Sodium in PDB 5hya: Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium EXCHANGERNCX_MJ Soaked with 150 Mm Na+ and Nominal CA2+

The structure of Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium EXCHANGERNCX_MJ Soaked with 150 Mm Na+ and Nominal CA2+, PDB code: 5hya 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)	37.67 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.490, 72.879, 96.206, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.7

The structure of Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium EXCHANGERNCX_MJ Soaked with 150 Mm Na+ and Nominal CA2+ also contains other interesting chemical elements:

Calcium

(Ca)

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 EXCHANGERNCX_MJ Soaked with 150 Mm Na+ and Nominal CA2+ (pdb code 5hya). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium EXCHANGERNCX_MJ Soaked with 150 Mm Na+ and Nominal CA2+, PDB code: 5hya:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium EXCHANGERNCX_MJ Soaked with 150 Mm Na+ and Nominal 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 EXCHANGERNCX_MJ Soaked with 150 Mm Na+ and Nominal CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:18.8 occ:1.00 OE2 A:GLU213 2.3 17.6 1.0 OG1 A:THR50 2.3 18.1 1.0 O A:ALA47 2.3 17.7 1.0 OG A:SER51 2.4 16.6 1.0 OG A:SER236 2.4 17.0 1.0 N A:SER51 2.9 16.6 1.0 CB A:SER236 3.1 16.4 1.0 CD A:GLU213 3.2 21.3 1.0 CB A:SER51 3.2 16.2 1.0 C A:THR50 3.2 19.4 1.0 C A:ALA47 3.3 20.6 1.0 CB A:THR50 3.4 16.8 1.0 CA A:SER51 3.4 19.4 1.0 CG A:GLU213 3.5 19.7 1.0 CA A:ALA47 3.7 16.6 1.0 CA A:THR50 3.7 19.8 1.0 CA A:SER236 3.7 17.4 1.0 O A:THR50 3.8 20.7 1.0 O A:HOH508 4.1 19.9 1.0 N A:THR50 4.1 18.9 1.0 OE1 A:GLU213 4.3 22.1 1.0 O A:MET46 4.3 20.5 1.0 NA A:NA402 4.4 21.3 1.0 OD1 A:ASN232 4.4 30.3 1.0 CB A:ALA47 4.5 15.6 1.0 N A:ILE48 4.5 19.9 1.0 CG2 A:THR50 4.7 19.1 1.0 N A:SER236 4.7 16.5 1.0 C A:SER236 4.8 16.9 1.0 N A:ALA47 4.9 17.4 1.0 O A:SER236 4.9 14.3 1.0 C A:SER51 4.9 19.9 1.0 O A:ASN232 5.0 17.5 1.0 CA A:ILE48 5.0 17.6 1.0 C A:ILE48 5.0 17.8 1.0

Sodium binding site 2 out of 3 in the Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium EXCHANGERNCX_MJ Soaked with 150 Mm Na+ and Nominal 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 EXCHANGERNCX_MJ Soaked with 150 Mm Na+ and Nominal CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:21.3 occ:1.00 OE1 A:GLU54 2.3 20.5 1.0 O A:THR209 2.3 21.5 1.0 O A:THR50 2.3 20.7 1.0 OE1 A:GLU213 2.3 22.1 1.0 OE2 A:GLU213 2.6 17.6 1.0 OE2 A:GLU54 2.6 20.6 1.0 CD A:GLU54 2.8 23.6 1.0 CD A:GLU213 2.8 21.3 1.0 C A:THR209 3.3 21.2 1.0 C A:THR50 3.3 19.4 1.0 O A:HOH508 3.6 19.9 1.0 CA A:SER51 3.8 19.4 1.0 CA A:SER210 3.9 19.3 1.0 N A:SER51 4.0 16.6 1.0 N A:SER210 4.0 19.4 1.0 CG A:GLU54 4.3 20.9 1.0 CG A:PRO53 4.3 26.6 1.0 CG A:GLU213 4.3 19.7 1.0 CD A:PRO53 4.4 22.1 1.0 CD A:PRO212 4.4 19.1 1.0 NA A:NA401 4.4 18.8 1.0 CA A:THR209 4.4 19.1 1.0 CA A:THR50 4.5 19.8 1.0 NA A:NA403 4.5 20.7 0.9 CB A:PRO53 4.5 25.8 1.0 CG A:PRO212 4.5 19.8 1.0 CB A:THR50 4.5 16.8 1.0 CB A:THR209 4.5 18.5 1.0 C A:SER51 4.6 19.9 1.0 OG A:SER51 4.6 16.6 1.0 CB A:PRO212 4.6 18.3 1.0 C A:SER210 4.6 20.9 1.0 OG A:SER210 4.7 23.9 1.0 N A:GLU54 4.7 20.4 1.0 N A:GLU213 4.7 16.7 1.0 CB A:SER51 4.8 16.2 1.0 CB A:SER210 4.9 22.4 1.0 OG1 A:THR50 4.9 18.1 1.0 CB A:GLU54 5.0 20.9 1.0 OG1 A:THR209 5.0 21.1 1.0

Sodium binding site 3 out of 3 in the Structural Mechanisms of Extracellular Ion Exchange and Induced Binding-Site Occlusion in the Sodium-Calcium EXCHANGERNCX_MJ Soaked with 150 Mm Na+ and Nominal 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 EXCHANGERNCX_MJ Soaked with 150 Mm Na+ and Nominal CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:20.7 occ:0.92 OG A:SER77 2.2 21.4 1.0 OE2 A:GLU54 2.3 20.6 1.0 O A:ALA206 2.3 19.0 1.0 OG1 A:THR209 2.4 21.1 1.0 OG A:SER210 2.4 23.9 1.0 N A:SER210 2.9 19.4 1.0 CB A:SER77 3.0 19.3 1.0 CB A:SER210 3.1 22.4 1.0 CD A:GLU54 3.2 23.6 1.0 C A:THR209 3.3 21.2 1.0 CA A:SER210 3.4 19.3 1.0 C A:ALA206 3.4 21.3 1.0 CB A:THR209 3.4 18.5 1.0 CG A:GLU54 3.5 20.9 1.0 CA A:THR209 3.8 19.1 1.0 CA A:ALA206 3.8 23.3 1.0 CA A:SER77 3.8 17.6 1.0 O A:THR209 3.8 21.5 1.0 N A:THR209 4.1 19.7 1.0 O A:HOH508 4.2 19.9 1.0 OE1 A:GLU54 4.2 20.5 1.0 OD1 A:ASN73 4.3 26.9 1.0 CB A:ALA206 4.3 19.2 1.0 NA A:NA402 4.5 21.3 1.0 N A:PHE207 4.5 20.6 1.0 O A:ASN73 4.6 19.9 1.0 N A:SER77 4.7 16.7 1.0 CG2 A:THR209 4.7 20.5 1.0 O A:VAL205 4.8 24.4 1.0 C A:SER210 4.9 20.9 1.0 C A:SER77 4.9 16.3 1.0 O A:PHE207 5.0 21.2 1.0 C A:PHE207 5.0 23.9 1.0 CA A:PHE207 5.0 21.2 1.0 CB A:GLU54 5.0 20.9 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