Magnesium in PDB 1l6y: Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4-Oxosebacic Acid

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

The structure of Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4-Oxosebacic Acid, PDB code: 1l6y 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 / 1.90
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 (%)	20.6 / 26.3

The structure of Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4-Oxosebacic 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-Oxosebacic Acid (pdb code 1l6y). 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-Oxosebacic Acid, PDB code: 1l6y:
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-Oxosebacic 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-Oxosebacic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:26.9 occ:1.00 O A:HOH483 2.0 25.5 1.0 O A:HOH422 2.0 31.4 1.0 O A:HOH433 2.1 30.2 1.0 OE1 A:GLU231 2.1 21.5 1.0 O A:HOH403 2.2 21.7 1.0 O A:HOH439 2.3 23.4 1.0 CD A:GLU231 3.1 18.3 1.0 OE2 A:GLU231 3.3 29.9 1.0 O A:HOH414 4.0 29.7 1.0 OD1 A:ASP235 4.0 34.5 1.0 O B:HOH425 4.0 29.4 1.0 O A:HOH409 4.2 29.2 1.0 O A:SER192 4.3 29.2 1.0 OD1 A:ASP168 4.3 38.1 1.0 O A:GLU231 4.3 20.8 1.0 CG A:GLU231 4.4 29.5 1.0 O A:HOH404 4.5 25.6 1.0 NE2 A:GLN170 4.5 22.6 1.0 O A:MET167 4.5 25.9 1.0 CA A:ASP168 4.5 33.3 1.0 OD2 A:ASP235 4.5 28.1 1.0 CG A:ASP235 4.7 64.0 1.0 CB A:GLU231 4.7 34.4 1.0 CA A:GLU231 4.8 22.8 1.0 C A:MET167 4.9 36.7 1.0 C A:GLU231 4.9 15.7 1.0 CG B:PRO7 4.9 30.8 1.0 N A:ASP168 4.9 45.2 1.0 O A:HOH446 5.0 43.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4-Oxosebacic 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-Oxosebacic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:29.3 occ:1.00 OE1 B:GLU231 1.9 23.6 1.0 O B:HOH427 2.2 28.8 1.0 O B:HOH412 2.2 23.4 1.0 O B:HOH448 2.2 27.2 1.0 O B:HOH430 2.4 24.0 1.0 O B:HOH421 2.6 32.4 1.0 CD B:GLU231 3.1 78.0 1.0 OE2 B:GLU231 3.6 24.3 1.0 OD1 B:ASP235 3.9 21.3 1.0 O B:SER192 4.0 27.6 1.0 O B:HOH458 4.0 28.3 1.0 O B:GLU231 4.2 25.3 1.0 O B:HOH419 4.3 28.3 1.0 OD2 B:ASP235 4.4 25.4 1.0 O B:HOH424 4.4 30.0 1.0 CG B:GLU231 4.4 24.8 1.0 O A:HOH487 4.4 28.8 1.0 O B:HOH434 4.4 30.5 1.0 O B:HOH418 4.4 31.9 1.0 O B:MET167 4.4 28.4 1.0 CG B:ASP235 4.5 22.0 1.0 CB B:GLU231 4.5 31.4 1.0 CA B:GLU231 4.6 15.3 1.0 OD1 B:ASP168 4.7 44.4 1.0 C B:GLU231 4.7 30.6 1.0 NE2 B:GLN170 4.7 43.6 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