Calcium in PDB 8c5d: Glutathione Transferase P1-1 From Mus Musculus

All present enzymatic activity of Glutathione Transferase P1-1 From Mus Musculus:
2.5.1.18;

The structure of Glutathione Transferase P1-1 From Mus Musculus, PDB code: 8c5d was solved by A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.68 / 1.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.617, 77.366, 101.444, 90, 90, 90
R / Rfree (%)	17.5 / 20

The structure of Glutathione Transferase P1-1 From Mus Musculus also contains other interesting chemical elements:

Sodium	(Na)	11 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Glutathione Transferase P1-1 From Mus Musculus (pdb code 8c5d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Glutathione Transferase P1-1 From Mus Musculus, PDB code: 8c5d:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Glutathione Transferase P1-1 From Mus Musculus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Glutathione Transferase P1-1 From Mus Musculus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca509 b:20.6 occ:1.00 HG3 A:ARG13 2.6 20.6 1.0 H'1 A:GTB502 2.7 24.1 1.0 O A:HOH617 3.1 18.7 1.0 O A:HOH745 3.1 19.2 1.0 NA A:NA503 3.2 23.8 1.0 HH A:TYR7 3.4 21.1 1.0 H A:ARG13 3.4 18.0 1.0 HG22 A:VAL104 3.4 21.1 1.0 HA3 A:GLY12 3.4 17.7 1.0 HG21 A:VAL104 3.4 21.1 1.0 HA2 A:GLY12 3.4 17.7 1.0 C' A:GTB502 3.5 20.1 1.0 SG2 A:GTB502 3.5 18.4 1.0 CG A:ARG13 3.6 17.1 1.0 OH A:TYR7 3.7 17.5 1.0 N A:ARG13 3.7 15.0 1.0 CA A:GLY12 3.8 14.7 1.0 HD2 A:ARG13 3.8 20.2 1.0 CG2 A:VAL104 3.9 17.6 1.0 HE A:ARG13 3.9 20.3 1.0 H'2 A:GTB502 4.0 24.1 1.0 C A:GLY12 4.0 14.6 1.0 HE2 A:TYR108 4.0 22.7 1.0 HH A:TYR108 4.1 23.6 1.0 CD A:ARG13 4.1 16.8 1.0 H6' A:GTB502 4.1 27.1 1.0 HG2 A:ARG13 4.2 20.6 1.0 HB2 A:ARG13 4.2 19.9 1.0 NE A:ARG13 4.2 16.9 1.0 CB A:ARG13 4.3 16.5 1.0 HG23 A:VAL104 4.4 21.1 1.0 CA A:ARG13 4.6 15.2 1.0 HG11 A:VAL104 4.6 23.3 1.0 O A:HOH752 4.6 18.2 1.0 HG13 A:VAL104 4.6 23.3 1.0 C1' A:GTB502 4.6 21.4 1.0 HA A:ARG13 4.7 18.3 1.0 C6' A:GTB502 4.7 22.5 1.0 HD3 A:ARG100 4.8 18.2 1.0 CE2 A:TYR108 4.8 18.9 1.0 OH A:TYR108 4.8 19.7 1.0 CG1 A:VAL104 4.9 19.4 1.0 O A:GLY12 5.0 15.9 1.0

Calcium binding site 2 out of 4 in the Glutathione Transferase P1-1 From Mus Musculus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Glutathione Transferase P1-1 From Mus Musculus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca510 b:29.2 occ:1.00 HD22 A:ASN110 2.6 35.7 1.0 O A:HOH695 3.0 21.1 1.0 HA A:LEU106 3.1 22.3 1.0 HB3 A:ASN110 3.1 32.7 1.0 O A:HOH720 3.1 26.0 1.0 O A:HOH841 3.1 35.3 1.0 HD12 A:LEU106 3.3 26.6 1.0 HB2 A:LEU106 3.4 23.5 1.0 ND2 A:ASN110 3.4 29.8 1.0 HG22 A:THR105 3.5 24.8 1.0 HD13 A:LEU106 3.7 26.6 1.0 HA3 A:GLY114 3.8 32.0 1.0 CA A:LEU106 3.8 18.6 1.0 CB A:ASN110 3.9 27.2 1.0 CD1 A:LEU106 3.9 22.2 1.0 CB A:LEU106 4.0 19.6 1.0 HD21 A:ASN110 4.0 35.7 1.0 N A:LEU106 4.1 17.4 1.0 HB2 A:ASN110 4.1 32.7 1.0 CG A:ASN110 4.2 29.1 1.0 HD2 A:TYR118 4.2 21.6 1.0 H A:LEU106 4.3 20.9 1.0 CG2 A:THR105 4.4 20.7 1.0 C A:THR105 4.6 17.9 1.0 HB2 A:TYR118 4.6 25.0 1.0 CG A:LEU106 4.6 21.2 1.0 HG21 A:THR105 4.6 24.8 1.0 O A:HOH893 4.7 27.0 1.0 CA A:GLY114 4.7 26.7 1.0 HB A:THR105 4.7 22.6 1.0 O A:THR105 4.7 19.4 1.0 HD11 A:LEU106 4.7 26.6 1.0 O A:HOH782 4.7 34.8 1.0 O A:ASN110 4.8 26.1 1.0 HB3 A:LEU106 4.8 23.5 1.0 O A:HOH868 4.9 24.9 1.0 O A:GLY114 4.9 25.0 1.0 HA2 A:GLY114 4.9 32.0 1.0 O A:HOH901 5.0 29.9 1.0

Calcium binding site 3 out of 4 in the Glutathione Transferase P1-1 From Mus Musculus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Glutathione Transferase P1-1 From Mus Musculus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca307 b:27.2 occ:1.00 H'1 B:GTB302 2.6 31.6 1.0 HG3 B:ARG13 2.7 25.8 1.0 O B:HOH533 3.1 20.1 1.0 O B:HOH412 3.1 22.4 1.0 O B:HOH534 3.1 21.4 1.0 HH B:TYR7 3.3 27.3 1.0 HA3 B:GLY12 3.3 28.1 1.0 HG22 B:VAL104 3.3 24.9 1.0 HA2 B:GLY12 3.3 28.1 1.0 H B:ARG13 3.4 25.9 1.0 C' B:GTB302 3.4 26.4 1.0 HG21 B:VAL104 3.5 24.9 1.0 OH B:TYR7 3.5 22.8 1.0 SG2 B:GTB302 3.6 24.9 1.0 CG B:ARG13 3.6 21.5 1.0 CA B:GLY12 3.7 23.4 1.0 N B:ARG13 3.7 21.6 1.0 CG2 B:VAL104 3.9 20.7 1.0 H6' B:GTB302 4.0 34.7 1.0 C B:GLY12 4.0 22.9 1.0 HD2 B:ARG13 4.0 25.7 1.0 HE B:ARG13 4.0 24.8 1.0 H'2 B:GTB302 4.0 31.6 1.0 HE2 B:TYR108 4.0 29.3 1.0 HG2 B:ARG13 4.1 25.8 1.0 CD B:ARG13 4.2 21.4 1.0 HB2 B:ARG13 4.2 25.5 1.0 NE B:ARG13 4.3 20.7 1.0 CB B:ARG13 4.3 21.2 1.0 HH B:TYR108 4.4 30.6 1.0 HG11 B:VAL104 4.4 25.2 1.0 HG13 B:VAL104 4.4 25.2 1.0 HG23 B:VAL104 4.4 24.9 1.0 C1' B:GTB302 4.5 28.9 1.0 O B:HOH532 4.5 22.0 1.0 CA B:ARG13 4.6 22.1 1.0 C6' B:GTB302 4.6 28.9 1.0 HA B:ARG13 4.7 26.5 1.0 HD3 B:ARG100 4.7 23.6 1.0 CG1 B:VAL104 4.8 21.0 1.0 CE2 B:TYR108 4.8 24.4 1.0 OH B:TYR108 4.9 25.5 1.0 O B:GLY12 4.9 21.8 1.0 CZ B:TYR7 4.9 22.7 1.0 CB B:VAL104 4.9 20.3 1.0

Calcium binding site 4 out of 4 in the Glutathione Transferase P1-1 From Mus Musculus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Glutathione Transferase P1-1 From Mus Musculus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca308 b:98.2 occ:1.00 O A:HOH874 2.7 38.0 1.0 O B:HOH431 2.8 36.7 1.0 HB2 B:LEU48 3.2 27.1 1.0 HE1 B:TYR63 3.2 29.9 1.0 HH B:TYR63 3.2 33.3 1.0 HA B:LEU48 3.4 26.7 1.0 O B:THR46 3.4 28.6 1.0 O A:HOH886 3.5 40.4 1.0 O B:HOH501 3.6 38.2 1.0 H B:LEU48 3.6 28.4 1.0 HD13 B:LEU48 3.7 29.9 1.0 N B:LEU48 3.7 23.6 1.0 CE1 B:TYR63 3.8 24.9 1.0 OH B:TYR63 3.8 27.8 1.0 CA B:LEU48 3.8 22.2 1.0 CB B:LEU48 4.0 22.6 1.0 O B:HOH562 4.0 37.1 1.0 CZ B:TYR63 4.1 25.2 1.0 O B:HOH524 4.2 37.6 1.0 HA B:CYS47 4.3 31.1 1.0 C B:CYS47 4.4 23.5 1.0 C B:THR46 4.5 28.0 1.0 CD1 B:LEU48 4.5 24.9 1.0 HB3 B:LEU48 4.6 27.1 1.0 HD12 B:LEU48 4.7 29.9 1.0 CD1 B:TYR63 4.7 24.4 1.0 HE22 A:GLN135 4.8 53.2 1.0 CA B:CYS47 4.8 25.9 1.0 CG B:LEU48 4.8 23.5 1.0 HD1 B:TYR63 4.9 29.3 1.0 HD22 B:LEU48 4.9 28.1 1.0 O B:HOH557 5.0 31.5 1.0

O.Kupreienko, F.Pouliou, K.Konstandinidis, I.Axarli, E.Douni, A.C.Papageorgiou, N.E.Labrou. Inhibition Analysis and High-Resolution Crystal Structure of Mus Musculus Glutathione Transferase P1-1. Biomolecules V. 13 2023.
ISSN: ESSN 2218-273X
PubMed: 37189361
DOI: 10.3390/BIOM13040613