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Calcium in PDB 3hjm: Crystal Structure of Human Glutathione Transferase Pi Y108V Mutant

Enzymatic activity of Crystal Structure of Human Glutathione Transferase Pi Y108V Mutant

All present enzymatic activity of Crystal Structure of Human Glutathione Transferase Pi Y108V Mutant:
2.5.1.18;

Protein crystallography data

The structure of Crystal Structure of Human Glutathione Transferase Pi Y108V Mutant, PDB code: 3hjm was solved by L.J.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.55 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.002, 90.393, 75.981, 90.00, 97.49, 90.00
R / Rfree (%) 18 / 23

Other elements in 3hjm:

The structure of Crystal Structure of Human Glutathione Transferase Pi Y108V Mutant also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Glutathione Transferase Pi Y108V Mutant (pdb code 3hjm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Human Glutathione Transferase Pi Y108V Mutant, PDB code: 3hjm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3hjm

Go back to Calcium Binding Sites List in 3hjm
Calcium binding site 1 out of 5 in the Crystal Structure of Human Glutathione Transferase Pi Y108V Mutant


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 Human Glutathione Transferase Pi Y108V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca211

b:40.1
occ:1.00
 O A:HOH219 2.3 18.5 1.0
O A:GLY77 2.4 15.5 1.0
O A:HOH376 2.6 19.6 1.0
OE1 A:GLN147 2.6 30.2 1.0
O A:HOH547 2.7 23.5 1.0
O A:HOH377 3.2 26.3 1.0
C A:GLY77 3.7 15.9 1.0
CD A:GLN147 3.8 25.8 1.0
O A:HOH390 4.1 35.4 1.0
CB A:GLN147 4.2 20.7 1.0
O A:HOH297 4.4 24.9 1.0
CA A:GLY77 4.5 16.2 1.0
CG A:GLN147 4.6 23.3 1.0
O A:ILE148 4.6 15.7 1.0
N A:LEU78 4.6 16.1 1.0
O A:HOH237 4.7 20.3 1.0
CA A:LEU78 4.8 16.4 1.0
NE2 A:GLN147 4.8 31.4 1.0
CD2 A:LEU78 4.8 17.7 1.0

Calcium binding site 2 out of 5 in 3hjm

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Calcium binding site 2 out of 5 in the Crystal Structure of Human Glutathione Transferase Pi Y108V Mutant


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 Human Glutathione Transferase Pi Y108V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca211

b:25.2
occ:1.00
 O B:HOH288 2.2 15.0 1.0
O B:HOH291 2.5 18.6 1.0
OE1 B:GLN147 2.5 24.1 1.0
O B:GLY77 2.5 13.8 1.0
O B:HOH314 2.6 22.1 1.0
O B:HOH290 2.6 16.0 1.0
O B:HOH289 2.7 15.7 1.0
CD B:GLN147 3.7 20.6 1.0
C B:GLY77 3.7 12.9 1.0
CB B:GLN147 4.2 16.7 1.0
O B:HOH509 4.3 22.6 1.0
CD2 B:LEU78 4.5 11.9 1.0
O B:HOH226 4.5 12.1 1.0
CA B:GLY77 4.5 13.6 1.0
CG B:GLN147 4.5 18.9 1.0
O B:HOH371 4.5 23.8 1.0
O B:HOH231 4.5 12.7 1.0
N B:LEU78 4.6 12.7 1.0
O B:ILE148 4.6 10.6 1.0
NE2 B:GLN147 4.6 22.4 1.0
CA B:LEU78 4.7 12.5 1.0
O B:HOH510 4.7 26.3 1.0
O B:HOH503 4.8 32.1 1.0
O B:LEU76 4.8 13.9 1.0

Calcium binding site 3 out of 5 in 3hjm

Go back to Calcium Binding Sites List in 3hjm
Calcium binding site 3 out of 5 in the Crystal Structure of Human Glutathione Transferase Pi Y108V Mutant


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 Human Glutathione Transferase Pi Y108V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca210

b:31.9
occ:1.00
 O C:HOH240 2.4 14.7 1.0
O C:GLY77 2.5 15.9 1.0
OE1 C:GLN147 2.5 22.3 1.0
O C:HOH216 2.6 18.2 1.0
O C:HOH327 2.7 20.5 1.0
C C:GLY77 3.7 15.1 1.0
CD C:GLN147 3.7 21.8 1.0
O C:HOH537 3.8 38.8 1.0
CB C:GLN147 4.3 18.1 1.0
CA C:GLY77 4.4 15.5 1.0
CG C:GLN147 4.5 19.5 1.0
O C:HOH264 4.5 16.2 1.0
O C:ILE148 4.6 14.3 1.0
N C:LEU78 4.7 15.0 1.0
O C:HOH265 4.7 14.5 1.0
CD2 C:LEU78 4.7 13.1 1.0
NE2 C:GLN147 4.7 25.7 1.0
CA C:LEU78 4.8 14.9 1.0
O C:LEU76 4.9 14.9 1.0

Calcium binding site 4 out of 5 in 3hjm

Go back to Calcium Binding Sites List in 3hjm
Calcium binding site 4 out of 5 in the Crystal Structure of Human Glutathione Transferase Pi Y108V Mutant


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 Human Glutathione Transferase Pi Y108V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca211

b:49.1
occ:1.00
 O C:HOH615 2.3 33.4 1.0
OD1 C:ASP171 2.6 32.4 1.0
OD2 C:ASP171 2.8 30.3 1.0
CG C:ASP171 3.1 27.1 1.0
O C:HOH534 3.2 39.4 1.0
CB C:ASP171 4.6 24.5 1.0
O C:HOH247 4.9 32.6 1.0
CA C:GLY168 5.0 27.7 1.0

Calcium binding site 5 out of 5 in 3hjm

Go back to Calcium Binding Sites List in 3hjm
Calcium binding site 5 out of 5 in the Crystal Structure of Human Glutathione Transferase Pi Y108V Mutant


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 Human Glutathione Transferase Pi Y108V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca211

b:20.3
occ:1.00
 O D:HOH243 2.4 13.5 1.0
OE1 D:GLN147 2.4 16.5 1.0
O D:GLY77 2.4 15.1 1.0
O D:HOH244 2.6 14.9 1.0
O D:HOH245 2.7 23.6 1.0
O D:HOH254 2.7 17.1 1.0
O D:HOH246 2.7 25.8 1.0
C D:GLY77 3.6 14.4 1.0
CD D:GLN147 3.6 17.7 1.0
O D:HOH431 4.2 18.7 1.0
CB D:GLN147 4.3 15.4 1.0
CA D:GLY77 4.4 14.8 1.0
O D:HOH226 4.4 10.2 1.0
O D:HOH220 4.5 10.6 1.0
CG D:GLN147 4.5 17.8 1.0
NE2 D:GLN147 4.5 18.4 1.0
O D:HOH354 4.6 24.8 1.0
CD2 D:LEU78 4.6 11.5 1.0
N D:LEU78 4.6 13.9 1.0
O D:ILE148 4.7 12.1 1.0
O D:HOH617 4.7 26.9 1.0
O D:HOH242 4.7 20.0 1.0
O D:LEU76 4.7 16.0 1.0
CA D:LEU78 4.8 13.2 1.0

Reference:

I.Quesada-Soriano, L.J.Parker, A.Primavera, J.M.Casas-Solvas, A.Vargas-Berenguel, C.Baron, C.J.Morton, A.P.Mazzetti, M.Lo Bello, M.W.Parker, L.Garcia-Fuentes. Influence of the H-Site Residue 108 on Human Glutathione Transferase P1-1 Ligand Binding: Structure-Thermodynamic Relationships and Thermal Stability. Protein Sci. V. 18 2454 2009.
ISSN: ISSN 0961-8368
PubMed: 19780048
DOI: 10.1002/PRO.253
Page generated: Tue Jul 8 13:00:07 2025

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