Sodium in PDB 5yjg: Structural Insights Into Periostin Functions

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

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

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 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

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