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:
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
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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 Sites List in 2c18
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
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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 Sites List in 2c18
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 Sites List in 2c18
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
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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
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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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