Sodium in PDB 7beu: Human Glutathione Transferase M1-1

All present enzymatic activity of Human Glutathione Transferase M1-1:
2.5.1.18;

The structure of Human Glutathione Transferase M1-1, PDB code: 7beu 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)	52.80 / 1.59
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.118, 211.188, 49.435, 90, 116.23, 90
R / Rfree (%)	18.8 / 22.6

The binding sites of Sodium atom in the Human Glutathione Transferase M1-1 (pdb code 7beu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Human Glutathione Transferase M1-1, PDB code: 7beu:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Human Glutathione Transferase M1-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Glutathione Transferase M1-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:35.2 occ:1.00 O A:HOH671 2.0 42.2 1.0 O A:HOH691 2.8 32.3 1.0 O D:HOH495 2.9 41.1 1.0 NH1 A:ARG81 3.2 18.5 1.0 SG A:CYS86 3.3 29.2 1.0 CG A:ARG81 3.6 15.3 1.0 CD A:ARG81 3.8 20.9 1.0 CB A:CYS77 4.0 12.5 1.0 CB A:CYS86 4.0 27.1 1.0 SG A:CYS77 4.2 20.2 1.0 CZ A:ARG81 4.3 19.3 1.0 O A:CYS77 4.3 17.1 1.0 OD2 D:ASP97 4.5 20.5 1.0 NE A:ARG81 4.5 18.5 1.0 O A:HOH415 4.6 37.3 1.0 O A:HOH673 4.6 36.6 1.0 CA A:CYS77 4.6 13.7 1.0 O A:HOH533 4.7 44.2 1.0 C A:CYS77 4.8 16.1 1.0 O D:HOH345 4.9 26.0 1.0

Sodium binding site 2 out of 7 in the Human Glutathione Transferase M1-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Glutathione Transferase M1-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:37.7 occ:1.00 O C:HOH633 2.2 37.6 1.0 O C:HOH668 2.4 45.5 1.0 O B:PRO57 2.7 19.3 1.0 N B:PRO57 3.0 14.6 1.0 CD B:PRO57 3.0 16.6 1.0 C B:PHE56 3.2 13.3 1.0 CD1 C:LEU136 3.3 17.9 1.0 C B:PRO57 3.5 14.9 1.0 CA B:PHE56 3.6 18.1 1.0 CA B:PRO57 3.7 18.5 1.0 O B:PHE56 3.8 16.1 1.0 O B:HOH564 3.9 44.4 1.0 CB B:PRO57 4.1 23.6 1.0 CB B:PHE56 4.1 16.0 1.0 CG B:PRO57 4.1 20.7 1.0 O C:HOH654 4.3 29.0 1.0 NA C:NA302 4.4 37.4 1.0 CE B:LYS49 4.7 34.5 1.0 CG C:LEU136 4.7 14.5 1.0 N B:ASN58 4.7 17.1 1.0 CD2 C:LEU136 5.0 17.3 1.0 N B:PHE56 5.0 13.5 1.0

Sodium binding site 3 out of 7 in the Human Glutathione Transferase M1-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Glutathione Transferase M1-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:34.6 occ:1.00 O B:HOH501 2.8 30.0 1.0 OD2 B:ASP182 4.4 24.5 1.0

Sodium binding site 4 out of 7 in the Human Glutathione Transferase M1-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Glutathione Transferase M1-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:43.9 occ:1.00 OD2 B:ASP8 2.7 37.5 1.0 O B:HOH632 2.7 44.2 1.0 CG2 B:THR33 2.8 30.6 1.0 O B:HOH536 3.3 48.3 1.0 CG B:ASP8 3.5 33.5 1.0 CB B:ASP8 3.6 22.2 1.0 CB B:THR33 3.7 40.5 1.0 CA B:THR33 4.4 39.4 1.0 O B:HOH568 4.7 52.4 1.0 OD1 B:ASP8 4.7 28.1 1.0 OG1 B:THR33 4.9 48.6 1.0 O B:HOH554 5.0 17.9 1.0

Sodium binding site 5 out of 7 in the Human Glutathione Transferase M1-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Human Glutathione Transferase M1-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:65.9 occ:1.00 O B:HOH460 2.4 32.0 1.0 O B:HOH572 2.6 41.8 1.0 O B:HOH630 2.7 35.6 1.0 OG B:SER194 4.2 27.9 1.0 O B:HOH544 4.3 45.1 1.0 O B:GLU188 4.8 23.1 1.0 NZ B:LYS198 4.9 51.9 1.0 CB B:SER194 5.0 20.8 1.0

Sodium binding site 6 out of 7 in the Human Glutathione Transferase M1-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Human Glutathione Transferase M1-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:42.0 occ:1.00 O C:HOH689 2.5 28.1 1.0 O C:HOH630 2.9 31.4 1.0 O C:HOH483 2.9 26.8 1.0 CB C:GLU132 3.7 25.2 1.0 CA C:GLU129 4.2 19.9 1.0 CG C:GLU132 4.3 33.0 1.0 O C:GLU128 4.3 22.1 1.0 O C:HOH580 4.5 39.9 1.0 CG C:GLU129 4.5 23.0 1.0 O C:HOH530 4.6 31.4 1.0 O C:GLU129 4.6 21.7 1.0 CB C:GLU129 4.7 20.7 1.0 C C:GLU129 4.8 21.1 1.0 CA C:GLU132 5.0 19.0 1.0

Sodium binding site 7 out of 7 in the Human Glutathione Transferase M1-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Human Glutathione Transferase M1-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:37.4 occ:1.00 OE2 C:GLU132 2.4 43.1 1.0 O C:HOH530 3.0 31.4 1.0 O C:HOH654 3.0 29.0 1.0 O C:HOH668 3.1 45.5 1.0 CG C:LYS133 3.4 27.6 1.0 O C:HOH669 3.6 41.9 1.0 CD C:GLU132 3.6 43.7 1.0 CA C:LYS133 3.8 17.8 1.0 CD1 C:LEU136 3.8 17.9 1.0 N C:LYS133 3.9 17.6 1.0 CB C:LYS133 4.1 21.6 1.0 OE1 C:GLU132 4.2 45.7 1.0 O C:HOH633 4.3 37.6 1.0 C C:GLU132 4.3 20.8 1.0 NA B:NA301 4.4 37.7 1.0 O C:GLU132 4.5 19.3 1.0 CB C:GLU132 4.6 25.2 1.0 CD C:LYS133 4.6 22.2 1.0 CG C:GLU132 4.7 33.0 1.0 CE C:LYS133 4.8 21.1 1.0 O C:HOH589 4.8 21.4 1.0 CG C:LEU136 4.8 14.5 1.0 O C:HOH689 4.9 28.1 1.0

C.S.Bodourian, N.Poudel, A.C.Papageorgiou, M.Antoniadi, N.D.Georgakis, H.Abe, N.E.Labrou. Ligandability Assessment of Human Glutathione Transferase M1-1 Using Pesticides As Chemical Probes. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 35408962
DOI: 10.3390/IJMS23073606