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Potassium in PDB 3wd6: Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh

Protein crystallography data

The structure of Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh, PDB code: 3wd6 was solved by K.Yamamoto, M.Suzuki, A.Higashiura, A.Nakagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.84 / 2.50
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.861, 89.894, 182.149, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.6

Other elements in 3wd6:

The structure of Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh also contains other interesting chemical elements:

Iodine (I) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh (pdb code 3wd6). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh, PDB code: 3wd6:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 3wd6

Go back to Potassium Binding Sites List in 3wd6
Potassium binding site 1 out of 8 in the Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K301

b:36.8
occ:1.00
 SG2 A:GSH306 3.9 35.5 1.0
CE1 A:PHE133 3.9 9.7 1.0
CD1 A:ILE134 4.0 48.6 1.0
K A:K302 4.0 0.7 1.0
CD A:PRO39 4.2 20.7 1.0
CG A:PRO39 4.2 20.5 1.0
CE2 A:TYR40 4.5 25.7 1.0
CZ A:PHE133 4.5 17.6 1.0
CG1 A:ILE134 4.7 50.7 1.0
CD1 A:PHE133 4.8 24.9 1.0
CD2 A:TYR40 4.8 24.1 1.0
CB A:ILE134 4.8 42.3 1.0

Potassium binding site 2 out of 8 in 3wd6

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Potassium binding site 2 out of 8 in the Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K302

b:0.7
occ:1.00
 OE1 A:GSH306 3.7 24.4 1.0
K A:K301 4.0 36.8 1.0
CE2 A:TYR40 4.6 25.7 1.0
O A:HOH486 4.6 31.8 1.0
CA2 A:GSH306 4.8 25.7 1.0
CD1 A:GSH306 4.8 23.0 1.0
CD1 A:ILE134 4.9 48.6 1.0
CG1 A:ILE134 5.0 50.7 1.0
SG2 A:GSH306 5.0 35.5 1.0

Potassium binding site 3 out of 8 in 3wd6

Go back to Potassium Binding Sites List in 3wd6
Potassium binding site 3 out of 8 in the Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K303

b:69.4
occ:1.00
 OE2 A:GLU236 3.9 73.1 1.0
CB A:ALA232 4.3 30.2 1.0
O A:ALA232 4.4 36.6 1.0
C A:ALA232 4.5 33.6 1.0
CD A:GLU236 4.7 66.2 1.0
N A:LYS233 4.8 29.7 1.0
CG A:GLU236 4.9 56.4 1.0
CB A:GLU236 4.9 48.5 1.0

Potassium binding site 4 out of 8 in 3wd6

Go back to Potassium Binding Sites List in 3wd6
Potassium binding site 4 out of 8 in the Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K301

b:25.9
occ:1.00
 NZ A:LYS29 3.6 30.0 1.0
O B:HOH447 3.7 36.9 1.0
N B:ASP195 3.8 36.9 1.0
N B:HIS194 3.8 37.5 1.0
C B:HIS194 3.9 36.5 1.0
CB B:HIS194 3.9 34.1 1.0
CA B:PHE192 4.0 31.9 1.0
CA B:HIS194 4.0 36.8 1.0
CB B:ASP195 4.1 36.6 1.0
O B:ALA191 4.2 30.0 1.0
C B:PHE192 4.2 35.9 1.0
CE A:LYS29 4.2 31.5 1.0
O B:HIS194 4.4 39.5 1.0
CA B:ASP195 4.4 36.3 1.0
N B:ALA193 4.6 34.5 1.0
O B:PHE192 4.6 36.4 1.0
CB B:PHE192 4.8 33.8 1.0
CD2 B:PHE192 4.8 39.0 1.0
CG B:HIS194 4.9 35.3 1.0

Potassium binding site 5 out of 8 in 3wd6

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Potassium binding site 5 out of 8 in the Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K302

b:21.1
occ:1.00
 SG2 B:GSH304 3.6 32.2 1.0
CG B:PRO39 4.0 18.5 1.0
O B:HOH504 4.0 20.3 1.0
CE1 B:PHE133 4.1 11.3 1.0
CD B:PRO39 4.1 19.6 1.0
CD1 B:ILE134 4.2 48.8 1.0
CE2 B:TYR40 4.4 18.1 1.0
CG1 B:ILE134 4.5 43.9 1.0
CB B:ILE134 4.7 40.2 1.0
CD1 B:PHE133 4.7 22.0 1.0
CD2 B:TYR40 4.8 20.5 1.0

Potassium binding site 6 out of 8 in 3wd6

Go back to Potassium Binding Sites List in 3wd6
Potassium binding site 6 out of 8 in the Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K302

b:56.9
occ:1.00
 O C:HOH429 3.4 36.6 1.0
SG2 C:GSH306 3.9 42.5 1.0
O C:HOH430 4.2 44.6 1.0
CD1 C:ILE134 4.2 71.4 1.0
CG1 C:ILE134 4.3 74.9 1.0
CG C:PRO39 4.3 43.6 1.0
CE2 C:TYR40 4.4 32.4 1.0
CD C:PRO39 4.4 42.0 1.0
CD2 C:TYR40 4.8 31.8 1.0

Potassium binding site 7 out of 8 in 3wd6

Go back to Potassium Binding Sites List in 3wd6
Potassium binding site 7 out of 8 in the Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K303

b:0.0
occ:1.00
 OH C:TYR40 3.7 32.4 1.0
O C:GLN130 4.0 56.7 1.0
C C:GLN130 4.2 53.1 1.0
CB C:GLN130 4.3 47.1 1.0
CG2 C:ILE134 4.3 68.8 1.0
CA C:SER131 4.4 54.1 1.0
N C:SER131 4.4 52.0 1.0
CB C:ILE134 4.7 73.3 1.0
OE1 C:GLN130 4.7 49.8 1.0
CA C:GLN130 4.9 51.6 1.0
CZ C:TYR40 5.0 32.1 1.0

Potassium binding site 8 out of 8 in 3wd6

Go back to Potassium Binding Sites List in 3wd6
Potassium binding site 8 out of 8 in the Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of Bombyx Mori Omega-Class Glutathione Transferase in Complex with Gsh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K302

b:69.8
occ:1.00
 NZ D:LYS72 3.6 43.7 1.0
N D:PHE26 3.9 49.4 1.0
OE2 D:GLU85 4.0 62.0 1.0
OE1 D:GLU82 4.0 37.8 1.0
OD1 D:ASP86 4.1 50.8 1.0
CE D:LYS72 4.2 38.4 1.0
CD2 D:LEU23 4.2 38.1 1.0
CA D:PRO25 4.2 47.0 1.0
CB D:PHE26 4.3 51.0 1.0
C D:PRO25 4.3 45.1 1.0
CD D:GLU85 4.4 58.9 1.0
CG D:LEU23 4.5 41.5 1.0
CG D:GLU85 4.5 50.4 1.0
O D:PRO24 4.5 46.6 1.0
CA D:PHE26 4.6 50.0 1.0
CD D:GLU82 4.8 38.1 1.0
OE2 D:GLU82 4.8 39.6 1.0
CD1 D:LEU23 5.0 39.3 1.0
NH1 D:ARG31 5.0 38.4 1.0

Reference:

K.Yamamoto, M.Suzuki, A.Higashiura, A.Nakagawa. Three-Dimensional Structure of A Bombyx Mori Omega-Class Glutathione Transferase. Biochem.Biophys.Res.Commun. V. 438 588 2013.
ISSN: ISSN 0006-291X
PubMed: 23939046
DOI: 10.1016/J.BBRC.2013.08.011
Page generated: Mon Aug 12 09:51:58 2024

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