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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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