Chlorine 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
Calcium (Ca) 3 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Chlorine atom in the Structural Insights Into Periostin Functions (pdb code 5yjh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 18 binding sites of Chlorine where determined in the Structural Insights Into Periostin Functions, PDB code: 5yjh:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 18 in 5yjh

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Chlorine binding site 1 out of 18 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl702

b:83.0
occ:1.00
N A:SER67 3.4 85.7 1.0
CA A:LYS66 3.9 0.4 1.0
CB A:SER67 4.0 67.2 1.0
O A:LYS65 4.0 0.1 1.0
C A:LYS66 4.1 0.3 1.0
OG A:SER67 4.1 67.1 1.0
CA A:SER67 4.3 75.7 1.0
C A:LYS65 4.8 0.9 1.0
CB A:LYS66 4.8 0.5 1.0
N A:LYS66 4.8 0.6 1.0

Chlorine binding site 2 out of 18 in 5yjh

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Chlorine binding site 2 out of 18 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl703

b:93.7
occ:1.00
CG2 A:THR59 3.7 77.9 1.0
CE A:LYS61 3.7 0.7 1.0
OG1 A:THR59 3.8 77.8 1.0
NZ A:LYS61 3.8 0.3 1.0
N A:THR59 4.1 80.5 1.0
CB A:THR59 4.3 76.0 1.0
O A:HOH946 4.4 57.7 1.0
CB A:SER58 4.6 67.9 1.0
CA A:SER58 4.8 63.1 1.0
CA A:THR59 4.8 82.7 1.0
C A:SER58 5.0 69.8 1.0

Chlorine binding site 3 out of 18 in 5yjh

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Chlorine binding site 3 out of 18 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl704

b:0.8
occ:1.00
CE A:LYS172 3.4 99.0 1.0
NZ A:LYS172 4.0 82.1 1.0
CB A:ASN171 4.0 63.6 1.0
CD A:LYS172 4.3 80.6 1.0
CG A:LYS172 4.3 62.5 1.0
ND2 A:ASN171 4.6 93.6 1.0
CG A:ASN171 4.9 80.0 1.0
O A:PRO186 4.9 55.8 1.0
N A:ASN171 4.9 64.1 1.0
CA A:ASN171 4.9 59.1 1.0

Chlorine binding site 4 out of 18 in 5yjh

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Chlorine binding site 4 out of 18 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl705

b:69.8
occ:1.00
N A:GLY82 3.2 59.1 1.0
O A:HOH837 3.4 60.5 1.0
CA A:GLY82 3.7 56.7 1.0
O A:TYR83 4.0 53.9 1.0
C A:GLY82 4.1 52.9 1.0
N A:TYR83 4.2 53.8 1.0
C A:PRO81 4.2 57.5 1.0
O A:HOH950 4.3 50.1 1.0
CA A:PRO81 4.4 56.3 1.0
SD A:MET84 4.5 73.8 1.0
CD2 A:LEU96 4.6 45.0 1.0
O A:GLY82 4.8 54.7 1.0
O A:CYS80 4.9 56.1 1.0
C A:TYR83 4.9 55.6 1.0

Chlorine binding site 5 out of 18 in 5yjh

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Chlorine binding site 5 out of 18 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl706

b:67.1
occ:1.00
NE2 A:GLN422 3.3 55.0 1.0
O A:LEU391 3.8 57.0 1.0
CD A:LYS426 4.1 44.7 1.0
CD2 A:LEU391 4.1 54.4 1.0
CG A:GLN422 4.1 59.3 1.0
CA A:LEU391 4.1 50.0 1.0
CD A:GLN422 4.2 56.2 1.0
CB A:LEU391 4.3 44.8 1.0
C A:LEU391 4.3 47.7 1.0
CG A:ARG423 4.5 67.9 1.0
O A:GLN422 4.7 60.9 1.0
NZ A:LYS426 4.8 56.4 1.0
CG A:LEU391 4.8 49.3 1.0
CB A:LYS426 4.9 45.5 1.0

Chlorine binding site 6 out of 18 in 5yjh

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Chlorine binding site 6 out of 18 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl707

b:72.7
occ:1.00
N A:LEU440 3.4 53.8 1.0
CG A:GLN479 3.4 57.6 1.0
O A:HOH944 3.6 52.4 1.0
NE2 A:GLN479 3.7 71.0 1.0
CD A:GLN479 3.9 72.6 1.0
CB A:LEU440 3.9 41.4 1.0
CE1 A:HIS486 4.0 48.1 1.0
CA A:GLY439 4.0 41.3 1.0
C A:GLY439 4.2 49.7 1.0
CB A:SER477 4.3 46.1 1.0
CA A:LEU440 4.3 45.0 1.0
O A:LYS478 4.3 49.9 1.0
C A:LYS478 4.4 45.0 1.0
CB A:GLN479 4.5 47.7 1.0
N A:GLN479 4.6 41.8 1.0
ND1 A:HIS486 4.7 47.0 1.0
CB A:ALA484 4.7 44.9 1.0
N A:LYS478 4.7 45.3 1.0
C A:SER477 4.8 45.9 1.0
CA A:LYS478 4.9 45.3 1.0
CA A:GLN479 4.9 44.0 1.0
OE1 A:GLN479 4.9 80.5 1.0
NE2 A:HIS486 5.0 45.3 1.0

Chlorine binding site 7 out of 18 in 5yjh

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Chlorine binding site 7 out of 18 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl708

b:87.5
occ:1.00
NZ A:LYS502 3.1 73.3 1.0
NZ A:LYS497 3.2 87.8 1.0
CE A:LYS497 3.7 82.2 1.0
CE A:LYS502 3.8 76.9 1.0
CD A:LYS497 3.8 84.7 1.0
NE2 A:GLN505 4.0 88.4 1.0
OE1 A:GLN505 4.7 98.3 1.0
CD A:LYS502 4.8 72.1 1.0
CD A:GLN505 4.8 93.7 1.0
CG A:LYS497 4.9 71.8 1.0

Chlorine binding site 8 out of 18 in 5yjh

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Chlorine binding site 8 out of 18 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl709

b:76.4
occ:1.00
NE A:ARG85 3.5 78.4 1.0
NH2 A:ARG85 3.7 82.6 1.0
N A:CYS79 3.7 66.8 1.0
CG A:GLU78 3.7 72.4 1.0
SG A:CYS79 3.9 61.1 1.0
CZ A:ARG85 4.0 89.4 1.0
CB A:CYS79 4.0 56.7 1.0
CB A:GLU78 4.3 56.5 1.0
CA A:GLU78 4.4 63.9 1.0
CA A:CYS79 4.5 65.6 1.0
CD A:GLU78 4.5 77.4 1.0
OE2 A:GLU78 4.5 76.5 1.0
C A:GLU78 4.6 63.9 1.0
CD A:ARG85 4.6 84.7 1.0
CG A:ARG85 4.8 85.4 1.0

Chlorine binding site 9 out of 18 in 5yjh

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Chlorine binding site 9 out of 18 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl710

b:77.1
occ:1.00
N A:MET316 3.4 43.1 1.0
N A:GLY317 3.6 53.0 1.0
O A:GLY317 3.9 61.6 1.0
ND2 A:ASN201 3.9 50.5 1.0
O A:SER314 4.0 46.0 1.0
CA A:MET316 4.1 44.1 1.0
C A:MET316 4.1 51.1 1.0
CB A:MET316 4.2 47.9 1.0
C A:GLY317 4.3 58.4 1.0
CA A:ILE315 4.3 42.7 1.0
C A:ILE315 4.4 45.1 1.0
CA A:GLY317 4.4 56.9 1.0
CG A:MET316 4.9 47.2 1.0

Chlorine binding site 10 out of 18 in 5yjh

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Chlorine binding site 10 out of 18 in the Structural Insights Into Periostin Functions


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Structural Insights Into Periostin Functions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl711

b:79.0
occ:1.00
O A:HOH825 3.5 47.2 1.0
O A:HOH816 4.0 49.9 1.0
N A:GLY214 4.3 40.3 1.0
O A:ILE211 4.4 48.4 1.0
CA A:GLY214 4.5 41.7 1.0
O A:ILE212 4.6 48.7 1.0
CG2 A:THR176 4.8 37.4 1.0
O A:HOH902 4.8 48.1 1.0
O A:PHE57 4.9 49.0 1.0
O A:GLY202 5.0 58.0 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: Sat Dec 12 12:40:52 2020

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