A:ASP121 3.6 53.3 0.6 OD1 A:ASP127 3.8 33.1 1.0 O23 A:OLC418 4.0 72.3 1.0 CA A:PHE123 4.1 32.6 1.0 O A:HOH502 4.2 45.6 1.0 N A:PHE123 4.3 28.1 1.0 CA A:GLY119 4.3 27.8 1.0 C22 A:OLC418 4.3 69.8 1.0 C A:ASP121 4.3 36.5 1.0 N A:GLY122 4.4 29.6 1.0 N A:GLY119 4.4 29.5 1.0 N A:SER124 4.4 30.2 1.0 O A:ASP121 4.5 35.7 1.0 CA A:GLY122 4.6 25.3 1.0 CA A:ILE118 4.6 31.9 1.0 CB A:ASP121 4.6 36.5 1.0 N A:ASP121 4.7 32.2 1.0 CB A:ASP127 4.8 25.3 1.0 C A:GLY119 4.8 31.8 1.0 C A:PHE123 4.8 32.7 1.0 CA A:ASP121 4.8 34.4 1.0 CB A:ILE118 4.8 34.6 1.0

Calcium 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 20 Mm Na+ and Zero CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 20 Mm Na+ and Zero CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:74.5 occ:1.00 ND1 A:HIS33 3.0 42.3 0.4 ND1 A:HIS33 3.1 40.3 0.6 CE1 A:HIS33 3.6 46.0 0.4 CE1 A:HIS33 3.8 38.4 0.6 CG A:HIS33 4.2 37.9 0.4 CG A:HIS33 4.2 41.5 0.6 CG2 A:VAL161 4.2 49.8 1.0 CA A:HIS33 4.5 33.9 0.6 CA A:HIS33 4.5 34.0 0.4 CB A:HIS33 4.6 36.6 0.6 CB A:HIS33 4.7 36.7 0.4 O A:HIS33 4.8 35.4 1.0 O A:HOH520 4.8 33.7 1.0 NE2 A:HIS33 4.8 40.5 0.4

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