Sodium in PDB 7opy: Camel GSTM1-1 in Complex with S-(P-Nitrobenzyl)Glutathione

All present enzymatic activity of Camel GSTM1-1 in Complex with S-(P-Nitrobenzyl)Glutathione:
2.5.1.18;

The structure of Camel GSTM1-1 in Complex with S-(P-Nitrobenzyl)Glutathione, PDB code: 7opy 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)	88.69 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.388, 177.376, 59.42, 90, 115, 90
R / Rfree (%)	19.3 / 25.2

The binding sites of Sodium atom in the Camel GSTM1-1 in Complex with S-(P-Nitrobenzyl)Glutathione (pdb code 7opy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Camel GSTM1-1 in Complex with S-(P-Nitrobenzyl)Glutathione, PDB code: 7opy:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Camel GSTM1-1 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 Camel GSTM1-1 in Complex with S-(P-Nitrobenzyl)Glutathione within 5.0Å range: probe atom residue distance (Å) B Occ F:Na802 b:64.2 occ:1.00 O F:HOH1032 2.6 49.3 1.0 O F:HOH1033 3.2 45.9 1.0 O F:LEU46 3.3 34.5 1.0 CB F:LEU46 4.0 33.1 1.0 C F:LEU46 4.1 44.2 1.0 CE2 F:PHE50 4.1 44.0 1.0 CD2 F:PHE50 4.2 46.0 1.0 O F:HOH962 4.4 31.5 1.0 CA F:LEU46 4.4 32.3 1.0 O F:HOH1035 4.5 60.2 1.0 O F:HOH1029 4.6 54.5 1.0 CG F:LEU46 5.0 36.3 1.0

Sodium binding site 2 out of 4 in the Camel GSTM1-1 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 Camel GSTM1-1 in Complex with S-(P-Nitrobenzyl)Glutathione within 5.0Å range: probe atom residue distance (Å) B Occ F:Na803 b:58.6 occ:1.00 O F:ARG144 2.4 54.1 1.0 O F:GLY142 2.4 52.5 1.0 C F:LYS143 3.1 60.3 1.0 O F:HOH957 3.2 47.8 1.0 N F:ARG144 3.3 53.2 1.0 CA F:LYS143 3.3 57.7 1.0 C F:ARG144 3.4 60.5 1.0 C F:GLY142 3.4 52.7 1.0 O F:LYS143 3.5 60.6 1.0 CD2 F:LEU141 3.6 58.5 1.0 CG F:LEU141 3.7 50.4 1.0 N F:LYS143 3.8 52.2 1.0 CA F:ARG144 3.9 58.9 1.0 CB F:ASN179 4.2 53.5 1.0 CD1 F:LEU141 4.3 46.0 1.0 O F:LEU141 4.5 48.8 1.0 NH2 F:ARG186 4.5 62.8 1.0 N F:THR145 4.5 61.9 1.0 ND2 F:ASN179 4.7 48.7 1.0 CB F:LYS143 4.7 62.4 1.0 C F:LEU141 4.7 49.8 1.0 CA F:GLY142 4.8 45.6 1.0 CB F:ARG144 4.8 52.1 1.0 O F:ASN179 4.8 55.7 1.0 CB F:LEU141 4.9 40.0 1.0 N F:GLY142 4.9 46.6 1.0 CA F:THR145 4.9 69.7 1.0 CG F:ASN179 5.0 54.5 1.0

Sodium binding site 3 out of 4 in the Camel GSTM1-1 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 Camel GSTM1-1 in Complex with S-(P-Nitrobenzyl)Glutathione within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:50.0 occ:1.00 O A:LEU136 2.7 43.0 1.0 O C:ASP55 2.9 34.3 1.0 N A:PHE140 3.3 38.2 1.0 CB A:PHE140 3.4 49.5 1.0 C A:LEU136 3.5 36.7 1.0 C C:ASP55 3.6 35.6 1.0 CA A:PHE140 3.6 38.6 1.0 CA C:ASP55 3.7 35.4 1.0 CA A:LEU136 3.7 41.1 1.0 CB C:ASP55 3.8 41.4 1.0 CB A:GLU139 3.9 49.8 1.0 C A:GLU139 4.0 41.2 1.0 OD2 C:ASP55 4.2 46.8 1.0 CE1 C:PHE56 4.2 30.8 1.0 CB A:LEU136 4.2 33.2 1.0 CZ C:PHE56 4.4 35.3 1.0 OE1 A:GLU139 4.4 56.4 1.0 CG C:ASP55 4.4 44.1 1.0 CA A:GLU139 4.5 47.4 1.0 CG A:PHE140 4.5 40.6 1.0 CD2 A:LEU136 4.5 33.7 1.0 CD1 C:PHE56 4.5 35.7 1.0 CD1 A:PHE140 4.6 40.6 1.0 N C:PHE56 4.7 42.2 1.0 N A:PHE137 4.8 34.0 1.0 CE2 C:PHE56 4.8 27.9 1.0 O A:GLU139 4.8 43.3 1.0 N A:GLU139 4.8 41.1 1.0 O A:LYS135 4.9 41.2 1.0 CG C:PHE56 5.0 28.0 1.0 CG A:LEU136 5.0 47.1 1.0

Sodium binding site 4 out of 4 in the Camel GSTM1-1 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 Camel GSTM1-1 in Complex with S-(P-Nitrobenzyl)Glutathione within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:77.9 occ:1.00 O B:HOH919 2.5 73.2 1.0 O B:HOH975 3.5 46.5 1.0 O B:ASN84 3.6 54.6 1.0 CD2 B:LEU85 4.1 66.0 1.0 C B:ASN84 4.5 52.6 1.0 CB B:ASN84 4.6 60.8 1.0 O B:HOH978 4.7 42.4 1.0 O B:LEU152 4.7 53.1 1.0 CG B:LEU85 4.8 56.6 1.0 OH B:TYR22 4.9 63.6 1.0

F.Perperopoulou, N.Poudel, A.C.Papageorgiou, F.S.Ataya, N.E.Labrou. Structural and Functional Characterization of Camelus Dromedarius Glutathione Transferase M1-1. Life V. 12 2022.
ISSN: ESSN 2075-1729
PubMed: 35054499
DOI: 10.3390/LIFE12010106