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Magnesium in PDB 2c18: 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa

Enzymatic activity of 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa

All present enzymatic activity of 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa:
4.2.1.24;

Protein crystallography data

The structure of 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa, PDB code: 2c18 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 / 1.93
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 125.596, 125.596, 86.573, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 18.6

Other elements in 2c18:

The structure of 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa (pdb code 2c18). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa, PDB code: 2c18:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 2c18

Go back to Magnesium Binding Sites List in 2c18
Magnesium binding site 1 out of 7 in the 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic 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-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg347

b:53.3
occ:1.00
 O B:HOH2316 2.1 17.9 1.0
O B:HOH2172 2.4 37.4 1.0
O B:ALA318 4.0 13.2 1.0
OD1 B:ASP319 4.0 17.0 1.0
O B:GLY317 4.1 16.7 1.0
NZ B:LYS273 4.3 18.0 0.5
C B:GLY317 4.5 15.8 1.0
O B:HOH2085 4.5 50.6 1.0
O B:LYS314 4.5 13.8 1.0
C B:ALA318 4.6 13.6 1.0
CE B:LYS314 4.6 18.4 1.0
CA B:GLY317 4.7 15.1 1.0
O B:HOH2317 4.8 34.0 1.0
CG B:ASP319 4.9 16.0 1.0
O B:HOH2286 5.0 7.0 0.2

Magnesium binding site 2 out of 7 in 2c18

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Magnesium binding site 2 out of 7 in the 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic 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-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg348

b:27.6
occ:0.50
 O B:HOH2305 2.0 40.2 1.0
O A:HOH2242 2.2 30.3 1.0
O A:HOH2238 2.3 37.0 1.0
O A:HOH2234 2.3 24.9 1.0
O B:TRP300 3.9 18.8 1.0
O A:HOH2235 4.0 26.2 1.0
O A:HOH2239 4.1 48.2 1.0
OD1 A:ASP216 4.2 24.0 0.7
O B:GLY299 4.2 20.9 1.0
OD2 A:ASP216 4.3 24.1 0.7
O A:GLY212 4.3 17.1 1.0
CA A:GLY212 4.3 16.2 1.0
C A:GLY212 4.4 16.8 1.0
C B:TRP300 4.5 18.2 1.0
O A:HOH2233 4.6 19.4 1.0
CG A:ASP216 4.6 22.7 0.7

Magnesium binding site 3 out of 7 in 2c18

Go back to Magnesium Binding Sites List in 2c18
Magnesium binding site 3 out of 7 in the 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic 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 3 of 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg349

b:29.9
occ:0.50
 O B:HOH2033 2.1 44.5 1.0
O B:HOH2067 2.3 32.1 1.0
O B:GLU30 4.5 14.6 1.0
O B:HOH2065 4.9 25.4 1.0

Magnesium binding site 4 out of 7 in 2c18

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Magnesium binding site 4 out of 7 in the 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic 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 4 of 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1337

b:17.2
occ:1.00
 O A:HOH2214 2.0 13.4 1.0
O A:HOH2273 2.1 12.7 1.0
O A:HOH2218 2.1 11.8 1.0
OE1 A:GLU245 2.1 14.0 1.0
O A:HOH2270 2.1 12.5 1.0
O A:HOH2272 2.2 14.2 1.0
CD A:GLU245 3.1 11.5 1.0
OE2 A:GLU245 3.5 11.3 1.0
NH1 A:ARG181 3.7 19.5 1.0
OD1 A:ASP249 3.8 11.3 1.0
O A:HOH2215 4.1 12.4 1.0
O A:HOH2275 4.1 12.0 1.0
O A:HOH2276 4.2 14.8 1.0
OD2 A:ASP249 4.2 11.4 1.0
O A:MET178 4.3 13.4 1.0
CG A:ASP249 4.4 13.4 1.0
CG A:GLU245 4.5 10.0 1.0
OD1 A:ASP179 4.5 14.2 1.0
O A:SER203 4.5 15.0 1.0
O A:GLU245 4.7 10.1 1.0
CB A:GLU245 4.7 11.1 1.0
O B:HOH2037 4.7 17.0 1.0
CA A:ASP179 4.7 12.3 1.0
SD A:MET177 4.8 14.8 1.0
CA A:GLU245 4.8 11.2 1.0
CE A:MET177 4.9 15.2 1.0
CZ A:ARG181 5.0 15.0 1.0
C A:MET178 5.0 13.0 1.0

Magnesium binding site 5 out of 7 in 2c18

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Magnesium binding site 5 out of 7 in the 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic 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 5 of 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1338

b:23.9
occ:1.00
 OD1 A:ASP131 2.0 24.1 1.0
OD2 A:ASP139 2.0 21.3 1.0
O A:HOH2176 2.1 27.3 1.0
O A:HOH2172 2.1 22.7 1.0
O A:HOH2212 2.1 19.9 1.0
OD1 A:ASP176 2.2 18.7 1.0
CG A:ASP131 2.9 21.8 1.0
CG A:ASP139 3.2 20.1 1.0
OD2 A:ASP131 3.3 24.7 1.0
CG A:ASP176 3.4 18.7 1.0
CB A:ASP139 3.8 19.6 1.0
O4 A:LSO260 3.9 27.9 1.0
CB A:ASP131 4.0 20.2 1.0
OD2 A:ASP176 4.0 17.6 1.0
OD1 A:ASP139 4.2 20.3 1.0
CB A:ALA129 4.2 15.3 1.0
C7 A:LSO260 4.3 23.7 1.0
O A:HOH2168 4.3 21.7 1.0
NZ A:LYS205 4.5 26.0 1.0
CA A:ASP139 4.5 19.3 1.0
CA A:ASP176 4.5 16.6 1.0
CB A:ASP176 4.5 17.2 1.0
CL A:CL1340 4.6 18.0 1.0
OG A:SER175 4.6 13.5 1.0
O A:SER175 4.7 17.7 1.0
N A:ASP131 4.7 17.9 1.0
NZ A:LYS229 4.8 21.9 1.0
N A:ASP176 4.9 15.9 1.0
C8 A:LSO260 4.9 25.2 1.0
C A:SER175 5.0 15.9 1.0
CA A:ASP131 5.0 19.8 1.0

Magnesium binding site 6 out of 7 in 2c18

Go back to Magnesium Binding Sites List in 2c18
Magnesium binding site 6 out of 7 in the 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic 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 6 of 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1337

b:15.7
occ:1.00
 O B:HOH2233 2.0 14.4 1.0
O B:HOH2237 2.1 11.3 1.0
OE1 B:GLU245 2.2 16.2 1.0
O B:HOH2276 2.2 12.9 1.0
O B:HOH2234 2.2 13.0 1.0
O B:HOH2277 2.2 13.3 1.0
CD B:GLU245 3.2 15.1 1.0
OE2 B:GLU245 3.5 13.8 1.0
NH1 B:ARG181 3.7 15.4 1.0
OD1 B:ASP249 3.9 12.6 1.0
O B:HOH2232 4.1 12.8 1.0
O B:HOH2280 4.1 10.7 1.0
O B:HOH2281 4.1 13.6 1.0
OD2 B:ASP249 4.2 12.7 1.0
O B:MET178 4.2 13.8 1.0
OD1 B:ASP179 4.4 15.9 1.0
CG B:ASP249 4.4 13.9 1.0
CG B:GLU245 4.5 14.9 1.0
CA B:ASP179 4.6 12.9 1.0
O B:SER203 4.7 14.7 1.0
O A:HOH2033 4.7 18.1 1.0
O B:GLU245 4.8 14.0 1.0
CB B:GLU245 4.8 12.6 1.0
SD B:MET177 4.8 15.9 1.0
CA B:GLU245 4.9 13.1 1.0
C B:MET178 4.9 14.0 1.0
CE B:MET177 5.0 15.0 1.0

Magnesium binding site 7 out of 7 in 2c18

Go back to Magnesium Binding Sites List in 2c18
Magnesium binding site 7 out of 7 in the 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic 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 7 of 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1338

b:30.0
occ:0.70
 OD1 B:ASP176 1.9 29.4 1.0
O B:HOH2251 1.9 34.0 1.0
O B:HOH2229 2.0 24.4 1.0
OD1 B:ASP131 2.2 33.7 1.0
O B:HOH2203 2.2 2.0 0.2
OD1 B:ASP139 2.2 27.5 1.0
CG B:ASP131 3.0 27.6 1.0
CG B:ASP176 3.1 26.2 1.0
CG B:ASP139 3.3 24.7 1.0
OD2 B:ASP131 3.6 34.4 1.0
CB B:ASP139 3.7 24.7 1.0
O4 B:LSO260 3.8 37.5 1.0
OD2 B:ASP176 3.8 24.7 1.0
CB B:ASP131 4.0 24.0 1.0
NZ B:LYS205 4.1 21.6 1.0
CA B:ASP176 4.2 21.4 1.0
CB B:ASP176 4.2 23.1 1.0
CB B:ALA129 4.2 16.4 1.0
O B:HOH2231 4.3 3.5 1.0
OD2 B:ASP139 4.3 24.0 1.0
C7 B:LSO260 4.4 28.1 1.0
CA B:ASP139 4.5 24.7 1.0
O B:HOH2198 4.5 19.7 1.0
O B:SER175 4.5 20.0 1.0
OG B:SER175 4.6 15.7 1.0
N B:ASP176 4.6 20.3 1.0
C B:SER175 4.8 19.3 1.0
N B:ASP131 4.8 20.9 1.0
O B:HOH2264 4.9 38.8 1.0
C8 B:LSO260 4.9 29.8 1.0
NZ B:LYS229 5.0 27.1 1.0
CA B:ASP131 5.0 22.8 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 22:08:03 2024

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