Magnesium in PDB 1l6s: 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: 1l6s was solved by E.K.Jaffe, J.Kervinen, J.Martins, 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)	40.00 / 1.70
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	129.000, 129.000, 142.800, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 24.3

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 1l6s). 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: 1l6s:
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:20.4 occ:1.00 O A:HOH433 2.0 19.0 1.0 O A:HOH439 2.1 19.7 1.0 O A:HOH483 2.1 17.2 1.0 OE1 A:GLU231 2.1 21.1 1.0 O A:HOH403 2.2 16.4 1.0 O A:HOH422 2.2 20.7 1.0 CD A:GLU231 3.1 19.4 1.0 OE2 A:GLU231 3.4 22.9 1.0 OD1 A:ASP235 4.0 20.7 1.0 O A:HOH414 4.1 24.5 1.0 O A:HOH425 4.1 18.3 1.0 O A:HOH409 4.2 21.0 1.0 O A:SER192 4.3 20.4 1.0 O A:MET167 4.3 19.6 1.0 O A:GLU231 4.3 18.0 1.0 OD1 A:ASP168 4.5 18.5 1.0 OD2 A:ASP235 4.5 18.7 1.0 CG A:GLU231 4.5 14.0 1.0 CG A:ASP235 4.6 25.1 1.0 NE2 A:GLN170 4.6 30.8 1.0 O A:HOH404 4.6 21.7 1.0 O A:HOH446 4.7 24.8 1.0 CA A:ASP168 4.7 25.5 1.0 CB A:GLU231 4.8 12.3 1.0 O A:HOH410 4.8 20.6 1.0 CA A:GLU231 4.9 16.0 1.0 C A:MET167 4.9 27.0 1.0 C A:GLU231 5.0 17.5 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:24.4 occ:1.00 O B:HOH430 2.1 19.0 1.0 O B:HOH421 2.1 18.1 1.0 OE1 B:GLU231 2.1 20.0 1.0 O B:HOH427 2.1 20.8 1.0 O B:HOH412 2.2 17.6 1.0 O B:HOH448 2.3 23.0 1.0 CD B:GLU231 3.1 27.0 1.0 OE2 B:GLU231 3.5 24.1 1.0 OD1 B:ASP235 3.9 23.3 1.0 O B:HOH424 4.0 19.4 1.0 O B:HOH419 4.0 21.6 1.0 O B:SER192 4.2 17.0 1.0 NE2 B:GLN170 4.2 34.6 1.0 O B:GLU231 4.3 17.9 1.0 O B:HOH458 4.3 21.7 1.0 O B:MET167 4.3 23.9 1.0 O B:HOH418 4.3 18.4 1.0 OD2 B:ASP235 4.3 24.1 1.0 CG B:ASP235 4.5 16.5 1.0 CG B:GLU231 4.5 19.7 1.0 OD1 B:ASP168 4.6 25.1 1.0 O B:HOH434 4.7 18.5 1.0 CB B:GLU231 4.8 19.0 1.0 CA B:ASP168 4.8 20.9 1.0 O B:HOH487 4.9 21.6 1.0 C B:MET167 4.9 29.6 1.0 CA B:GLU231 4.9 17.7 1.0 C B:GLU231 4.9 16.6 1.0

E.K.Jaffe, J.Kervinen, J.Martins, F.Stauffer, R.Neier, A.Wlodawer, A.Zdanov. Species-Specific Inhibition of Porphobilinogen Synthase By 4-Oxosebacic Acid J.Biol.Chem. V. 277 19792 2002.
ISSN: ISSN 0021-9258
PubMed: 11909869
DOI: 10.1074/JBC.M201486200