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Zinc 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
Calcium (Ca) 6 atoms
Chlorine (Cl) 16 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 1 in 5yjg

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn733

b:0.8
occ:1.00
N A:LYS586 3.2 53.3 1.0
O A:LYS586 3.6 57.0 1.0
CA A:LYS586 4.0 57.8 1.0
CB A:LYS586 4.1 56.4 1.0
CA A:LEU585 4.1 57.1 1.0
C A:LEU585 4.1 54.5 1.0
C A:LYS586 4.2 58.7 1.0
CB A:LEU585 4.2 53.3 1.0
CD2 A:LEU585 4.3 48.1 1.0
O A:HOH963 4.4 51.1 1.0
CG2 A:THR568 4.5 52.4 1.0
CZ A:PHE572 4.5 51.3 1.0
O A:PRO569 4.5 54.6 1.0
CE2 A:PHE572 4.7 53.8 1.0
O A:HOH916 4.7 57.3 1.0
CG A:LEU585 4.9 55.0 1.0
CG A:PRO569 4.9 46.0 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: Wed Dec 16 11:23:12 2020

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