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Magnesium in PDB 2c19: 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa

Enzymatic activity of 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa

All present enzymatic activity of 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa:
4.2.1.24;

Protein crystallography data

The structure of 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa, PDB code: 2c19 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 / 2.05
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 127.203, 127.203, 85.848, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 20.1

Other elements in 2c19:

The structure of 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa (pdb code 2c19). 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-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa, PDB code: 2c19:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2c19

Go back to Magnesium Binding Sites List in 2c19
Magnesium binding site 1 out of 2 in the 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid 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-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1336

b:14.9
occ:1.00
 O A:HOH2268 2.0 11.8 1.0
OE1 A:GLU245 2.0 14.6 1.0
O A:HOH2267 2.1 12.2 1.0
O A:HOH2270 2.2 11.8 1.0
O A:HOH2217 2.2 15.3 1.0
O A:HOH2271 2.3 15.2 1.0
CD A:GLU245 3.1 14.2 1.0
OE2 A:GLU245 3.5 11.8 1.0
NH1 A:ARG181 3.7 12.2 1.0
OD1 A:ASP249 3.8 15.4 1.0
O A:HOH2275 4.0 11.7 1.0
O A:HOH2216 4.1 7.9 0.8
O A:HOH2276 4.2 11.6 1.0
O A:MET178 4.2 12.9 1.0
OD2 A:ASP249 4.3 14.1 1.0
CG A:ASP249 4.4 13.5 1.0
CG A:GLU245 4.4 12.5 1.0
OD1 A:ASP179 4.4 14.2 1.0
O A:SER203 4.6 13.4 1.0
CA A:ASP179 4.6 12.9 1.0
O A:GLU245 4.6 10.6 1.0
O B:HOH2035 4.7 13.3 1.0
CB A:GLU245 4.7 11.8 1.0
CA A:GLU245 4.8 11.8 1.0
SD A:MET177 4.9 13.1 1.0
C A:MET178 5.0 12.9 1.0
N A:GLY180 5.0 13.2 1.0

Magnesium binding site 2 out of 2 in 2c19

Go back to Magnesium Binding Sites List in 2c19
Magnesium binding site 2 out of 2 in the 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid 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-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1336

b:13.9
occ:1.00
 OE1 B:GLU245 2.1 11.7 1.0
O B:HOH2281 2.1 11.2 1.0
O B:HOH2284 2.1 13.3 1.0
O B:HOH2280 2.2 15.8 1.0
O B:HOH2240 2.2 14.2 1.0
O B:HOH2283 2.2 14.4 1.0
CD B:GLU245 3.1 13.2 1.0
OE2 B:GLU245 3.4 13.1 1.0
NH1 B:ARG181 3.7 13.7 1.0
OD1 B:ASP249 3.8 14.5 1.0
O B:HOH2239 4.1 12.4 1.0
O B:HOH2286 4.1 12.7 1.0
O B:HOH2288 4.2 13.0 1.0
OD2 B:ASP249 4.3 15.0 1.0
O B:MET178 4.3 15.6 1.0
CG B:ASP249 4.4 14.3 1.0
CG B:GLU245 4.4 12.5 1.0
O B:SER203 4.5 13.7 1.0
OD1 B:ASP179 4.6 15.1 1.0
O A:HOH2040 4.6 14.1 1.0
CA B:ASP179 4.7 15.0 1.0
CB B:GLU245 4.7 12.1 1.0
O B:GLU245 4.8 13.4 1.0
CA B:GLU245 4.9 12.6 1.0
SD B:MET177 4.9 14.1 1.0
CE B:MET177 4.9 9.1 1.0
N B:GLY180 5.0 15.0 1.0

Reference:

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
Page generated: Tue Aug 13 22:08:31 2024

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