Iron in PDB 2pbj: Gsh-Heme Bound Microsomal Prostaglandin E Synthase

All present enzymatic activity of Gsh-Heme Bound Microsomal Prostaglandin E Synthase:
5.3.99.3;

The structure of Gsh-Heme Bound Microsomal Prostaglandin E Synthase, PDB code: 2pbj was solved by F.Takusagawa, T.Yamada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.000, 122.490, 110.970, 90.00, 111.00, 90.00
R / Rfree (%)	24.2 / 26.9

The structure of Gsh-Heme Bound Microsomal Prostaglandin E Synthase also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Iron atom in the Gsh-Heme Bound Microsomal Prostaglandin E Synthase (pdb code 2pbj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Gsh-Heme Bound Microsomal Prostaglandin E Synthase, PDB code: 2pbj:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Gsh-Heme Bound Microsomal Prostaglandin E Synthase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Gsh-Heme Bound Microsomal Prostaglandin E Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe476 b:43.2 occ:1.00 FE A:HEM476 0.0 43.2 1.0 ND A:HEM476 1.9 44.4 1.0 NA A:HEM476 2.0 44.8 1.0 NC A:HEM476 2.0 44.0 1.0 NB A:HEM476 2.0 42.4 1.0 SG2 A:GSH477 2.7 36.5 1.0 C1D A:HEM476 3.0 45.2 1.0 C4D A:HEM476 3.0 45.4 1.0 C1B A:HEM476 3.0 41.9 1.0 C4B A:HEM476 3.0 41.5 1.0 C1C A:HEM476 3.0 43.2 1.0 C4C A:HEM476 3.0 44.4 1.0 C1A A:HEM476 3.0 44.5 1.0 C4A A:HEM476 3.0 43.6 1.0 CHC A:HEM476 3.4 42.3 1.0 CHA A:HEM476 3.4 45.0 1.0 CHD A:HEM476 3.4 44.7 1.0 CHB A:HEM476 3.4 41.4 1.0 CB2 A:GSH477 3.6 36.0 1.0 C2C A:HEM476 4.2 42.8 1.0 C2A A:HEM476 4.2 44.6 1.0 C3A A:HEM476 4.2 44.3 1.0 C2B A:HEM476 4.2 42.1 1.0 C3C A:HEM476 4.2 44.3 1.0 C2D A:HEM476 4.2 45.4 1.0 C3D A:HEM476 4.2 46.0 1.0 C3B A:HEM476 4.3 40.9 1.0 CA2 A:GSH477 4.4 37.6 1.0

Iron binding site 2 out of 4 in the Gsh-Heme Bound Microsomal Prostaglandin E Synthase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Gsh-Heme Bound Microsomal Prostaglandin E Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe476 b:43.6 occ:1.00 FE B:HEM476 0.0 43.6 1.0 NC B:HEM476 1.9 43.9 1.0 NB B:HEM476 2.0 42.8 1.0 ND B:HEM476 2.0 44.5 1.0 NA B:HEM476 2.0 44.5 1.0 SG2 B:GSH477 2.6 28.9 1.0 C4B B:HEM476 3.0 41.5 1.0 C1C B:HEM476 3.0 42.5 1.0 C1D B:HEM476 3.0 45.2 1.0 C1B B:HEM476 3.0 42.0 1.0 C4C B:HEM476 3.0 43.4 1.0 C4D B:HEM476 3.0 45.1 1.0 C4A B:HEM476 3.0 43.0 1.0 C1A B:HEM476 3.1 44.6 1.0 CHC B:HEM476 3.3 41.8 1.0 CHD B:HEM476 3.4 44.1 1.0 CHB B:HEM476 3.4 41.9 1.0 CHA B:HEM476 3.4 44.9 1.0 CB2 B:GSH477 3.6 34.7 1.0 C2C B:HEM476 4.2 42.4 1.0 C3C B:HEM476 4.2 43.2 1.0 C2B B:HEM476 4.2 41.0 1.0 C3A B:HEM476 4.3 44.8 1.0 C2A B:HEM476 4.3 45.2 1.0 C3B B:HEM476 4.3 40.9 1.0 C2D B:HEM476 4.3 46.2 1.0 C3D B:HEM476 4.3 46.2 1.0 CA2 B:GSH477 4.4 35.9 1.0

Iron binding site 3 out of 4 in the Gsh-Heme Bound Microsomal Prostaglandin E Synthase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Gsh-Heme Bound Microsomal Prostaglandin E Synthase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe476 b:43.1 occ:1.00 FE C:HEM476 0.0 43.1 1.0 NA C:HEM476 1.9 43.8 1.0 NC C:HEM476 2.0 42.8 1.0 ND C:HEM476 2.0 43.1 1.0 NB C:HEM476 2.0 41.5 1.0 SG2 C:GSH477 2.7 32.4 1.0 C1B C:HEM476 3.0 40.8 1.0 C1D C:HEM476 3.0 43.0 1.0 C4D C:HEM476 3.0 44.2 1.0 C4B C:HEM476 3.0 40.7 1.0 C1C C:HEM476 3.0 41.9 1.0 C4A C:HEM476 3.0 43.1 1.0 C1A C:HEM476 3.0 44.0 1.0 C4C C:HEM476 3.0 43.1 1.0 CHC C:HEM476 3.4 41.0 1.0 CHB C:HEM476 3.4 40.6 1.0 CHA C:HEM476 3.4 43.5 1.0 CHD C:HEM476 3.4 43.2 1.0 CB2 C:GSH477 3.6 33.5 1.0 C2C C:HEM476 4.2 42.0 1.0 C2A C:HEM476 4.2 44.6 1.0 C3A C:HEM476 4.2 43.9 1.0 C2B C:HEM476 4.2 40.7 1.0 C3C C:HEM476 4.2 43.0 1.0 C2D C:HEM476 4.3 43.2 1.0 C3D C:HEM476 4.3 44.9 1.0 C3B C:HEM476 4.3 39.9 1.0 CA2 C:GSH477 4.4 35.9 1.0

Iron binding site 4 out of 4 in the Gsh-Heme Bound Microsomal Prostaglandin E Synthase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Gsh-Heme Bound Microsomal Prostaglandin E Synthase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe476 b:43.9 occ:1.00 FE D:HEM476 0.0 43.9 1.0 NA D:HEM476 2.0 42.7 1.0 ND D:HEM476 2.0 43.3 1.0 NC D:HEM476 2.0 42.8 1.0 NB D:HEM476 2.0 42.0 1.0 SG2 D:GSH477 2.7 28.7 1.0 C1D D:HEM476 3.0 43.9 1.0 C4D D:HEM476 3.0 44.5 1.0 C4B D:HEM476 3.0 40.7 1.0 C1B D:HEM476 3.0 41.0 1.0 C1C D:HEM476 3.0 42.2 1.0 C1A D:HEM476 3.0 43.3 1.0 C4A D:HEM476 3.0 42.4 1.0 C4C D:HEM476 3.0 42.6 1.0 CHC D:HEM476 3.4 41.2 1.0 CHA D:HEM476 3.4 43.8 1.0 CHB D:HEM476 3.4 40.6 1.0 CHD D:HEM476 3.4 43.1 1.0 CB2 D:GSH477 3.7 32.3 1.0 C2A D:HEM476 4.2 44.2 1.0 C3A D:HEM476 4.2 43.6 1.0 C2C D:HEM476 4.2 42.6 1.0 C2B D:HEM476 4.2 39.9 1.0 C3D D:HEM476 4.2 45.9 1.0 C2D D:HEM476 4.2 44.8 1.0 C3C D:HEM476 4.3 42.9 1.0 C3B D:HEM476 4.3 39.7 1.0 CA2 D:GSH477 4.4 35.1 1.0

T.Yamada, F.Takusagawa. PGH2 Degradation Pathway Catalyzed By Gsh-Heme Complex Bound Microsomal Prostaglandin E2 Synthase Type 2: the First Example of A Dual-Function Enzyme. Biochemistry V. 46 8414 2007.
ISSN: ISSN 0006-2960
PubMed: 17585783
DOI: 10.1021/BI700605M