Calcium 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
Chlorine	(Cl)	16 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Structural Insights Into Periostin Functions (pdb code 5yjg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structural Insights Into Periostin Functions, PDB code: 5yjg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 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:Ca719 b:0.1 occ:1.00 OD2 A:ASP258 3.0 0.3 1.0 CB A:ASP258 3.3 98.5 1.0 CG A:ASP258 3.5 0.6 1.0 NZ A:LYS294 3.8 97.9 1.0 CE A:LYS294 4.1 99.2 1.0 OD1 A:ASP258 4.7 0.1 1.0 CA A:ASP258 4.7 92.6 1.0 O A:SER257 4.7 89.1 1.0

Calcium binding site 2 out of 6 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:Ca720 b:93.4 occ:1.00 O A:HOH1124 2.5 71.9 1.0 O A:HOH1079 2.6 72.2 1.0 O A:HOH1037 2.6 76.3 1.0 N A:LYS379 3.7 55.2 1.0 CA A:GLY378 4.0 51.8 1.0 C A:GLY378 4.4 54.1 1.0 CD A:LYS379 4.4 81.8 1.0 CB A:LYS379 4.5 63.8 1.0 CA A:LYS379 4.7 58.4 1.0 O A:HOH1016 4.8 62.7 1.0 CG A:LYS379 5.0 71.7 1.0

Calcium binding site 3 out of 6 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:Ca721 b:75.1 occ:1.00 O A:HOH923 2.5 62.3 1.0 O A:HOH809 2.9 47.0 1.0 O A:HOH808 3.1 51.7 1.0 CA A:GLY103 3.7 43.2 1.0 CD2 A:TYR102 3.8 43.6 1.0 CE1 A:HIS100 3.9 42.2 1.0 CE2 A:TYR102 4.0 42.6 1.0 N A:GLY103 4.2 41.2 1.0 NE2 A:GLN114 4.3 44.0 1.0 O A:HOH844 4.4 55.0 1.0 OD2 A:ASP99 4.5 46.8 1.0 NE2 A:HIS100 4.7 49.7 1.0 O A:HOH1009 4.7 54.7 1.0 OE2 A:GLU127 4.7 47.9 1.0 NH2 A:ARG123 4.8 46.4 1.0 C A:TYR102 4.9 43.1 1.0 O A:HOH1076 4.9 58.3 1.0 ND1 A:HIS100 4.9 40.2 1.0

Calcium binding site 4 out of 6 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 4 of Structural Insights Into Periostin Functions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca722 b:71.7 occ:1.00 O A:HOH1177 2.5 68.3 1.0 O A:HOH1122 2.7 61.6 1.0 OG1 A:THR176 3.2 42.1 1.0 O A:HOH897 3.3 52.9 1.0 O A:HOH1121 3.5 52.5 1.0 N A:LYS177 3.9 42.6 1.0 NE2 A:HIS198 3.9 43.3 1.0 O A:HOH893 4.0 43.6 1.0 CB A:THR176 4.0 40.5 1.0 CA A:LYS177 4.1 44.8 1.0 C A:THR176 4.1 41.9 1.0 CB A:LYS177 4.3 47.1 1.0 CE1 A:HIS198 4.4 47.5 1.0 O A:THR176 4.4 45.3 1.0 CA A:THR176 4.7 42.5 1.0

Calcium binding site 5 out of 6 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 5 of Structural Insights Into Periostin Functions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca723 b:73.0 occ:1.00 O A:HOH1069 2.4 60.0 1.0 O A:HOH824 2.4 46.3 1.0 O A:VAL571 3.1 52.2 1.0 O A:HOH856 3.5 42.6 1.0 O A:HOH1159 3.6 45.4 1.0 O A:HOH1018 3.6 53.0 1.0 ND2 A:ASN445 3.8 41.2 1.0 CE1 A:TYR462 3.9 47.5 1.0 OD1 A:ASN445 4.0 43.1 1.0 N A:VAL571 4.1 48.4 1.0 C A:VAL571 4.1 51.3 1.0 CE1 A:PHE572 4.1 47.9 1.0 CG A:ASN445 4.3 37.9 1.0 CD1 A:PHE572 4.4 42.2 1.0 CZ A:PHE572 4.5 51.3 1.0 CZ A:TYR462 4.5 51.3 1.0 OH A:TYR462 4.5 45.5 1.0 CD1 A:TYR462 4.5 49.1 1.0 CA A:VAL571 4.6 44.7 1.0 O A:VAL461 4.8 39.3 1.0 C A:GLY570 4.8 48.5 1.0 CA A:GLY570 4.9 48.2 1.0 CD1 A:PHE460 4.9 43.5 1.0 CG A:PHE572 5.0 50.2 1.0 CB A:PHE460 5.0 42.8 1.0

Calcium binding site 6 out of 6 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 6 of Structural Insights Into Periostin Functions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca724 b:77.9 occ:1.00 O A:HOH1194 2.4 53.6 1.0 O A:HOH913 2.6 50.1 1.0 O A:HOH930 4.2 55.0 1.0 CB A:HIS213 4.2 46.5 1.0 O A:HOH1008 4.4 63.8 1.0 CD1 A:LEU46 4.4 45.5 1.0 CG A:PHE57 4.5 51.8 1.0 CD1 A:PHE57 4.6 47.7 1.0 CG2 A:ILE212 4.6 44.9 1.0 ND1 A:HIS213 4.6 49.0 1.0 O A:VAL108 4.6 49.0 1.0 CB A:PHE57 4.7 44.9 1.0 CG A:HIS213 4.8 50.3 1.0 CD2 A:PHE57 4.8 51.6 1.0 O A:HOH1179 4.9 72.4 1.0 CD2 A:LEU46 5.0 52.4 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