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Calcium in PDB 5jcw: Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate

Enzymatic activity of Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate

All present enzymatic activity of Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate:
2.5.1.18;

Protein crystallography data

The structure of Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate, PDB code: 5jcw was solved by V.Kumari, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.98 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.365, 88.943, 69.483, 90.00, 97.85, 90.00
R / Rfree (%) 15.4 / 19.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate (pdb code 5jcw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate, PDB code: 5jcw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5jcw

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Calcium binding site 1 out of 8 in the Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:25.3
occ:1.00
 O A:TRP28 2.4 23.1 1.0
O A:HOH546 2.4 30.9 1.0
O A:HOH564 2.4 28.4 1.0
O A:HOH458 2.4 31.0 1.0
O A:HOH538 2.7 35.7 1.0
O A:HOH592 2.8 31.2 1.0
C A:TRP28 3.6 27.1 1.0
N A:TRP28 4.4 21.5 1.0
OE1 A:GLU197 4.4 24.0 1.0
CA A:LYS29 4.4 23.1 1.0
N A:LYS29 4.5 18.9 1.0
CA A:TRP28 4.6 24.5 1.0
O A:HOH609 4.7 41.8 1.0
N A:GLU30 4.8 21.4 1.0
OE2 A:GLU197 4.8 32.0 1.0
CG A:TRP28 4.9 18.6 1.0
CD2 A:TRP28 4.9 21.6 1.0
CD1 A:TRP28 4.9 20.7 1.0
CE2 A:TRP28 5.0 21.5 1.0
C A:LYS29 5.0 22.9 1.0

Calcium binding site 2 out of 8 in 5jcw

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Calcium binding site 2 out of 8 in the Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:32.5
occ:1.00
 O A:HOH575 2.3 31.5 1.0
O A:GLY77 2.4 23.0 1.0
OE1 A:GLN147 2.5 36.0 1.0
O A:HOH470 2.5 24.5 1.0
O A:HOH549 2.5 29.6 1.0
O A:HOH556 2.5 29.1 1.0
O A:HOH531 2.6 26.9 1.0
C A:GLY77 3.6 26.5 1.0
CD A:GLN147 3.7 40.4 1.0
CB A:GLN147 4.2 28.9 1.0
O A:HOH447 4.5 26.6 1.0
CA A:GLY77 4.5 23.2 1.0
CD2 A:LEU78 4.5 23.6 1.0
CG A:GLN147 4.5 31.6 1.0
O A:HOH509 4.5 23.3 1.0
N A:LEU78 4.6 22.1 1.0
NE2 A:GLN147 4.6 42.1 1.0
O A:HOH478 4.6 39.4 1.0
O A:HOH542 4.7 41.3 1.0
CA A:LEU78 4.7 19.3 1.0
H3 A:ACT303 4.7 28.2 1.0
O A:ILE148 4.7 21.6 1.0
O A:LEU76 4.9 28.6 1.0

Calcium binding site 3 out of 8 in 5jcw

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Calcium binding site 3 out of 8 in the Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca306

b:26.3
occ:0.75
 OD1 A:ASP171 2.3 32.6 1.0
O A:HOH401 2.4 42.9 1.0
O A:HOH573 2.4 29.8 1.0
O A:HOH479 2.6 34.7 1.0
CG A:ASP171 3.4 36.7 1.0
CA A:ASP171 3.8 27.8 1.0
CB A:ASP171 4.0 29.2 1.0
O A:HOH402 4.4 34.2 1.0
OD2 A:ASP171 4.4 31.7 1.0
O A:HOH619 4.6 32.0 1.0
O A:ASP171 4.6 28.5 1.0
N A:ASP171 4.7 26.6 1.0
OG A:SER177 4.8 29.4 1.0
C A:ASP171 4.8 33.5 1.0
O A:HOH594 4.9 39.5 1.0

Calcium binding site 4 out of 8 in 5jcw

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Calcium binding site 4 out of 8 in the Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca307

b:67.7
occ:1.00
 OD1 A:ASP116 2.3 54.7 1.0
O A:HOH405 2.4 50.1 1.0
O A:ALA113 2.6 43.8 1.0
CG A:ASP116 3.1 51.2 1.0
O A:HOH602 3.2 53.5 1.0
OD2 A:ASP116 3.3 60.9 1.0
OD2 A:ASP117 3.7 52.5 1.0
C A:ALA113 3.7 47.0 1.0
O A:HOH439 3.8 44.5 1.0
CG A:ASP117 4.2 48.0 1.0
OD1 A:ASP117 4.3 47.8 1.0
CA A:ALA113 4.4 42.8 1.0
CB A:ASP116 4.5 45.1 1.0
N A:GLY114 4.8 36.6 1.0
N A:ASP117 4.9 35.7 1.0
CA A:GLY114 5.0 34.4 1.0

Calcium binding site 5 out of 8 in 5jcw

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Calcium binding site 5 out of 8 in the Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:34.8
occ:1.00
 O B:HOH572 2.3 36.7 1.0
O B:HOH477 2.4 36.7 1.0
O B:HOH560 2.5 35.4 0.9
O B:TRP28 2.6 29.6 1.0
O B:HOH567 2.6 36.0 0.9
O B:HOH585 2.8 41.8 1.0
C B:TRP28 3.8 31.5 1.0
OE1 B:GLU197 4.4 27.9 1.0
O B:HOH594 4.5 42.0 1.0
CA B:LYS29 4.5 29.5 1.0
N B:TRP28 4.6 27.9 1.0
N B:LYS29 4.7 29.1 1.0
OE2 B:GLU197 4.7 34.1 1.0
N B:GLU30 4.8 25.5 1.0
O B:HOH409 4.8 44.2 1.0
CE2 B:TRP28 4.8 25.0 1.0
NE1 B:TRP28 4.8 25.3 1.0
CA B:TRP28 4.8 31.9 1.0
CD2 B:TRP28 4.9 22.6 1.0
CD1 B:TRP28 4.9 22.4 1.0
CG B:TRP28 4.9 20.4 1.0
CD B:GLU197 5.0 32.7 1.0
C B:LYS29 5.0 25.2 1.0
CG B:GLU30 5.0 27.8 1.0

Calcium binding site 6 out of 8 in 5jcw

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Calcium binding site 6 out of 8 in the Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:26.8
occ:1.00
 O B:HOH523 2.3 18.4 0.9
O B:HOH539 2.4 26.6 1.0
O B:HOH528 2.4 26.9 1.0
O B:GLY77 2.4 23.3 1.0
OE1 B:GLN147 2.5 28.4 1.0
O B:HOH587 2.6 31.5 1.0
O B:HOH489 2.6 24.8 1.0
C B:GLY77 3.6 24.0 1.0
CD B:GLN147 3.7 35.0 1.0
CB B:GLN147 4.2 21.5 1.0
O B:HOH522 4.4 20.8 1.0
O B:HOH601 4.5 40.1 1.0
CA B:GLY77 4.5 24.0 1.0
CD2 B:LEU78 4.5 21.5 1.0
O B:HOH571 4.5 31.2 1.0
CG B:GLN147 4.5 27.5 1.0
O B:HOH476 4.6 22.1 1.0
N B:LEU78 4.6 21.1 1.0
NE2 B:GLN147 4.6 33.0 1.0
O B:HOH510 4.6 34.7 1.0
O B:HOH500 4.7 37.9 1.0
O B:ILE148 4.7 17.1 1.0
CA B:LEU78 4.7 20.1 1.0
H2 B:ACT303 4.8 25.2 1.0
O B:HOH645 4.8 54.5 1.0
O B:LEU76 4.8 23.9 1.0

Calcium binding site 7 out of 8 in 5jcw

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Calcium binding site 7 out of 8 in the Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca306

b:21.6
occ:0.85
 OD1 B:ASP171 2.3 23.8 1.0
O B:HOH512 2.4 29.5 1.0
O B:HOH546 2.4 24.1 1.0
O B:HOH568 2.9 38.2 1.0
CG B:ASP171 3.4 27.4 1.0
CA B:ASP171 4.0 25.0 1.0
CB B:ASP171 4.0 27.6 1.0
OD2 B:ASP171 4.4 24.8 1.0
O B:HOH410 4.5 28.2 1.0
O B:HOH638 4.5 25.9 1.0
O B:ASP171 4.6 28.2 1.0
OG B:SER177 4.8 24.4 1.0
C B:ASP171 4.8 24.6 1.0
N B:ASP171 4.9 24.1 1.0
O B:HOH609 4.9 28.9 1.0

Calcium binding site 8 out of 8 in 5jcw

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Calcium binding site 8 out of 8 in the Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of HGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca307

b:56.5
occ:1.00
 O B:HOH564 2.3 41.8 1.0
O B:HOH404 2.4 41.0 1.0
O B:HOH566 2.5 41.8 1.0
O B:ALA113 2.6 41.8 1.0
OD1 B:ASP116 2.6 44.9 1.0
O B:HOH457 3.0 50.9 1.0
O B:HOH486 3.3 58.2 1.0
CG B:ASP116 3.5 43.5 1.0
C B:ALA113 3.7 40.6 1.0
OD2 B:ASP116 3.7 49.3 1.0
O B:HOH449 4.0 35.5 1.0
OD2 B:ASP117 4.0 52.3 1.0
CG B:ASP117 4.3 46.0 1.0
CA B:ALA113 4.4 39.5 1.0
OD1 B:ASP117 4.6 46.7 1.0
N B:ASP117 4.7 34.3 1.0
N B:GLY114 4.7 37.8 1.0
CA B:GLY114 4.9 34.9 1.0
CB B:ASP116 4.9 38.8 1.0
N B:ASP116 5.0 32.3 1.0
CB B:ASP117 5.0 36.6 1.0

Reference:

V.Kumari, M.A.Dyba, R.J.Holland, Y.H.Liang, S.V.Singh, X.Ji. Irreversible Inhibition of Glutathione S-Transferase By Phenethyl Isothiocyanate (Peitc), A Dietary Cancer Chemopreventive Phytochemical. Plos One V. 11 63821 2016.
ISSN: ESSN 1932-6203
PubMed: 27684484
DOI: 10.1371/JOURNAL.PONE.0163821
Page generated: Mon Jul 15 06:26:00 2024

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