Magnesium in PDB 2c13: 5-Hydroxy-Levulinic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa

All present enzymatic activity of 5-Hydroxy-Levulinic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa:
4.2.1.24;

The structure of 5-Hydroxy-Levulinic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa, PDB code: 2c13 was solved by F.Frere, M.Nentwich, S.Gacond, D.W.Heinz, R.Neier, N.Frankenberg-Dinkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	89.80 / 2.15
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	126.314, 126.314, 85.481, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 20.4

The structure of 5-Hydroxy-Levulinic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the 5-Hydroxy-Levulinic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa (pdb code 2c13). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the 5-Hydroxy-Levulinic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa, PDB code: 2c13:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the 5-Hydroxy-Levulinic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 5-Hydroxy-Levulinic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1336 b:10.8 occ:1.00 O A:HOH2185 2.0 14.1 1.0 OE1 A:GLU245 2.0 12.7 1.0 O A:HOH2181 2.1 8.6 1.0 O A:HOH2182 2.1 14.4 1.0 O A:HOH2183 2.1 6.8 1.0 O A:HOH2144 2.2 20.2 1.0 CD A:GLU245 3.1 12.4 1.0 OE2 A:GLU245 3.5 10.3 1.0 NH1 A:ARG181 3.7 9.8 1.0 OD1 A:ASP249 3.8 11.7 1.0 O A:HOH2143 4.0 14.5 1.0 O A:HOH2189 4.1 7.4 1.0 O A:HOH2188 4.2 12.3 1.0 OD2 A:ASP249 4.3 13.3 1.0 O A:MET178 4.3 13.0 1.0 CG A:GLU245 4.4 10.2 1.0 CG A:ASP249 4.4 13.4 1.0 O A:SER203 4.5 12.0 1.0 OD1 A:ASP179 4.5 12.9 1.0 O A:GLU245 4.5 9.3 1.0 CB A:GLU245 4.6 12.0 1.0 O B:HOH2023 4.6 12.4 1.0 CA A:ASP179 4.7 11.7 1.0 CA A:GLU245 4.7 11.2 1.0 SD A:MET177 4.8 13.5 1.0 CZ A:ARG181 5.0 12.3 1.0 CE A:MET177 5.0 6.6 1.0

Magnesium binding site 2 out of 2 in the 5-Hydroxy-Levulinic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 5-Hydroxy-Levulinic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1336 b:10.8 occ:1.00 O B:HOH2189 2.1 11.2 1.0 O B:HOH2149 2.1 13.1 1.0 OE1 B:GLU245 2.1 11.8 1.0 O B:HOH2191 2.1 14.6 1.0 O B:HOH2146 2.2 10.9 1.0 O B:HOH2145 2.2 10.9 1.0 CD B:GLU245 3.2 13.0 1.0 OE2 B:GLU245 3.6 10.5 1.0 NH1 B:ARG181 3.7 13.6 1.0 OD1 B:ASP249 3.9 13.1 1.0 O B:HOH2144 4.0 8.1 1.0 O B:HOH2195 4.0 8.2 1.0 O B:HOH2194 4.2 11.3 1.0 OD2 B:ASP249 4.3 14.9 1.0 O B:MET178 4.4 13.5 1.0 OD1 B:ASP179 4.4 13.8 1.0 CG B:GLU245 4.5 9.4 1.0 CG B:ASP249 4.5 12.8 1.0 O B:SER203 4.6 13.1 1.0 CB B:GLU245 4.6 9.8 1.0 O B:GLU245 4.7 10.6 1.0 O A:HOH2024 4.7 14.4 1.0 CA B:ASP179 4.7 12.4 1.0 CA B:GLU245 4.7 10.1 1.0 SD B:MET177 4.8 15.2 1.0 CZ B:ARG181 5.0 12.2 1.0

F.Frere, M.Nentwich, S.Gacond, D.W.Heinz, R.Neier, N.Frankenberg-Dinkel. Probing the Active Site of Pseudomonas Aeruginosa Porphobilinogen Synthase Using Newly Developed Inhibitors. Biochemistry V. 45 8243 2006.
ISSN: ISSN 0006-2960
PubMed: 16819823
DOI: 10.1021/BI052611F