Calcium 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
Chlorine (Cl) 18 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structural Insights Into Periostin Functions (pdb code 5yjh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structural Insights Into Periostin Functions, PDB code: 5yjh:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5yjh

Go back to Calcium Binding Sites List in 5yjh
Calcium binding site 1 out of 3 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca729

b:72.8
occ:1.00
O A:HOH949 2.1 76.4 1.0
O A:HOH929 2.8 52.9 1.0
OG1 A:THR176 3.7 51.4 1.0
CE1 A:HIS198 4.0 52.7 1.0
N A:LYS177 4.1 40.5 1.0
CA A:LYS177 4.1 45.7 1.0
O A:HOH870 4.2 44.6 1.0
NE2 A:HIS198 4.2 51.2 1.0
CB A:LYS177 4.2 46.4 1.0
C A:THR176 4.4 49.4 1.0
CB A:THR176 4.5 39.3 1.0
O A:THR176 4.7 50.5 1.0

Calcium binding site 2 out of 3 in 5yjh

Go back to Calcium Binding Sites List in 5yjh
Calcium binding site 2 out of 3 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca730

b:66.2
occ:1.00
O A:HOH813 3.0 50.3 1.0
O A:HOH876 3.2 42.4 1.0
ND2 A:ASN445 3.3 36.4 1.0
OD1 A:ASN445 3.4 43.3 1.0
O A:VAL571 3.5 50.1 1.0
CG A:ASN445 3.8 34.7 1.0
CE1 A:TYR462 4.2 45.1 1.0
N A:VAL571 4.4 41.3 1.0
CE1 A:PHE572 4.4 50.9 1.0
O A:VAL461 4.5 40.1 1.0
C A:VAL571 4.5 49.6 1.0
CZ A:TYR462 4.7 48.6 1.0
OH A:TYR462 4.7 54.1 1.0
CZ A:PHE572 4.7 59.2 1.0
CD1 A:PHE460 4.7 53.2 1.0
CD1 A:PHE572 4.8 49.4 1.0
CD1 A:TYR462 4.8 47.4 1.0
CB A:PHE460 4.9 48.5 1.0
O A:HOH917 4.9 34.1 1.0
CA A:VAL571 5.0 44.1 1.0

Calcium binding site 3 out of 3 in 5yjh

Go back to Calcium Binding Sites List in 5yjh
Calcium binding site 3 out of 3 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca731

b:91.3
occ:1.00
CG2 A:ILE212 4.3 40.7 1.0
CB A:HIS213 4.4 49.1 1.0
O A:VAL108 4.6 48.9 1.0
CD1 A:PHE57 4.8 55.1 1.0
CD2 A:LEU46 4.9 40.0 1.0
CD1 A:LEU46 4.9 54.3 1.0
CG A:PHE57 4.9 56.6 1.0
CG1 A:VAL225 4.9 43.2 1.0
CB A:PHE57 4.9 50.4 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: Sat Dec 12 05:54:30 2020

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