Atomistry » Sodium » PDB 5xuz-5yr7 » 5yjg
Atomistry »
  Sodium »
    PDB 5xuz-5yr7 »
      5yjg »

Sodium in PDB 5yjg: Structural Insights Into Periostin Functions

Protein crystallography data

The structure of Structural Insights Into Periostin Functions, PDB code: 5yjg was solved by H.Liu, J.Liu, F.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.14 / 2.40
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 105.605, 105.605, 331.225, 90.00, 90.00, 120.00
R / Rfree (%) 21.2 / 24.8

Other elements in 5yjg:

The structure of Structural Insights Into Periostin Functions also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms
Zinc (Zn) 1 atom
Calcium (Ca) 6 atoms
Chlorine (Cl) 16 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structural Insights Into Periostin Functions (pdb code 5yjg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structural Insights Into Periostin Functions, PDB code: 5yjg:

Sodium binding site 1 out of 1 in 5yjg

Go back to Sodium Binding Sites List in 5yjg
Sodium binding site 1 out of 1 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na701

b:72.8
occ:1.00
O A:HOH957 2.7 35.4 1.0
O A:HOH1071 3.0 57.7 1.0
O A:HOH881 3.1 53.8 1.0
CD1 A:PHE577 3.4 58.2 1.0
O A:HOH852 3.4 53.7 1.0
OD1 A:ASN583 3.5 54.6 1.0
CD1 A:TYR462 3.6 49.1 1.0
CB A:TYR462 3.7 42.2 1.0
CE1 A:PHE577 3.9 63.0 1.0
CG A:TYR462 3.9 49.2 1.0
O A:HOH859 4.0 57.0 1.0
O A:GLY576 4.0 56.5 1.0
CA A:PHE577 4.1 59.1 1.0
O A:HOH924 4.2 45.1 1.0
CG A:ASN583 4.4 55.2 1.0
CG A:PHE577 4.5 54.4 1.0
C A:GLY576 4.5 54.4 1.0
CE1 A:TYR462 4.5 47.5 1.0
N A:PHE577 4.6 52.2 1.0
N A:ARG463 4.6 40.0 1.0
CA A:TYR462 4.7 43.9 1.0
CB A:PHE577 4.8 54.2 1.0
ND2 A:ASN583 4.9 63.8 1.0
CD2 A:TYR462 5.0 45.4 1.0

Reference:

J.Liu, J.Zhang, F.Xu, Z.Lin, Z.Li, H.Liu. Structural Characterizations of Human Periostin Dimerization and Cysteinylation. Febs Lett. V. 592 1789 2018.
ISSN: ISSN 1873-3468
PubMed: 29754429
DOI: 10.1002/1873-3468.13091
Page generated: Tue Dec 15 11:50:57 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy