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Sodium in PDB 5yjh: Structural Insights Into Periostin Functions

Protein crystallography data

The structure of Structural Insights Into Periostin Functions, PDB code: 5yjh 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) 44.04 / 2.96
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 105.529, 105.529, 330.342, 90.00, 90.00, 120.00
R / Rfree (%) 21.3 / 24.2

Other elements in 5yjh:

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

Magnesium (Mg) 9 atoms
Zinc (Zn) 1 atom
Calcium (Ca) 3 atoms
Chlorine (Cl) 18 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structural Insights Into Periostin Functions (pdb code 5yjh). 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: 5yjh:

Sodium binding site 1 out of 1 in 5yjh

Go back to Sodium Binding Sites List in 5yjh
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:58.5
occ:1.00
O A:HOH818 2.7 50.5 1.0
O A:HOH839 2.9 61.0 1.0
OD1 A:ASN583 3.6 52.4 1.0
CD1 A:TYR462 3.7 47.4 1.0
CE1 A:PHE577 4.0 59.5 1.0
CD1 A:PHE577 4.1 60.1 1.0
CD1 A:PHE572 4.2 49.4 1.0
CE1 A:PHE572 4.3 50.9 1.0
CE1 A:TYR462 4.4 45.1 1.0
O A:HOH827 4.4 61.7 1.0
CG A:TYR462 4.6 46.9 1.0
CG A:ASN583 4.6 52.0 1.0
CB A:TYR462 4.7 44.8 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 11:50:58 2020

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