Calcium in PDB 5hxr: 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 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 2.5 Mm Na+ and 10MM CA2+, PDB code: 5hxr 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)	31.30 / 2.46
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.700, 72.522, 96.942, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 26

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 10MM CA2+ (pdb code 5hxr). 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 2.5 Mm Na+ and 10MM CA2+, PDB code: 5hxr:
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 2.5 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 2.5 Mm Na+ and 10MM CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:62.4 occ:1.00 O A:ILE118 2.4 62.3 1.0 O23 A:OLC404 2.4 66.1 1.0 O A:GLY122 2.4 55.0 1.0 OD2 A:ASP127 2.5 54.4 1.0 OD1 A:ASP121 2.5 73.2 1.0 O A:HOH511 2.6 59.8 0.8 CG A:ASP121 3.3 66.2 1.0 C22 A:OLC404 3.5 74.5 1.0 CG A:ASP127 3.5 56.2 1.0 C A:ILE118 3.6 61.8 1.0 OD2 A:ASP121 3.6 70.2 1.0 C A:GLY122 3.6 57.5 1.0 C24 A:OLC404 3.6 79.3 1.0 OD1 A:ASP127 3.9 57.6 1.0 O25 A:OLC404 3.9 89.7 1.0 C A:ASP121 4.3 59.2 1.0 N A:GLY122 4.4 56.7 1.0 O A:ASP121 4.4 65.1 1.0 CA A:PHE123 4.4 51.8 1.0 N A:PHE123 4.4 52.0 1.0 N A:SER124 4.5 49.4 1.0 CA A:ILE118 4.5 61.8 1.0 N A:GLY119 4.5 57.1 1.0 CA A:GLY119 4.5 58.4 1.0 CB A:ASP121 4.6 58.6 1.0 CA A:GLY122 4.6 59.4 1.0 N A:ASP121 4.7 64.0 1.0 O A:HOH501 4.7 64.3 0.9 CB A:ILE118 4.7 58.5 1.0 CA A:ASP121 4.7 60.7 1.0 C21 A:OLC404 4.8 82.7 1.0 CB A:ASP127 4.8 54.2 1.0 C A:PHE123 4.9 57.7 1.0 C A:GLY119 5.0 63.3 1.0 O20 A:OLC404 5.0 84.1 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 2.5 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 2.5 Mm Na+ and 10MM CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:56.5 occ:0.55 CA A:CA402 0.0 56.5 0.6 O A:THR209 2.3 64.9 1.0 OE2 A:GLU213 2.4 67.3 0.6 OE1 A:GLU213 2.4 61.8 1.0 OE1 A:GLU54 2.4 63.3 1.0 O A:THR50 2.5 67.6 1.0 OE2 A:GLU54 2.6 70.1 1.0 CD A:GLU213 2.7 61.8 1.0 CD A:GLU54 2.8 67.8 0.4 CA A:CA402 3.0 62.9 0.5 O A:HOH506 3.3 71.7 1.0 C A:THR209 3.4 70.1 1.0 C A:THR50 3.5 64.7 1.0 CA A:SER51 3.9 64.8 1.0 CA A:SER210 4.1 63.7 1.0 N A:SER51 4.1 66.7 1.0 N A:SER210 4.2 64.7 1.0 CG A:GLU213 4.2 51.9 1.0 CG A:GLU54 4.4 68.3 1.0 CA A:THR209 4.5 70.9 1.0 OG A:SER51 4.5 65.6 1.0 CB A:THR50 4.5 54.3 1.0 CA A:THR50 4.6 61.8 1.0 CB A:THR209 4.6 65.5 1.0 CG A:PRO53 4.6 76.8 1.0 CB A:PRO53 4.6 71.9 1.0 OG1 A:THR50 4.7 55.0 1.0 CD A:PRO212 4.8 51.0 1.0 C A:SER51 4.8 64.3 1.0 CB A:SER51 4.8 61.7 1.0 C A:SER210 4.9 62.8 1.0 CG A:PRO212 4.9 62.9 1.0 CD A:PRO53 4.9 69.0 1.0 CB A:PRO212 4.9 61.7 1.0 OG1 A:THR209 4.9 70.2 1.0 N A:GLU213 5.0 61.1 1.0 CB A:GLU213 5.0 59.6 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 2.5 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 2.5 Mm Na+ and 10MM CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:62.9 occ:0.45 CA A:CA402 0.0 62.9 0.5 O A:HOH506 2.5 71.7 1.0 OE2 A:GLU54 2.5 70.1 1.0 OD1 A:ASP240 2.5 56.0 1.0 CD A:GLU54 2.8 67.8 0.4 OD2 A:ASP240 2.8 61.4 1.0 OE2 A:GLU213 2.9 67.3 0.6 CA A:CA402 3.0 56.5 0.6 CG A:ASP240 3.0 54.5 1.0 OE1 A:GLU54 3.1 63.3 1.0 OG A:SER51 3.2 65.6 1.0 CG A:GLU54 3.7 68.3 1.0 CD A:GLU213 3.7 61.8 1.0 O A:SER236 4.1 52.6 1.0 CB A:SER51 4.1 61.7 1.0 ND2 A:ASN81 4.2 57.1 1.0 CB A:SER77 4.2 55.5 1.0 CA A:SER51 4.2 64.8 1.0 CB A:SER236 4.3 54.3 1.0 OE1 A:GLU213 4.3 61.8 1.0 CB A:GLU54 4.5 58.0 1.0 OG A:SER77 4.5 71.1 1.0 CB A:ASP240 4.5 56.6 1.0 C A:SER236 4.6 46.1 1.0 O A:THR50 4.6 67.6 1.0 CG A:GLU213 4.7 51.9 1.0 O A:THR209 4.7 64.9 1.0 CA A:SER236 4.8 55.0 1.0 OG A:SER236 4.9 50.7 1.0 N A:SER51 5.0 66.7 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