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

Calcium Binding Sites:

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 5yjg

Go back to Calcium Binding Sites List in 5yjg
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 5yjg

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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 5yjg

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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 5yjg

Go back to Calcium Binding Sites List in 5yjg
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 5yjg

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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 5yjg

Go back to Calcium Binding Sites List in 5yjg
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

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 05:54:28 2020

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