Sodium in PDB 5hxe: Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 100 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 100 Mm Na+ and Zero CA2+, PDB code: 5hxe 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)	26.99 / 2.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.765, 72.854, 96.356, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23.9

The structure of Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 100 Mm Na+ and Zero CA2+ also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

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 100 Mm Na+ and Zero CA2+ (pdb code 5hxe). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 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 100 Mm Na+ and Zero CA2+, PDB code: 5hxe:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 100 Mm Na+ and Zero CA2+


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 100 Mm Na+ and Zero CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:41.2 occ:1.00 O A:GLY122 2.3 35.4 1.0 O A:ILE118 2.4 42.9 1.0 OD2 A:ASP127 2.5 40.9 1.0 OD1 A:ASP121 2.5 43.3 1.0 O A:HOH545 2.6 44.3 0.9 O A:HOH527 2.6 45.8 1.0 CG A:ASP121 3.4 42.8 1.0 CG A:ASP127 3.5 35.5 1.0 C A:GLY122 3.5 34.8 1.0 C A:ILE118 3.6 35.2 1.0 OD2 A:ASP121 3.8 52.3 1.0 OD1 A:ASP127 3.8 37.1 1.0 O A:HOH513 3.9 45.7 1.0 O A:HOH536 4.0 51.9 1.0 O A:HOH554 4.0 50.8 1.0 CA A:PHE123 4.2 31.7 1.0 C A:ASP121 4.2 39.4 1.0 O A:ASP121 4.2 43.0 1.0 N A:PHE123 4.3 33.2 1.0 N A:SER124 4.3 31.8 1.0 N A:GLY122 4.4 39.1 1.0 CA A:GLY119 4.4 32.6 1.0 N A:GLY119 4.5 36.8 1.0 CA A:GLY122 4.5 31.6 1.0 CA A:ILE118 4.6 36.0 1.0 N A:ASP121 4.7 38.1 1.0 CB A:ASP121 4.7 34.2 1.0 CB A:ASP127 4.8 32.5 1.0 CA A:ASP121 4.8 36.4 1.0 C A:PHE123 4.8 33.9 1.0 CB A:ILE118 4.8 39.5 1.0 C A:GLY119 4.9 33.8 1.0 OG A:SER124 4.9 37.8 1.0

Sodium binding site 2 out of 4 in the Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 100 Mm Na+ and Zero CA2+


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 100 Mm Na+ and Zero CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:26.1 occ:0.90 OE2 A:GLU213 2.3 32.6 1.0 OG A:SER236 2.3 25.0 1.0 OG1 A:THR50 2.4 30.4 1.0 O A:ALA47 2.4 29.7 1.0 OG A:SER51 2.4 30.6 1.0 CB A:SER236 3.0 25.7 1.0 N A:SER51 3.0 26.5 1.0 CD A:GLU213 3.2 35.5 1.0 CB A:SER51 3.3 28.9 1.0 C A:THR50 3.3 32.5 1.0 C A:ALA47 3.4 31.8 1.0 CB A:THR50 3.4 30.8 1.0 CA A:SER51 3.4 33.4 1.0 CG A:GLU213 3.5 34.2 1.0 CA A:SER236 3.7 29.4 1.0 CA A:ALA47 3.8 31.4 1.0 O A:THR50 3.8 33.9 1.0 CA A:THR50 3.8 31.4 1.0 O A:HOH507 4.0 32.0 1.0 N A:THR50 4.2 34.1 1.0 OD1 A:ASN232 4.3 40.5 1.0 OE1 A:GLU213 4.3 34.3 1.0 NA A:NA403 4.4 30.1 0.9 O A:MET46 4.5 36.2 1.0 CB A:ALA47 4.5 25.7 1.0 N A:ILE48 4.6 32.8 1.0 N A:SER236 4.6 24.5 1.0 C A:SER236 4.7 24.5 1.0 CG2 A:THR50 4.7 31.7 1.0 O A:ASN232 4.8 32.3 1.0 O A:SER236 4.8 25.8 1.0 N A:ALA47 4.9 33.0 1.0 OD1 A:ASP240 4.9 28.8 1.0 C A:SER51 5.0 33.3 1.0 CB A:GLU213 5.0 26.1 1.0

Sodium binding site 3 out of 4 in the Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 100 Mm Na+ and Zero CA2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 100 Mm Na+ and Zero CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:30.1 occ:0.95 O A:THR209 2.2 37.2 1.0 OE1 A:GLU54 2.3 35.9 1.0 O A:THR50 2.4 33.9 1.0 OE2 A:GLU213 2.4 32.6 1.0 OE1 A:GLU213 2.4 34.3 1.0 OE2 A:GLU54 2.4 33.6 1.0 CD A:GLU54 2.7 37.7 1.0 CD A:GLU213 2.7 35.5 1.0 C A:THR209 3.3 33.4 1.0 O A:HOH507 3.4 32.0 1.0 C A:THR50 3.4 32.5 1.0 CA A:SER210 3.9 36.6 1.0 CA A:SER51 3.9 33.4 1.0 N A:SER210 4.0 32.8 1.0 N A:SER51 4.1 26.5 1.0 CG A:GLU213 4.2 34.2 1.0 CG A:GLU54 4.2 37.3 1.0 CG A:PRO53 4.3 36.5 1.0 NA A:NA404 4.3 36.8 0.8 NA A:NA402 4.4 26.1 0.9 CD A:PRO212 4.4 31.0 1.0 CD A:PRO53 4.4 34.8 1.0 CA A:THR209 4.4 35.4 1.0 CB A:PRO53 4.4 41.1 1.0 CG A:PRO212 4.5 37.7 1.0 CB A:THR209 4.5 38.4 1.0 CA A:THR50 4.5 31.4 1.0 CB A:THR50 4.6 30.8 1.0 CB A:PRO212 4.6 32.2 1.0 C A:SER210 4.6 35.6 1.0 OG A:SER51 4.7 30.6 1.0 C A:SER51 4.7 33.3 1.0 N A:GLU213 4.8 32.8 1.0 N A:GLU54 4.8 32.7 1.0 OG A:SER210 4.8 42.0 1.0 OG1 A:THR209 4.9 34.4 1.0 CB A:SER51 4.9 28.9 1.0 OG1 A:THR50 5.0 30.4 1.0 CB A:GLU54 5.0 30.0 1.0 CB A:GLU213 5.0 26.1 1.0 CB A:SER210 5.0 36.3 1.0 O A:SER210 5.0 34.1 1.0

Sodium binding site 4 out of 4 in the Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 100 Mm Na+ and Zero CA2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium Exchanger NCX_MJ Soaked with 100 Mm Na+ and Zero CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:36.8 occ:0.77 OG A:SER77 2.3 35.2 1.0 OE2 A:GLU54 2.4 33.6 1.0 O A:ALA206 2.4 39.4 1.0 OG1 A:THR209 2.4 34.4 1.0 OG A:SER210 2.6 42.0 1.0 CB A:SER77 3.0 32.5 1.0 N A:SER210 3.1 32.8 1.0 CD A:GLU54 3.2 37.7 1.0 C A:THR209 3.4 33.4 1.0 CB A:SER210 3.4 36.3 1.0 C A:ALA206 3.4 44.6 1.0 CG A:GLU54 3.4 37.3 1.0 CB A:THR209 3.5 38.4 1.0 CA A:SER210 3.5 36.6 1.0 CA A:ALA206 3.8 43.7 1.0 O A:THR209 3.8 37.2 1.0 CA A:SER77 3.8 32.3 1.0 CA A:THR209 3.9 35.4 1.0 O A:HOH507 4.1 32.0 1.0 OD1 A:ASN73 4.2 40.7 1.0 OE1 A:GLU54 4.2 35.9 1.0 N A:THR209 4.3 28.6 1.0 CB A:ALA206 4.3 31.5 1.0 NA A:NA403 4.3 30.1 0.9 O A:ASN73 4.5 30.1 1.0 N A:PHE207 4.6 43.2 1.0 N A:SER77 4.7 30.6 1.0 CG2 A:THR209 4.8 33.8 1.0 CB A:GLU54 4.9 30.0 1.0 O A:VAL205 4.9 46.8 1.0 C A:SER77 5.0 29.9 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