Sodium in PDB 5jdm: 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 SR2+

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 SR2+, PDB code: 5jdm 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)	37.64 / 2.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.802, 72.267, 94.839, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 26.4

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 SR2+ also contains other interesting chemical elements:

Strontium

(Sr)

1 atom

The binding sites of Sodium 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 SR2+ (pdb code 5jdm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium 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 0.1MM SR2+, PDB code: 5jdm:
Jump to Sodium binding site number: 1; 2;

Sodium 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 2.5 Mm Na+ and 0.1MM SR2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 SR2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:46.8 occ:0.66 O A:ALA47 2.4 51.3 1.0 OG A:SER51 2.4 46.7 1.0 OG1 A:THR50 2.4 50.1 1.0 OG A:SER236 2.4 41.8 1.0 OE2 A:GLU213 2.5 50.3 1.0 N A:SER51 2.9 46.6 1.0 CB A:SER236 3.0 45.5 1.0 CB A:SER51 3.1 50.8 1.0 CD A:GLU213 3.2 46.1 1.0 C A:THR50 3.2 48.0 1.0 CA A:SER51 3.3 49.4 1.0 C A:ALA47 3.4 50.6 1.0 CB A:THR50 3.4 50.3 1.0 CG A:GLU213 3.5 44.6 1.0 CA A:SER236 3.6 46.0 1.0 O A:THR50 3.7 49.6 1.0 CA A:THR50 3.8 46.9 1.0 CA A:ALA47 3.8 49.6 1.0 O A:HOH502 4.1 49.6 1.0 N A:THR50 4.1 54.2 1.0 OE1 A:GLU213 4.2 52.8 1.0 NA A:NA402 4.4 49.6 0.9 O A:MET46 4.5 49.4 1.0 N A:ILE48 4.6 48.4 1.0 CB A:ALA47 4.6 40.7 1.0 N A:SER236 4.6 40.7 1.0 C A:SER236 4.6 42.8 1.0 O A:SER236 4.7 47.0 1.0 CG2 A:THR50 4.8 51.3 1.0 OD1 A:ASN232 4.8 43.7 1.0 C A:SER51 4.8 46.2 1.0 OD1 A:ASP240 4.8 51.0 0.8 C A:ILE48 5.0 48.7 1.0

Sodium 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 2.5 Mm Na+ and 0.1MM SR2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 0.1MM SR2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:49.6 occ:0.91 OE1 A:GLU213 2.3 52.8 1.0 OE1 A:GLU54 2.3 50.5 0.6 O A:THR50 2.3 49.6 1.0 OE2 A:GLU213 2.4 50.3 1.0 OE2 A:GLU54 2.4 60.4 1.0 O A:THR209 2.4 56.0 1.0 CD A:GLU213 2.7 46.1 1.0 CD A:GLU54 2.7 51.7 1.0 O A:HOH502 3.4 49.6 1.0 C A:THR50 3.4 48.0 1.0 C A:THR209 3.6 61.4 1.0 CA A:SER51 3.8 49.4 1.0 OG1 A:THR209 4.0 66.5 1.0 N A:SER51 4.0 46.6 1.0 CA A:SER210 4.1 56.5 1.0 CG A:GLU213 4.2 44.6 1.0 CG A:GLU54 4.2 53.1 1.0 N A:SER210 4.3 64.8 1.0 NA A:NA401 4.4 46.8 0.7 CD A:PRO53 4.4 49.8 1.0 CG A:PRO53 4.5 55.3 1.0 CB A:PRO53 4.5 56.3 1.0 OG A:SER51 4.5 46.7 1.0 CA A:THR50 4.6 46.9 1.0 C A:SER51 4.6 46.2 1.0 CB A:THR50 4.6 50.3 1.0 CA A:THR209 4.7 59.5 1.0 CD A:PRO212 4.7 45.7 1.0 N A:GLU54 4.7 52.2 1.0 CB A:PRO212 4.8 54.5 1.0 CB A:SER51 4.8 50.8 1.0 CG A:PRO212 4.8 55.8 1.0 N A:GLU213 4.9 46.0 1.0 C A:SER210 4.9 59.6 1.0 CB A:GLU213 4.9 40.8 1.0 OG A:SER210 4.9 83.9 1.0 CB A:GLU54 5.0 52.1 1.0 CB A:THR209 5.0 66.3 1.0 OG1 A:THR50 5.0 50.1 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