Calcium in PDB 5jdf: 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 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 1MM CA2+, PDB code: 5jdf 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)	34.52 / 2.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.801, 72.258, 95.803, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 28.1

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 1MM CA2+ (pdb code 5jdf). 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 1MM CA2+, PDB code: 5jdf:
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 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 1MM CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:62.7 occ:0.89 O A:ILE118 2.4 63.9 1.0 O A:GLY122 2.4 69.3 1.0 O A:HOH505 2.4 86.5 1.0 OD2 A:ASP127 2.5 57.4 1.0 OD1 A:ASP121 2.6 72.3 1.0 O25 A:OLC407 2.7 83.4 1.0 CG A:ASP121 3.1 71.2 1.0 OD2 A:ASP121 3.2 76.3 1.0 C A:GLY122 3.4 69.0 1.0 C24 A:OLC407 3.5 83.5 1.0 C A:ILE118 3.6 70.6 1.0 CG A:ASP127 3.6 65.6 1.0 OD1 A:ASP127 4.0 70.4 1.0 N A:GLY122 4.1 63.8 1.0 C A:ASP121 4.1 71.8 1.0 O23 A:OLC407 4.2 0.3 1.0 N A:PHE123 4.2 71.1 1.0 CA A:PHE123 4.3 67.1 1.0 CB A:ASP121 4.3 70.2 1.0 CA A:GLY122 4.3 67.4 1.0 O A:ASP121 4.3 71.9 1.0 N A:SER124 4.4 64.3 1.0 CA A:GLY119 4.4 60.1 1.0 N A:GLY119 4.4 65.1 1.0 N A:ASP121 4.4 71.6 1.0 CA A:ASP121 4.5 75.2 1.0 C22 A:OLC407 4.5 98.6 1.0 CA A:ILE118 4.6 70.5 1.0 C A:GLY119 4.7 57.0 1.0 C A:PHE123 4.9 65.5 1.0 CB A:ASP127 4.9 60.0 1.0 CB A:ILE118 4.9 62.5 1.0 OG A:SER124 4.9 71.8 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 1MM 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 1MM CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:69.9 occ:0.49 CA A:CA402 0.0 69.9 0.5 OE1 A:GLU54 2.3 65.5 1.0 O A:THR50 2.3 71.1 1.0 OE2 A:GLU213 2.3 73.2 1.0 O A:THR209 2.4 72.2 1.0 OE1 A:GLU213 2.4 64.8 1.0 OE2 A:GLU54 2.5 73.3 1.0 CD A:GLU213 2.7 67.3 1.0 CD A:GLU54 2.7 69.6 1.0 CA A:CA402 3.0 79.7 0.5 C A:THR50 3.3 67.9 1.0 C A:THR209 3.5 74.0 1.0 CA A:SER51 3.6 62.6 1.0 N A:SER51 3.9 66.8 1.0 CG A:GLU213 4.1 53.8 1.0 CG A:GLU54 4.2 69.5 1.0 N A:SER210 4.3 70.8 1.0 CA A:THR209 4.3 74.2 1.0 OG A:SER51 4.4 66.8 1.0 CB A:THR209 4.4 72.8 1.0 CA A:SER210 4.4 65.6 1.0 CD A:PRO53 4.4 69.7 1.0 C A:SER51 4.4 68.3 1.0 CG A:PRO53 4.4 78.8 1.0 CB A:PRO53 4.5 73.4 1.0 CA A:THR50 4.5 64.9 1.0 CB A:SER51 4.6 66.4 1.0 CB A:THR50 4.6 62.3 1.0 N A:GLU54 4.8 68.8 1.0 CD A:PRO212 4.8 55.6 1.0 O A:SER51 4.9 63.2 1.0 CG A:PRO212 4.9 73.6 1.0 CB A:PRO212 4.9 71.8 1.0 CB A:GLU54 5.0 69.7 1.0 OG1 A:THR209 5.0 78.9 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 2.5 Mm Na+ and 1MM 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 1MM CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:79.7 occ:0.45 CA A:CA402 0.0 79.7 0.5 OE2 A:GLU213 2.1 73.2 1.0 OE2 A:GLU54 2.2 73.3 1.0 OD2 A:ASP240 2.8 63.1 1.0 CD A:GLU54 2.9 69.6 1.0 CA A:CA402 3.0 69.9 0.5 OD1 A:ASP240 3.1 66.9 1.0 CD A:GLU213 3.2 67.3 1.0 CG A:ASP240 3.3 73.8 1.0 OE1 A:GLU54 3.4 65.5 1.0 CB A:SER77 3.7 61.3 1.0 OG A:SER51 3.7 66.8 1.0 ND2 A:ASN81 3.8 73.4 1.0 CG A:GLU54 3.8 69.5 1.0 OE1 A:GLU213 3.9 64.8 1.0 OG A:SER77 4.2 72.3 1.0 CB A:SER236 4.2 60.0 1.0 CG A:GLU213 4.3 53.8 1.0 OD1 A:ASN81 4.3 86.8 1.0 O A:SER236 4.5 44.5 1.0 CG A:ASN81 4.5 64.0 1.0 O A:THR209 4.5 72.2 1.0 CA A:SER51 4.6 62.6 1.0 CB A:SER51 4.6 66.4 1.0 CB A:GLU54 4.8 69.7 1.0 C A:SER236 4.8 50.4 1.0 CA A:SER77 4.8 62.3 1.0 OG A:SER210 4.8 80.7 1.0 CB A:ASP240 4.8 59.7 1.0 O A:THR50 4.9 71.1 1.0 OG A:SER236 4.9 59.6 1.0 C A:SER77 4.9 55.5 1.0 CA A:SER236 5.0 58.3 1.0 O A:SER77 5.0 59.3 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