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Magnesium in PDB 2woq: Porphobilinogen Synthase (Hemb) in Complex with 5-Acetamido-4- Oxohexanoic Acid (Alaremycin 2)

Enzymatic activity of Porphobilinogen Synthase (Hemb) in Complex with 5-Acetamido-4- Oxohexanoic Acid (Alaremycin 2)

All present enzymatic activity of Porphobilinogen Synthase (Hemb) in Complex with 5-Acetamido-4- Oxohexanoic Acid (Alaremycin 2):
4.2.1.24;

Protein crystallography data

The structure of Porphobilinogen Synthase (Hemb) in Complex with 5-Acetamido-4- Oxohexanoic Acid (Alaremycin 2), PDB code: 2woq was solved by I.U.Heinemann, C.Schulz, W.-D.Schubert, D.W.Heinz, Y.-G.Wang, Y.Kobayashi, Y.Awa, M.Wachi, D.Jahn, M.Jahn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.31 / 1.75
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 84.444, 84.444, 158.528, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 18

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Porphobilinogen Synthase (Hemb) in Complex with 5-Acetamido-4- Oxohexanoic Acid (Alaremycin 2) (pdb code 2woq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Porphobilinogen Synthase (Hemb) in Complex with 5-Acetamido-4- Oxohexanoic Acid (Alaremycin 2), PDB code: 2woq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2woq

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Magnesium binding site 1 out of 4 in the Porphobilinogen Synthase (Hemb) in Complex with 5-Acetamido-4- Oxohexanoic Acid (Alaremycin 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Porphobilinogen Synthase (Hemb) in Complex with 5-Acetamido-4- Oxohexanoic Acid (Alaremycin 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1334

b:21.7
occ:0.70
 O A:HOH2167 1.9 18.1 1.0
O A:HOH2169 2.0 28.7 1.0
O A:HOH2059 2.0 26.8 1.0
C9 A:EPE1338 4.1 28.5 0.5
CD A:LYS314 4.1 15.4 0.2
O A:ALA318 4.1 10.9 1.0
O A:HOH2168 4.2 29.1 1.0
OD1 A:ASP319 4.2 11.5 1.0
O A:GLY317 4.2 12.8 1.0
O A:LYS314 4.4 10.3 1.0
O A:HOH2148 4.5 29.0 1.0
C A:GLY317 4.5 12.1 1.0
C6 A:EPE1338 4.5 30.5 0.5
CE A:LYS314 4.6 24.1 0.8
C2 A:EPE1338 4.6 29.2 0.5
O3S A:EPE1338 4.6 28.6 0.5
CA A:GLY317 4.6 11.5 1.0
N1 A:EPE1338 4.6 28.6 0.5
CE A:LYS314 4.7 18.8 0.2
OD1 A:ASN31 4.7 15.7 1.0
C10 A:EPE1338 4.8 26.4 0.5
C A:ALA318 4.8 10.0 1.0

Magnesium binding site 2 out of 4 in 2woq

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Magnesium binding site 2 out of 4 in the Porphobilinogen Synthase (Hemb) in Complex with 5-Acetamido-4- Oxohexanoic Acid (Alaremycin 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Porphobilinogen Synthase (Hemb) in Complex with 5-Acetamido-4- Oxohexanoic Acid (Alaremycin 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1335

b:11.2
occ:1.00
 OE1 A:GLU245 2.0 9.4 1.0
O A:HOH2139 2.0 9.4 1.0
O A:HOH2107 2.1 7.2 1.0
O A:HOH2137 2.1 9.9 1.0
O A:HOH2108 2.1 9.0 1.0
O A:HOH2140 2.2 10.7 1.0
CD A:GLU245 3.0 11.1 1.0
OE2 A:GLU245 3.4 10.4 1.0
NH1 A:ARG181 3.8 14.4 1.0
OD1 A:ASP249 3.9 10.8 1.0
O A:HOH2106 4.0 9.4 1.0
O A:HOH2143 4.2 8.8 1.0
O A:HOH2144 4.2 7.1 1.0
OD2 A:ASP249 4.3 10.5 1.0
O A:MET178 4.4 7.8 1.0
CG A:GLU245 4.4 9.3 1.0
OD1 A:ASP179 4.5 8.9 1.0
CG A:ASP249 4.5 8.8 1.0
O A:SER203 4.6 8.8 1.0
O A:GLU245 4.6 7.7 1.0
CB A:GLU245 4.6 7.5 1.0
CA A:ASP179 4.7 5.0 1.0
CE A:MET177 4.7 10.6 0.7
CA A:GLU245 4.7 7.3 1.0
SD A:MET177 4.7 10.3 0.7
SD A:MET177 4.9 5.3 0.3

Magnesium binding site 3 out of 4 in 2woq

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Magnesium binding site 3 out of 4 in the Porphobilinogen Synthase (Hemb) in Complex with 5-Acetamido-4- Oxohexanoic Acid (Alaremycin 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Porphobilinogen Synthase (Hemb) in Complex with 5-Acetamido-4- Oxohexanoic Acid (Alaremycin 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1336

b:10.2
occ:0.50
 OD1 A:ASP176 1.9 14.3 0.7
O A:HOH2105 1.9 16.7 1.0
OD2 A:ASP139 2.0 18.9 1.0
O A:HOH2090 2.0 24.7 1.0
OD1 A:ASP131 2.0 17.5 1.0
CG A:ASP131 3.1 17.8 1.0
CG A:ASP176 3.1 11.4 0.7
CG A:ASP139 3.1 17.4 1.0
CB A:ASP139 3.7 14.3 1.0
CAB A:AYC1333 3.8 24.5 1.0
OD2 A:ASP176 3.8 9.1 0.7
CB A:ASP131 3.9 12.0 1.0
O A:SER175 4.0 12.2 1.0
CB A:ALA129 4.0 12.8 1.0
OD2 A:ASP131 4.0 22.9 1.0
O A:HOH2085 4.1 16.0 1.0
CAQ A:AYC1333 4.1 23.4 1.0
OG A:SER175 4.2 8.6 1.0
CB A:ASP176 4.2 12.4 0.7
OD1 A:ASP139 4.2 18.6 1.0
CA A:ASP176 4.2 9.8 0.7
NZ A:LYS205 4.3 14.4 1.0
CA A:ASP139 4.4 12.0 1.0
C A:SER175 4.4 10.7 1.0
O A:HOH2128 4.4 4.9 1.0
CA A:ASP176 4.5 3.7 0.3
NAP A:AYC1333 4.5 19.9 1.0
OAD A:AYC1333 4.5 22.2 1.0
N A:ASP176 4.5 9.6 0.7
N A:ASP131 4.6 9.0 1.0
N A:ASP176 4.8 5.4 0.3
CA A:ASP131 4.9 10.4 1.0
O A:HOH2173 5.0 19.6 1.0
CA A:ALA129 5.0 11.3 1.0

Magnesium binding site 4 out of 4 in 2woq

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Magnesium binding site 4 out of 4 in the Porphobilinogen Synthase (Hemb) in Complex with 5-Acetamido-4- Oxohexanoic Acid (Alaremycin 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Porphobilinogen Synthase (Hemb) in Complex with 5-Acetamido-4- Oxohexanoic Acid (Alaremycin 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1337

b:8.2
occ:0.50
 OD1 A:ASP37 2.1 11.9 1.0
O A:ASP319 2.1 11.3 1.0
O A:HOH2031 2.2 27.7 1.0
C A:ASP319 3.3 10.8 1.0
CG A:ASP37 3.3 13.7 1.0
CA A:ASP319 3.8 8.7 1.0
O A:HOH2027 4.0 24.5 1.0
CA A:ASP37 4.1 13.0 1.0
CB A:ASP37 4.1 12.8 1.0
O A:HOH2174 4.2 38.0 1.0
OD2 A:ASP37 4.3 11.2 1.0
O A:ASP36 4.3 14.6 1.0
CE A:LYS314 4.3 24.1 0.8
NZ A:LYS314 4.4 17.3 0.2
CB A:ASP319 4.4 9.4 1.0
N A:GLY320 4.4 11.4 1.0
N A:ASP37 4.4 11.1 1.0
CE A:LYS314 4.4 18.8 0.2
C A:ASP36 4.5 13.5 1.0
NZ A:LYS314 4.5 20.9 0.8
CA A:GLY320 4.8 10.7 1.0
CD A:LYS314 5.0 18.9 0.8
O A:ALA318 5.0 10.9 1.0
CB A:ASP36 5.0 13.6 1.0

Reference:

I.U.Heinemann, C.Schulz, W.D.Schubert, D.W.Heinz, Y.G.Wang, Y.Kobayashi, Y.Awa, M.Wachi, D.Jahn, M.Jahn. Structure of the Heme Biosynthetic Pseudomonas Aeruginosa Porphobilinogen Synthase in Complex with the Antibiotic Alaremycin. Antimicrob. Agents V. 54 267 2010CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 19822707
DOI: 10.1128/AAC.00553-09
Page generated: Sun Aug 10 15:45:13 2025

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