Atomistry » Sodium » PDB 5hn3-5i9b » 5hxe
Atomistry »
  Sodium »
    PDB 5hn3-5i9b »
      5hxe »

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+

Protein crystallography data

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

Other elements in 5hxe:

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

Sodium Binding Sites:

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 5hxe

Go back to Sodium Binding Sites List in 5hxe
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 5hxe

Go back to Sodium Binding Sites List in 5hxe
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 5hxe

Go back to Sodium Binding Sites List in 5hxe
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 5hxe

Go back to Sodium Binding Sites List in 5hxe
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

Reference:

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
Page generated: Tue Dec 15 11:03:56 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy