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Fluorine in PDB 1gzg: Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid

Enzymatic activity of Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid

All present enzymatic activity of Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid:
4.2.1.24;

Protein crystallography data

The structure of Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid, PDB code: 1gzg was solved by F.Frere, W.-D.Schubert, F.Stauffer, N.Frankenberg, R.Neier, D.Jahn, D.W.Heinz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.29 / 1.66
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 127.131, 127.131, 86.145, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.8

Other elements in 1gzg:

The structure of Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Potassium (K) 2 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid (pdb code 1gzg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid, PDB code: 1gzg:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 1gzg

Go back to Fluorine Binding Sites List in 1gzg
Fluorine binding site 1 out of 6 in the Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1336

b:34.7
occ:1.00
F A:LAF1336 0.0 34.7 1.0
C5 A:LAF1336 1.4 30.2 1.0
NA A:NA1339 1.8 22.3 1.0
ND2 A:ASN139 2.5 27.8 1.0
C4 A:LAF1336 2.6 29.2 1.0
OG A:SER175 2.8 16.1 1.0
OD1 A:ASP131 2.9 25.8 1.0
NZ A:LYS205 3.1 24.9 1.0
O A:SER175 3.2 17.5 1.0
F A:LAF1337 3.4 25.1 1.0
CB A:SER175 3.6 16.5 1.0
CG A:ASP131 3.6 24.7 1.0
CG A:ASN139 3.6 28.6 1.0
CB A:ALA129 3.7 19.4 1.0
OD2 A:ASP131 3.8 29.5 1.0
C A:SER175 3.8 16.6 1.0
O A:HOH2196 3.9 36.1 1.0
C3 A:LAF1336 4.0 29.6 1.0
OD1 A:ASN139 4.2 31.2 1.0
C2 A:LAF1336 4.2 29.1 1.0
CA A:SER175 4.4 16.3 1.0
O A:HOH2240 4.4 22.6 1.0
C5 A:LAF1337 4.6 21.1 1.0
OD2 A:ASP127 4.6 18.5 1.0
N A:ASP176 4.6 16.4 1.0
CE A:LYS205 4.7 22.6 1.0
C1 A:LAF1336 4.7 29.8 1.0
CB A:ASP131 4.7 23.9 1.0
CB A:ASN139 4.7 27.8 1.0
OD1 A:ASP127 4.8 18.0 1.0
CA A:ASP176 4.9 16.6 1.0

Fluorine binding site 2 out of 6 in 1gzg

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Fluorine binding site 2 out of 6 in the Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1337

b:25.1
occ:1.00
F A:LAF1337 0.0 25.1 1.0
C5 A:LAF1337 1.4 21.1 1.0
C4 A:LAF1337 2.4 20.3 1.0
NA A:NA1339 2.7 22.3 1.0
NZ A:LYS260 2.8 19.1 1.0
C5 A:LAF1336 3.1 30.2 1.0
C4 A:LAF1336 3.2 29.2 1.0
OG A:SER175 3.3 16.1 1.0
CB A:SER175 3.4 16.5 1.0
F A:LAF1336 3.4 34.7 1.0
NZ A:LYS205 3.6 24.9 1.0
C3 A:LAF1336 3.7 29.6 1.0
C3 A:LAF1337 3.8 18.4 1.0
CE2 A:TYR202 3.9 15.5 1.0
CE1 A:PHE86 3.9 16.6 1.0
OH A:TYR202 4.0 16.8 1.0
OD1 A:ASP127 4.0 18.0 1.0
CZ A:TYR202 4.1 15.8 1.0
C2 A:LAF1336 4.1 29.1 1.0
O A:HOH2196 4.1 36.1 1.0
CE A:LYS260 4.3 17.3 1.0
CZ A:PHE86 4.4 15.9 1.0
CZ A:PHE214 4.5 16.7 1.0
CE A:LYS205 4.5 22.6 1.0
C2 A:LAF1337 4.6 17.4 1.0
OD2 A:ASP127 4.6 18.5 1.0
CD2 A:TYR202 4.7 15.2 1.0
CG A:ASP127 4.7 17.9 1.0
CA A:SER175 4.8 16.3 1.0
CE1 A:PHE214 4.9 17.6 1.0
CD1 A:PHE86 4.9 16.6 1.0
CD A:LYS260 4.9 15.3 1.0
O A:SER175 4.9 17.5 1.0
CE2 A:PHE214 4.9 15.7 1.0
CE1 A:TYR202 5.0 15.3 1.0
O A:HOH2264 5.0 16.0 1.0

Fluorine binding site 3 out of 6 in 1gzg

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Fluorine binding site 3 out of 6 in the Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1338

b:68.1
occ:0.35
F B:LAF1338 0.0 68.1 0.3
F B:LAF1338 1.2 35.4 0.3
C5 B:LAF1338 1.4 71.0 0.3
C5 B:LAF1338 1.4 68.5 0.3
NA B:NA1342 2.2 33.1 0.5
F B:LAF1338 2.3 71.1 0.3
C5 B:LAF1338 2.4 33.8 0.3
C4 B:LAF1338 2.5 71.0 0.3
C4 B:LAF1338 2.5 68.6 0.3
O B:HOH2199 2.6 55.7 1.0
OG B:SER175 2.8 30.6 1.0
OD1 B:ASP131 3.0 43.8 0.5
O4 B:LAF1338 3.0 71.0 0.3
O4 B:LAF1338 3.0 68.7 0.3
CB B:ALA129 3.3 33.6 1.0
OD1 B:ASP131 3.3 43.1 0.5
O B:SER175 3.4 30.3 1.0
O B:HOH2194 3.6 43.2 1.0
C4 B:LAF1338 3.7 33.1 0.3
CG B:ASP131 3.7 42.2 0.5
O B:HOH2195 3.8 24.1 0.5
C B:SER175 3.8 30.4 1.0
OD2 B:ASP131 3.8 43.0 0.5
CB B:SER175 3.8 30.0 1.0
OD1 B:ASP176 3.9 31.7 0.2
C3 B:LAF1338 3.9 71.0 0.3
ND2 B:ASN139 3.9 56.3 1.0
C3 B:LAF1338 3.9 68.7 0.3
OD2 B:ASP131 3.9 42.5 0.5
CG B:ASP131 4.0 42.0 0.5
NZ B:LYS205 4.2 32.0 0.7
NZ B:LYS205 4.2 33.7 0.3
N B:ASP176 4.2 30.6 0.2
N B:ASP176 4.3 30.4 0.8
CA B:ASP176 4.4 31.0 0.8
CA B:SER175 4.4 30.0 1.0
F B:LAF1337 4.5 29.4 1.0
CA B:ASP176 4.5 30.9 0.2
O B:HOH2315 4.6 32.3 1.0
CA B:ALA129 4.6 33.4 1.0
OD2 B:ASP127 4.6 22.9 1.0
CG B:ASN139 4.7 56.2 1.0
CG B:ASP176 4.7 31.2 0.2
OD1 B:ASP127 4.8 21.6 1.0
C2 B:LAF1338 4.9 70.9 0.3
C3 B:LAF1338 4.9 33.6 0.3
CB B:ASP131 5.0 41.4 0.5
C2 B:LAF1338 5.0 33.8 0.3

Fluorine binding site 4 out of 6 in 1gzg

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Fluorine binding site 4 out of 6 in the Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1338

b:71.1
occ:0.35
F B:LAF1338 0.0 71.1 0.3
NA B:NA1342 0.2 33.1 0.5
C5 B:LAF1338 1.4 71.0 0.3
C5 B:LAF1338 1.4 68.5 0.3
C5 B:LAF1338 1.8 33.8 0.3
F B:LAF1338 2.0 35.4 0.3
O B:HOH2194 2.1 43.2 1.0
F B:LAF1338 2.3 68.1 0.3
C4 B:LAF1338 2.5 68.6 0.3
C4 B:LAF1338 2.5 71.0 0.3
F B:LAF1337 2.6 29.4 1.0
OG B:SER175 2.8 30.6 1.0
O B:HOH2195 3.0 24.1 0.5
C3 B:LAF1338 3.0 68.7 0.3
C3 B:LAF1338 3.1 71.0 0.3
C4 B:LAF1338 3.2 33.1 0.3
C5 B:LAF1337 3.5 27.3 1.0
O4 B:LAF1338 3.6 71.0 0.3
CB B:SER175 3.6 30.0 1.0
O4 B:LAF1338 3.6 68.7 0.3
OD2 B:ASP127 3.7 22.9 1.0
C2 B:LAF1338 3.8 70.9 0.3
C2 B:LAF1338 3.8 33.8 0.3
OD1 B:ASP127 3.9 21.6 1.0
OD1 B:ASP131 4.0 43.8 0.5
OD2 B:ASP131 4.1 43.0 0.5
NZ B:LYS205 4.1 33.7 0.3
C3 B:LAF1338 4.1 33.6 0.3
NZ B:LYS205 4.1 32.0 0.7
CG B:ASP127 4.2 22.8 1.0
O B:HOH2073 4.3 31.9 1.0
OD2 B:ASP131 4.4 42.5 0.5
CB B:ALA129 4.4 33.6 1.0
O B:SER175 4.4 30.3 1.0
C2 B:LAF1338 4.5 68.7 0.3
CG B:ASP131 4.5 42.2 0.5
OD1 B:ASP131 4.6 43.1 0.5
C4 B:LAF1337 4.6 25.9 1.0
CZ B:PHE214 4.6 19.1 1.0
C1 B:LAF1338 4.6 34.4 0.3
CE1 B:PHE214 4.6 19.0 1.0
O B:HOH2199 4.6 55.7 1.0
C1 B:LAF1338 4.7 71.0 0.3
CE1 B:PHE86 4.8 19.7 1.0
C B:SER175 4.8 30.4 1.0
CA B:SER175 4.8 30.0 1.0
CG B:ASP131 5.0 42.0 0.5
O1 B:LAF1338 5.0 34.3 0.3

Fluorine binding site 5 out of 6 in 1gzg

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Fluorine binding site 5 out of 6 in the Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1338

b:35.4
occ:0.30
F B:LAF1338 0.0 35.4 0.3
C5 B:LAF1338 0.8 68.5 0.3
C5 B:LAF1338 0.9 71.0 0.3
F B:LAF1338 1.2 68.1 0.3
C5 B:LAF1338 1.4 33.8 0.3
C4 B:LAF1338 1.8 71.0 0.3
C4 B:LAF1338 1.8 68.6 0.3
F B:LAF1338 2.0 71.1 0.3
NA B:NA1342 2.0 33.1 0.5
O4 B:LAF1338 2.3 68.7 0.3
O4 B:LAF1338 2.5 71.0 0.3
C4 B:LAF1338 2.6 33.1 0.3
OG B:SER175 2.6 30.6 1.0
O B:SER175 2.8 30.3 1.0
C3 B:LAF1338 2.9 71.0 0.3
NZ B:LYS205 3.1 33.7 0.3
NZ B:LYS205 3.1 32.0 0.7
O B:HOH2199 3.1 55.7 1.0
C3 B:LAF1338 3.1 68.7 0.3
CB B:SER175 3.2 30.0 1.0
C B:SER175 3.4 30.4 1.0
F B:LAF1337 3.6 29.4 1.0
O B:HOH2194 3.8 43.2 1.0
C3 B:LAF1338 3.9 33.6 0.3
CA B:SER175 3.9 30.0 1.0
OD1 B:ASP131 4.0 43.8 0.5
O B:HOH2195 4.0 24.1 0.5
C2 B:LAF1338 4.1 70.9 0.3
O B:HOH2315 4.1 32.3 1.0
C2 B:LAF1338 4.1 33.8 0.3
N B:ASP176 4.1 30.6 0.2
N B:ASP176 4.2 30.4 0.8
CB B:ALA129 4.2 33.6 1.0
C2 B:LAF1338 4.3 68.7 0.3
OD2 B:ASP131 4.4 43.0 0.5
OD1 B:ASP131 4.4 43.1 0.5
CA B:ASP176 4.5 31.0 0.8
CA B:ASP176 4.6 30.9 0.2
CE B:LYS205 4.6 33.1 0.3
CE B:LYS205 4.6 27.7 0.7
CG B:ASP131 4.6 42.2 0.5
OD2 B:ASP131 4.6 42.5 0.5
C1 B:LAF1338 4.6 34.4 0.3
C5 B:LAF1337 4.6 27.3 1.0
OD1 B:ASP176 4.6 31.7 0.2
ND2 B:ASN139 4.7 56.3 1.0
C1 B:LAF1338 4.7 71.0 0.3
OD1 B:ASP127 4.8 21.6 1.0
OH1 B:LAF1338 4.8 34.2 0.3
N B:SER175 4.9 29.0 1.0
CG B:ASP131 4.9 42.0 0.5
OD2 B:ASP127 4.9 22.9 1.0
OH1 B:LAF1338 5.0 70.9 0.3

Fluorine binding site 6 out of 6 in 1gzg

Go back to Fluorine Binding Sites List in 1gzg
Fluorine binding site 6 out of 6 in the Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Complex of A MG2-Dependent Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutant D139N) with 5-Fluorolevulinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1337

b:29.4
occ:1.00
F B:LAF1337 0.0 29.4 1.0
C5 B:LAF1337 1.4 27.3 1.0
C4 B:LAF1337 2.4 25.9 1.0
F B:LAF1338 2.6 71.1 0.3
C5 B:LAF1338 2.7 33.8 0.3
NA B:NA1342 2.8 33.1 0.5
NZ B:LYS260 2.8 23.3 1.0
C4 B:LAF1338 3.0 33.1 0.3
C3 B:LAF1338 3.1 71.0 0.3
CB B:SER175 3.3 30.0 1.0
C5 B:LAF1338 3.4 68.5 0.3
C5 B:LAF1338 3.4 71.0 0.3
C3 B:LAF1338 3.5 33.6 0.3
OG B:SER175 3.5 30.6 1.0
C3 B:LAF1338 3.6 68.7 0.3
F B:LAF1338 3.6 35.4 0.3
NZ B:LYS205 3.6 33.7 0.3
NZ B:LYS205 3.7 32.0 0.7
C4 B:LAF1338 3.7 68.6 0.3
C4 B:LAF1338 3.7 71.0 0.3
C3 B:LAF1337 3.8 24.9 1.0
C2 B:LAF1338 3.8 33.8 0.3
C2 B:LAF1338 3.9 70.9 0.3
CE1 B:PHE86 3.9 19.7 1.0
OH B:TYR202 3.9 23.1 1.0
CE2 B:TYR202 3.9 22.3 1.0
O B:HOH2194 4.0 43.2 1.0
CZ B:TYR202 4.1 22.8 1.0
OD1 B:ASP127 4.2 21.6 1.0
CE B:LYS260 4.3 21.2 1.0
CZ B:PHE86 4.3 18.8 1.0
CZ B:PHE214 4.4 19.1 1.0
F B:LAF1338 4.5 68.1 0.3
C2 B:LAF1337 4.5 21.6 1.0
O4 B:LAF1338 4.6 68.7 0.3
CE B:LYS205 4.6 33.1 0.3
CA B:SER175 4.7 30.0 1.0
C2 B:LAF1338 4.7 68.7 0.3
O B:SER175 4.7 30.3 1.0
CD2 B:TYR202 4.7 21.8 1.0
CE B:LYS205 4.8 27.7 0.7
O4 B:LAF1338 4.8 71.0 0.3
CD1 B:PHE86 4.9 19.5 1.0
CE1 B:PHE214 4.9 19.0 1.0
CG B:ASP127 4.9 22.8 1.0
OD2 B:ASP127 4.9 22.9 1.0
CE2 B:PHE214 4.9 18.0 1.0
CD B:LYS260 5.0 19.3 1.0
CE1 B:TYR202 5.0 22.4 1.0

Reference:

F.Frere, W.D.Schubert, F.Stauffer, N.Frankenberg, R.Neier, D.Jahn, D.W.Heinz. Structure of Porphobilinogen Synthase From Pseudomonas Aeruginosa in Complex with 5-Fluorolevulinic Acid Suggests A Double Schiff Base Mechanism. J. Mol. Biol. V. 320 237 2002.
ISSN: ISSN 0022-2836
PubMed: 12079382
DOI: 10.1016/S0022-2836(02)00472-2
Page generated: Sun Dec 13 11:29:53 2020

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