Magnesium in PDB 1i8j: Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid

All present enzymatic activity of Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid:
4.2.1.24;

The structure of Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid, PDB code: 1i8j was solved by J.Kervinen, E.K.Jaffe, F.Stauffer, R.Neier, A.Wlodawer, A.Zdanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.00 / 1.90
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.741, 128.741, 142.760, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.7

The structure of Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid (pdb code 1i8j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid, PDB code: 1i8j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:21.2 occ:1.00 O A:HOH439 2.0 23.5 1.0 OE1 A:GLU231 2.0 19.1 1.0 O A:HOH433 2.1 20.4 1.0 O A:HOH483 2.1 18.6 1.0 O A:HOH422 2.2 24.2 1.0 O A:HOH403 2.2 21.3 1.0 CD A:GLU231 3.1 23.0 1.0 OE2 A:GLU231 3.4 27.1 1.0 O A:HOH414 4.0 25.7 1.0 OD1 A:ASP235 4.0 20.2 1.0 O A:HOH425 4.1 23.8 1.0 O A:SER192 4.2 22.4 1.0 O A:HOH409 4.3 22.8 1.0 O A:GLU231 4.3 18.8 1.0 O A:MET167 4.4 26.2 1.0 CG A:GLU231 4.4 20.0 1.0 OD1 A:ASP168 4.5 21.3 1.0 OD2 A:ASP235 4.5 19.8 1.0 NE2 A:GLN170 4.6 27.7 1.0 CG A:ASP235 4.6 25.2 1.0 O A:HOH404 4.6 20.1 1.0 CA A:ASP168 4.7 28.2 1.0 O A:HOH446 4.7 26.2 1.0 CB A:GLU231 4.7 17.7 1.0 O A:HOH410 4.7 20.5 1.0 CA A:GLU231 4.8 19.3 1.0 C A:GLU231 4.9 19.6 1.0 C A:MET167 4.9 25.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:26.1 occ:1.00 O B:HOH421 2.0 29.2 1.0 O B:HOH412 2.0 17.7 1.0 O B:HOH427 2.1 17.9 1.0 O B:HOH430 2.1 19.0 1.0 OE1 B:GLU231 2.1 25.1 1.0 O B:HOH448 2.2 30.6 1.0 CD B:GLU231 3.2 25.1 1.0 OE2 B:GLU231 3.7 25.2 1.0 OD1 B:ASP235 3.9 25.2 1.0 O B:HOH424 3.9 20.1 1.0 O B:HOH419 4.1 19.9 1.0 O B:SER192 4.1 21.0 1.0 O B:GLU231 4.1 21.9 1.0 OD2 B:ASP235 4.2 24.9 1.0 O B:MET167 4.2 25.8 1.0 O B:HOH418 4.3 18.4 1.0 NE2 B:GLN170 4.3 31.5 1.0 CG B:ASP235 4.4 19.2 1.0 O B:HOH434 4.5 21.6 1.0 O B:HOH458 4.5 23.1 1.0 CG B:GLU231 4.5 18.9 1.0 CB B:GLU231 4.7 18.2 1.0 OD1 B:ASP168 4.7 29.0 1.0 C B:GLU231 4.8 18.0 1.0 CA B:GLU231 4.8 19.5 1.0 O B:HOH487 4.8 27.4 1.0 CA B:ASP168 4.9 27.6 1.0 C B:MET167 5.0 28.7 1.0

J.Kervinen, E.K.Jaffe, F.Stauffer, R.Neier, A.Wlodawer, A.Zdanov. Mechanistic Basis For Suicide Inactivation of Porphobilinogen Synthase By 4,7-Dioxosebacic Acid, An Inhibitor That Shows Dramatic Species Selectivity. Biochemistry V. 40 8227 2001.
ISSN: ISSN 0006-2960
PubMed: 11444968
DOI: 10.1021/BI010656K