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Calcium in PDB 3kmn: Crystal Structure of the Human Apo Gst Pi C47S/Y108V Double Mutant

Enzymatic activity of Crystal Structure of the Human Apo Gst Pi C47S/Y108V Double Mutant

All present enzymatic activity of Crystal Structure of the Human Apo Gst Pi C47S/Y108V Double Mutant:
2.5.1.18;

Protein crystallography data

The structure of Crystal Structure of the Human Apo Gst Pi C47S/Y108V Double Mutant, PDB code: 3kmn 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) 34.61 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 74.320, 89.430, 69.200, 90.00, 89.98, 90.00
R / Rfree (%) 17.1 / 21

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Human Apo Gst Pi C47S/Y108V Double Mutant (pdb code 3kmn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Human Apo Gst Pi C47S/Y108V Double Mutant, PDB code: 3kmn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3kmn

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Calcium binding site 1 out of 6 in the Crystal Structure of the Human Apo Gst Pi C47S/Y108V Double 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 the Human Apo Gst Pi C47S/Y108V Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca210

b:25.5
occ:1.00
 O A:HOH310 2.3 27.6 1.0
O A:HOH215 2.3 17.8 1.0
O A:GLY77 2.3 15.1 1.0
O A:HOH217 2.4 26.7 1.0
O A:HOH416 2.4 38.2 1.0
OE1 A:GLN147 2.5 26.7 1.0
O A:HOH293 2.7 20.1 1.0
C A:GLY77 3.5 16.1 1.0
CD A:GLN147 3.7 26.7 1.0
CB A:GLN147 4.3 19.4 1.0
CA A:GLY77 4.4 16.6 1.0
N A:LEU78 4.5 15.7 1.0
CD2 A:LEU78 4.5 16.2 1.0
O A:HOH343 4.5 16.8 1.0
NE2 A:GLN147 4.6 27.8 1.0
O A:HOH252 4.6 34.7 1.0
O A:HOH408 4.6 19.6 1.0
O A:HOH288 4.6 32.3 1.0
CG A:GLN147 4.6 22.4 1.0
CA A:LEU78 4.6 15.8 1.0
O A:ILE148 4.7 17.4 1.0
O A:LEU76 4.8 18.7 1.0

Calcium binding site 2 out of 6 in 3kmn

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Calcium binding site 2 out of 6 in the Crystal Structure of the Human Apo Gst Pi C47S/Y108V Double 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 the Human Apo Gst Pi C47S/Y108V Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca211

b:18.2
occ:1.00
 O A:HOH356 2.3 33.7 1.0
O A:HOH395 2.3 29.1 1.0
O A:HOH272 2.3 16.4 1.0
OD1 A:ASP171 2.3 17.6 1.0
O A:HOH389 2.4 19.0 1.0
CG A:ASP171 3.5 16.8 1.0
CA A:ASP171 4.0 16.7 1.0
CB A:ASP171 4.0 17.1 1.0
OG A:SER177 4.2 15.6 0.5
O A:HOH354 4.2 24.0 1.0
OD2 A:ASP171 4.5 17.4 1.0
O A:ASP171 4.7 17.6 1.0
OG A:SER177 4.8 12.1 0.5
C A:ASP171 4.9 17.1 1.0
O A:HOH271 4.9 33.7 1.0
N A:ASP171 4.9 16.9 1.0

Calcium binding site 3 out of 6 in 3kmn

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Calcium binding site 3 out of 6 in the Crystal Structure of the Human Apo Gst Pi C47S/Y108V Double 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 the Human Apo Gst Pi C47S/Y108V Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca212

b:17.8
occ:1.00
 OD2 A:ASP171 2.3 17.4 1.0
O A:HOH227 2.4 30.2 1.0
O A:HOH413 2.5 24.0 1.0
O A:HOH357 2.7 29.1 1.0
CG A:ASP171 3.4 16.8 1.0
CB A:ASP171 4.1 17.1 1.0
OD1 A:ASP171 4.5 17.6 1.0
C A:ASP171 4.5 17.1 1.0
O A:ASP171 4.5 17.6 1.0
N A:ALA172 4.8 16.2 1.0
O A:HOH285 4.9 20.0 1.0
CA A:ASP171 5.0 16.7 1.0

Calcium binding site 4 out of 6 in 3kmn

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Calcium binding site 4 out of 6 in the Crystal Structure of the Human Apo Gst Pi C47S/Y108V Double 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 the Human Apo Gst Pi C47S/Y108V Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca210

b:19.7
occ:1.00
 O B:HOH269 2.4 29.4 1.0
O B:HOH301 2.4 14.4 1.0
O B:HOH271 2.4 19.7 1.0
OD1 B:ASP171 2.4 16.2 1.0
CG B:ASP171 3.5 16.9 1.0
CA B:ASP171 4.0 16.4 1.0
CB B:ASP171 4.0 16.5 1.0
OG B:SER177 4.2 13.5 0.2
O B:HOH324 4.2 22.1 1.0
OD2 B:ASP171 4.6 17.5 1.0
O B:ASP171 4.6 16.6 1.0
OG B:SER177 4.7 18.0 0.8
O B:HOH482 4.8 39.0 1.0
O B:HOH223 4.8 28.8 1.0
C B:ASP171 4.9 16.5 1.0
N B:ASP171 4.9 16.0 1.0

Calcium binding site 5 out of 6 in 3kmn

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Calcium binding site 5 out of 6 in the Crystal Structure of the Human Apo Gst Pi C47S/Y108V Double 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 the Human Apo Gst Pi C47S/Y108V Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca211

b:18.4
occ:1.00
 OD2 B:ASP171 2.3 17.5 1.0
O B:HOH281 2.4 26.1 1.0
O B:HOH448 2.5 29.8 1.0
O B:HOH280 2.5 27.3 1.0
CG B:ASP171 3.5 16.9 1.0
CB B:ASP171 4.1 16.5 1.0
OD1 B:ASP171 4.5 16.2 1.0
O B:ASP171 4.5 16.6 1.0
C B:ASP171 4.5 16.5 1.0
N B:ALA172 4.8 16.1 1.0
O B:HOH236 4.9 19.2 1.0
CA B:ASP171 5.0 16.4 1.0

Calcium binding site 6 out of 6 in 3kmn

Go back to Calcium Binding Sites List in 3kmn
Calcium binding site 6 out of 6 in the Crystal Structure of the Human Apo Gst Pi C47S/Y108V Double Mutant


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 the Human Apo Gst Pi C47S/Y108V Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca212

b:25.2
occ:1.00
 O B:HOH310 2.2 18.0 1.0
O B:HOH349 2.2 22.8 1.0
O B:GLY77 2.3 16.1 1.0
OE1 B:GLN147 2.4 27.8 1.0
O B:HOH216 2.5 28.7 1.0
O B:HOH328 2.5 33.6 1.0
O B:HOH248 2.6 20.5 1.0
C B:GLY77 3.5 16.9 1.0
CD B:GLN147 3.7 27.4 1.0
CB B:GLN147 4.3 19.8 1.0
CA B:GLY77 4.3 17.5 1.0
O B:HOH327 4.5 34.0 1.0
NE2 B:GLN147 4.5 30.2 1.0
N B:LEU78 4.5 16.2 1.0
CD2 B:LEU78 4.5 15.8 1.0
O B:HOH479 4.6 46.9 1.0
O B:HOH300 4.6 17.5 1.0
O B:HOH329 4.6 29.1 1.0
CG B:GLN147 4.6 23.0 1.0
O B:HOH305 4.6 19.9 1.0
CA B:LEU78 4.7 15.4 1.0
O B:ILE148 4.7 18.0 1.0
O B:LEU76 4.8 19.6 1.0

Reference:

I.Quesada-Soriano, L.J.Parker, A.Primavera, J.Wielens, J.K.Holien, J.M.Casas-Solvas, A.Vargas-Berenguel, A.Aguilera, N.Nuccetelli, A.P.Mazzetti, M.Lo Bello, M.W.Parker, L.Garcia-Fuentes. Diuretic Drug Binding to Human Glutathione Transferase P1-1: Potential Role of CYS101 Revealed in the Double Mutant C47S/Y108V To Be Published.
Page generated: Tue Jul 8 13:52:31 2025

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