Calcium in PDB 5jdh: 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 CA2+

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 CA2+, PDB code: 5jdh 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)	31.21 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.883, 72.218, 96.099, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.7

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 CA2+ also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

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 10 Mm Na+ and 10MM CA2+ (pdb code 5jdh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 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 10 Mm Na+ and 10MM CA2+, PDB code: 5jdh:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 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 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 10 Mm Na+ and 10MM CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:41.4 occ:1.00 O A:ILE118 2.3 35.1 1.0 O A:GLY122 2.4 38.4 1.0 O A:HOH540 2.4 45.4 1.0 OD1 A:ASP121 2.5 47.4 1.0 OD2 A:ASP127 2.5 38.6 1.0 O A:HOH531 2.8 49.8 1.0 CG A:ASP121 3.3 41.8 1.0 CG A:ASP127 3.5 37.9 1.0 C A:ILE118 3.5 37.3 1.0 C A:GLY122 3.6 43.3 1.0 OD2 A:ASP121 3.6 55.6 1.0 O A:HOH528 3.6 67.1 1.0 OD1 A:ASP127 3.8 39.2 1.0 C A:ASP121 4.3 45.4 1.0 CA A:PHE123 4.3 35.9 1.0 O A:HOH504 4.3 53.9 1.0 N A:GLY122 4.3 39.0 1.0 N A:PHE123 4.3 34.9 1.0 O A:ASP121 4.4 46.7 1.0 N A:SER124 4.4 28.7 1.0 CA A:ILE118 4.4 38.7 1.0 N A:GLY119 4.4 42.7 1.0 CA A:GLY119 4.5 40.2 1.0 CA A:GLY122 4.5 32.8 1.0 CB A:ASP121 4.6 40.1 1.0 N A:ASP121 4.7 41.1 1.0 CB A:ILE118 4.7 32.6 1.0 CA A:ASP121 4.7 41.6 1.0 CB A:ASP127 4.8 37.0 1.0 OG A:SER124 4.9 40.5 1.0 C A:PHE123 4.9 38.5 1.0 C A:GLY119 4.9 41.0 1.0 O23 A:OLC422 5.0 81.9 1.0

Calcium binding site 2 out of 3 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 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 10 Mm Na+ and 10MM CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:40.6 occ:0.52 CA A:CA404 0.0 40.6 0.5 O A:THR209 2.2 38.1 1.0 OE1 A:GLU213 2.3 50.2 1.0 O A:THR50 2.3 39.7 1.0 OE2 A:GLU213 2.3 56.4 1.0 OE1 A:GLU54 2.3 44.1 0.9 OE2 A:GLU54 2.6 42.3 1.0 CD A:GLU213 2.6 44.6 1.0 CD A:GLU54 2.8 55.3 1.0 CA A:CA404 3.1 48.8 0.5 C A:THR50 3.4 41.0 1.0 C A:THR209 3.4 42.0 1.0 CA A:SER51 3.8 43.1 1.0 O A:HOH509 3.9 55.2 0.6 N A:SER51 4.0 37.6 1.0 CG A:GLU213 4.1 37.1 1.0 CA A:SER210 4.2 41.2 1.0 N A:SER210 4.2 40.2 1.0 NA A:NA402 4.3 36.3 0.7 CG A:GLU54 4.3 53.7 1.0 CA A:THR209 4.4 47.6 1.0 CA A:THR50 4.5 33.8 1.0 CD A:PRO53 4.5 48.2 1.0 OG A:SER51 4.5 42.9 1.0 CB A:THR50 4.5 38.5 1.0 CG A:PRO53 4.6 52.4 1.0 CB A:THR209 4.6 47.2 1.0 C A:SER51 4.6 39.6 1.0 CB A:PRO53 4.6 44.2 1.0 CD A:PRO212 4.6 36.4 1.0 CB A:SER51 4.8 47.5 1.0 N A:GLU54 4.8 42.7 1.0 CG A:PRO212 4.8 42.0 1.0 C A:SER210 4.9 42.8 1.0 OG1 A:THR50 4.9 33.4 1.0 N A:GLU213 4.9 32.4 1.0 CB A:GLU213 4.9 42.9 1.0 OG1 A:THR209 5.0 43.5 1.0 CB A:PRO212 5.0 29.8 1.0 CB A:GLU54 5.0 37.9 1.0

Calcium binding site 3 out of 3 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 CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 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 CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:48.8 occ:0.48 CA A:CA404 0.0 48.8 0.5 OE2 A:GLU54 2.4 42.3 1.0 O A:HOH509 2.5 55.2 0.6 OE2 A:GLU213 2.5 56.4 1.0 OD2 A:ASP240 2.7 48.1 1.0 CD A:GLU54 2.8 55.3 1.0 OD1 A:ASP240 2.8 39.1 1.0 CG A:ASP240 3.1 45.3 1.0 CA A:CA404 3.1 40.6 0.5 OE1 A:GLU54 3.3 44.1 0.9 CD A:GLU213 3.4 44.6 1.0 OG A:SER51 3.6 42.9 1.0 CG A:GLU54 3.6 53.7 1.0 CB A:SER77 3.7 34.4 1.0 ND2 A:ASN81 3.8 39.0 1.0 OE1 A:GLU213 4.0 50.2 1.0 OG A:SER77 4.1 55.3 1.0 NA A:NA402 4.2 36.3 0.7 CB A:SER236 4.4 30.2 1.0 CG A:GLU213 4.4 37.1 1.0 O A:SER236 4.5 25.1 1.0 CB A:SER51 4.5 47.5 1.0 CB A:GLU54 4.5 37.9 1.0 CA A:SER51 4.5 43.1 1.0 OD1 A:ASN81 4.6 41.1 1.0 O A:THR209 4.6 38.1 1.0 CG A:ASN81 4.6 38.8 1.0 CB A:ASP240 4.6 33.3 1.0 OG A:SER210 4.7 56.9 1.0 O A:THR50 4.8 39.7 1.0 C A:SER236 4.9 23.7 1.0 OG A:SER236 4.9 31.4 1.0 CA A:SER77 4.9 41.2 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