Atomistry » Sodium » PDB 6z72-6zl3 » 6zb6
Atomistry »
  Sodium »
    PDB 6z72-6zl3 »
      6zb6 »

Sodium in PDB 6zb6: Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione

Protein crystallography data

The structure of Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione, PDB code: 6zb6 was solved by A.C.Papageorgiou, N.Poudel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.68 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.562, 98.500, 95.900, 90.00, 109.13, 90.00
R / Rfree (%) 16.4 / 20.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione (pdb code 6zb6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione, PDB code: 6zb6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 6zb6

Go back to Sodium Binding Sites List in 6zb6
Sodium binding site 1 out of 9 in the Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:50.2
occ:1.00
 O E:HOH570 2.5 46.3 1.0
O A:HOH543 2.7 53.6 1.0
OG1 A:THR108 2.8 25.4 1.0
OE1 E:GLN54 3.4 36.9 1.0
CG2 A:THR108 3.4 19.5 1.0
O E:HOH472 3.5 42.4 1.0
CB A:THR108 3.6 22.7 1.0
CD E:GLN54 3.6 37.3 1.0
NE2 E:GLN54 3.6 40.7 1.0
O E:HOH484 3.6 25.0 1.0
CA A:THR108 4.0 20.8 1.0
O A:HOH572 4.1 33.4 1.0
O A:HIS107 4.3 20.3 1.0
O A:HOH422 4.3 24.8 1.0
O E:HOH434 4.3 53.3 1.0
CG E:GLN54 4.6 33.9 1.0
CB E:PHE52 4.9 32.7 1.0
O E:HOH417 4.9 23.5 1.0
N A:THR108 5.0 23.5 1.0
C A:HIS107 5.0 22.5 1.0

Sodium binding site 2 out of 9 in 6zb6

Go back to Sodium Binding Sites List in 6zb6
Sodium binding site 2 out of 9 in the Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:52.3
occ:1.00
 N3 A:GTB301 3.2 25.5 1.0
C2' A:GTB301 3.3 50.7 1.0
O32 A:GTB301 3.8 37.8 1.0
OH A:TYR118 3.9 54.6 1.0
C3' A:GTB301 4.0 58.9 1.0
CA2 A:GTB301 4.0 25.2 1.0
C2 A:GTB301 4.1 21.6 1.0
CA3 A:GTB301 4.2 30.3 1.0
C3 A:GTB301 4.2 36.9 1.0
OE1 A:GTB301 4.2 26.0 1.0
C1' A:GTB301 4.3 45.4 1.0
O A:HOH558 4.4 57.5 1.0
NE2 A:GLN54 4.5 23.0 1.0
C' A:GTB301 4.5 35.6 1.0
O A:HOH451 4.8 28.0 1.0
CZ A:TYR118 4.9 51.6 1.0
CB2 A:GTB301 4.9 24.3 1.0
CE1 A:TYR118 4.9 46.5 1.0

Sodium binding site 3 out of 9 in 6zb6

Go back to Sodium Binding Sites List in 6zb6
Sodium binding site 3 out of 9 in the Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:77.1
occ:1.00
 O A:HOH488 2.6 46.1 1.0
OD1 A:ASP85 2.6 40.4 1.0
O A:HOH409 2.8 35.9 1.0
N A:LEU87 3.0 24.9 1.0
N A:LEU86 3.2 23.5 1.0
CB A:LEU87 3.4 25.0 1.0
CA A:ASP85 3.6 36.0 1.0
CA A:LEU87 3.7 22.5 1.0
C A:ASP85 3.7 34.5 1.0
CD A:LYS80 3.8 58.1 1.0
CG A:ASP85 3.8 42.7 1.0
CE A:LYS80 3.8 57.5 1.0
CG A:LEU87 3.8 27.4 1.0
C A:LEU86 4.0 28.0 1.0
N A:ARG88 4.0 23.6 1.0
O A:HOH442 4.1 34.7 1.0
CA A:LEU86 4.1 23.6 1.0
CB A:ASP85 4.3 38.4 1.0
CD1 A:LEU87 4.3 27.4 1.0
C A:LEU87 4.3 21.8 1.0
O A:VAL84 4.6 60.4 1.0
O A:ASP85 4.7 33.8 1.0
CB A:LEU86 4.8 21.2 1.0
N A:ASP85 4.8 40.1 1.0
OD2 A:ASP85 4.8 53.4 1.0
NZ A:LYS80 5.0 50.2 1.0
O A:LEU76 5.0 25.0 1.0
CB A:LEU76 5.0 24.4 1.0

Sodium binding site 4 out of 9 in 6zb6

Go back to Sodium Binding Sites List in 6zb6
Sodium binding site 4 out of 9 in the Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na303

b:55.0
occ:1.00
 N C:GLY61 3.2 28.6 1.0
O C:PRO3 3.7 40.1 1.0
O C:GLN59 3.8 25.8 1.0
CA C:GLY61 4.0 36.7 1.0
CG C:GLN59 4.0 27.0 1.0
CA C:ASP60 4.1 23.0 1.0
C C:ASP60 4.1 25.8 1.0
C C:GLN59 4.1 26.5 1.0
CD C:GLN59 4.3 38.2 1.0
CG C:LYS5 4.3 33.8 1.0
N C:ASP60 4.3 27.7 1.0
O C:HOH512 4.4 45.5 1.0
CE C:LYS5 4.4 55.3 1.0
O C:GLY61 4.5 33.4 1.0
NE2 C:GLN59 4.6 36.3 1.0
CB C:GLN59 4.6 18.4 1.0
CD C:LYS5 4.6 45.6 1.0
CA C:VAL4 4.7 31.1 1.0
N C:LYS5 4.7 27.2 1.0
C C:GLY61 4.7 35.7 1.0
OE1 C:GLN59 4.7 38.1 1.0
C C:PRO3 4.8 34.1 1.0
CB C:LYS5 5.0 26.7 1.0

Sodium binding site 5 out of 9 in 6zb6

Go back to Sodium Binding Sites List in 6zb6
Sodium binding site 5 out of 9 in the Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na306

b:49.6
occ:1.00
 O B:HOH570 2.5 57.7 1.0
O B:HOH413 2.8 53.3 1.0
OE1 B:GLU23 3.3 36.6 1.0
CA B:ALA206 3.4 31.0 1.0
N B:ALA206 3.6 31.3 1.0
C B:PRO205 3.8 34.9 1.0
CB B:ALA206 3.9 32.0 1.0
O B:PRO205 3.9 30.6 1.0
CB B:GLU23 4.0 24.0 1.0
O B:GLU23 4.0 32.9 1.0
CD B:LYS209 4.1 51.4 1.0
CB B:PRO205 4.3 45.8 1.0
CD B:GLU23 4.3 37.9 1.0
O B:HOH571 4.3 53.6 1.0
C B:GLU23 4.5 26.6 1.0
CB B:LYS209 4.6 33.7 1.0
CG B:GLU23 4.6 33.4 1.0
CA B:GLU23 4.7 25.3 1.0
CA B:PRO205 4.7 36.5 1.0
C B:ALA206 4.8 31.7 1.0
O B:HOH499 4.9 46.4 1.0

Sodium binding site 6 out of 9 in 6zb6

Go back to Sodium Binding Sites List in 6zb6
Sodium binding site 6 out of 9 in the Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na307

b:64.9
occ:1.00
 O F:HOH494 2.3 40.8 1.0
O B:HOH432 3.2 36.9 1.0
O F:GLY82 3.2 29.2 1.0
O B:PRO183 3.4 29.5 1.0
C F:GLY82 4.1 30.3 1.0
C B:PRO183 4.1 34.3 1.0
CA F:GLY82 4.1 32.0 1.0
NZ F:LYS80 4.4 32.1 1.0
O F:HOH436 4.4 44.6 1.0
CA B:PRO183 4.4 33.3 1.0
O B:HOH475 4.8 53.8 1.0
N B:ALA186 4.8 22.1 1.0
N B:ALA185 4.8 26.2 1.0
CB B:ALA186 4.9 25.3 1.0
O B:THR182 4.9 29.8 1.0
OD2 F:ASP85 5.0 37.2 1.0
N B:HIS184 5.0 26.6 1.0

Sodium binding site 7 out of 9 in 6zb6

Go back to Sodium Binding Sites List in 6zb6
Sodium binding site 7 out of 9 in the Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na303

b:41.9
occ:1.00
 O B:HOH496 2.7 46.6 1.0
O F:HOH488 2.8 39.7 1.0
O B:HOH483 2.8 30.6 1.0
NE F:ARG200 3.0 29.7 1.0
CG F:ARG200 3.2 49.2 1.0
O F:HOH419 3.4 26.9 1.0
CD F:ARG200 3.4 36.9 1.0
OE2 F:GLU158 3.8 31.2 1.0
CG B:GLU151 4.0 29.7 1.0
CZ F:ARG200 4.0 28.6 1.0
CD F:GLU158 4.2 31.6 1.0
OE1 F:GLU158 4.2 24.9 1.0
NH2 F:ARG200 4.3 26.9 1.0
CB F:ARG200 4.4 40.3 1.0
O B:HOH449 4.4 27.5 1.0
OE2 B:GLU151 4.4 30.9 1.0
O F:HOH463 4.5 29.1 1.0
CD B:GLU151 4.6 31.5 1.0
O B:HOH446 4.7 51.8 1.0
NA F:NA304 4.7 64.1 1.0
CA F:ARG200 4.9 30.3 1.0
OH F:TYR159 4.9 26.9 1.0

Sodium binding site 8 out of 9 in 6zb6

Go back to Sodium Binding Sites List in 6zb6
Sodium binding site 8 out of 9 in the Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na304

b:64.1
occ:1.00
 O F:HOH542 2.0 62.0 1.0
O B:HOH496 2.7 46.6 1.0
O B:HOH446 3.1 51.8 1.0
O F:HOH463 3.2 29.1 1.0
O F:GLU199 3.8 30.4 1.0
C F:GLU199 4.0 26.5 1.0
N F:ARG200 4.0 25.9 1.0
CA F:ARG200 4.2 30.3 1.0
CB F:ALA203 4.2 26.9 1.0
CB F:GLU199 4.3 28.3 1.0
CE1 B:HIS193 4.3 32.4 1.0
O F:HOH487 4.6 33.4 1.0
NA F:NA303 4.7 41.9 1.0
O F:HOH488 4.7 39.7 1.0
CA F:GLU199 4.8 29.1 1.0
ND1 B:HIS193 4.9 30.9 1.0

Sodium binding site 9 out of 9 in 6zb6

Go back to Sodium Binding Sites List in 6zb6
Sodium binding site 9 out of 9 in the Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Lolium Rigidum Gstf in Complex with S-(P- Nitrobenzyl) Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:50.2
occ:1.00
 OD2 D:ASP85 2.6 37.5 1.0
CA D:ARG88 3.4 22.5 1.0
O D:HOH464 3.5 40.1 1.0
C D:ARG88 3.5 31.0 1.0
N D:GLY90 3.5 41.7 1.0
CG D:ASP85 3.6 35.4 1.0
O D:ARG88 3.7 29.3 1.0
OD1 D:ASP85 3.8 32.5 1.0
CA D:GLY90 3.9 40.2 1.0
N D:ASN91 3.9 30.4 1.0
N D:GLU89 4.0 38.4 1.0
O D:HOH416 4.1 52.0 1.0
C D:GLY90 4.2 41.0 1.0
O D:HOH418 4.2 48.2 1.0
CB D:ARG88 4.2 24.8 1.0
CD D:ARG88 4.3 37.1 1.0
CB D:ASN91 4.4 26.3 1.0
N D:ARG88 4.5 22.5 1.0
O A:HOH524 4.6 59.5 1.0
C D:GLU89 4.6 43.3 1.0
O D:HOH473 4.6 43.8 1.0
CA D:ASN91 4.8 30.2 1.0
CG D:ARG88 4.8 23.1 1.0
CA D:GLU89 4.9 41.3 1.0
NE D:ARG88 4.9 43.0 1.0
CB D:ASP85 5.0 26.7 1.0

Reference:

N.Georgakis, N.Poudel, D.Vlachakis, A.C.Papageorgiou, N.E.Labrou. Phi Class Glutathione Transferases As Molecular Targets Towards Multiple-Herbicide Resistance: Inhibition Analysis and Pharmacophore Design. Plant Physiol Biochem. 2020.
ISSN: ESSN 1873-2690
PubMed: 33257232
DOI: 10.1016/J.PLAPHY.2020.11.018
Page generated: Tue Oct 8 15:25:33 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy