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Sodium 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:

Fluorine (F) 6 atoms
Magnesium (Mg) 2 atoms
Potassium (K) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1gzg

Go back to Sodium Binding Sites List in 1gzg
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na1339

b:22.3
occ:1.00
 F A:LAF1336 1.8 34.7 1.0
O A:HOH2196 2.4 36.1 1.0
C5 A:LAF1336 2.4 30.2 1.0
OG A:SER175 2.6 16.1 1.0
F A:LAF1337 2.7 25.1 1.0
OD1 A:ASP131 3.0 25.8 1.0
OD2 A:ASP127 3.1 18.5 1.0
OD2 A:ASP131 3.5 29.5 1.0
OD1 A:ASP127 3.6 18.0 1.0
C4 A:LAF1336 3.6 29.2 1.0
CB A:ALA129 3.7 19.4 1.0
CB A:SER175 3.7 16.5 1.0
CG A:ASP131 3.7 24.7 1.0
C5 A:LAF1337 3.7 21.1 1.0
CG A:ASP127 3.8 17.9 1.0
ND2 A:ASN139 4.1 27.8 1.0
NZ A:LYS205 4.3 24.9 1.0
O A:HOH2193 4.4 35.1 1.0
C2 A:LAF1336 4.5 29.1 1.0
O A:SER175 4.6 17.5 1.0
C3 A:LAF1336 4.6 29.6 1.0
CE1 A:PHE86 4.6 16.6 1.0
CZ A:PHE214 4.7 16.7 1.0
CE1 A:PHE214 4.9 17.6 1.0
C A:SER175 4.9 16.6 1.0
CA A:SER175 4.9 16.3 1.0
C4 A:LAF1337 4.9 20.3 1.0

Sodium binding site 2 out of 2 in 1gzg

Go back to Sodium Binding Sites List in 1gzg
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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
B:Na1342

b:33.1
occ:0.50
 F B:LAF1338 0.2 71.1 0.3
C5 B:LAF1338 1.4 71.0 0.3
C5 B:LAF1338 1.4 68.5 0.3
C5 B:LAF1338 1.9 33.8 0.3
O B:HOH2194 2.0 43.2 1.0
F B:LAF1338 2.0 35.4 0.3
F B:LAF1338 2.2 68.1 0.3
C4 B:LAF1338 2.7 68.6 0.3
C4 B:LAF1338 2.7 71.0 0.3
OG B:SER175 2.7 30.6 1.0
F B:LAF1337 2.8 29.4 1.0
O B:HOH2195 3.0 24.1 0.5
C3 B:LAF1338 3.2 68.7 0.3
C3 B:LAF1338 3.3 71.0 0.3
C4 B:LAF1338 3.4 33.1 0.3
OD2 B:ASP127 3.5 22.9 1.0
CB B:SER175 3.6 30.0 1.0
C5 B:LAF1337 3.6 27.3 1.0
O4 B:LAF1338 3.7 71.0 0.3
O4 B:LAF1338 3.7 68.7 0.3
OD1 B:ASP127 3.8 21.6 1.0
OD1 B:ASP131 3.9 43.8 0.5
C2 B:LAF1338 4.0 70.9 0.3
OD2 B:ASP131 4.0 43.0 0.5
C2 B:LAF1338 4.0 33.8 0.3
CG B:ASP127 4.1 22.8 1.0
CB B:ALA129 4.2 33.6 1.0
NZ B:LYS205 4.2 33.7 0.3
O B:HOH2073 4.2 31.9 1.0
NZ B:LYS205 4.3 32.0 0.7
C3 B:LAF1338 4.3 33.6 0.3
OD2 B:ASP131 4.3 42.5 0.5
OD1 B:ASP131 4.4 43.1 0.5
CG B:ASP131 4.4 42.2 0.5
O B:SER175 4.4 30.3 1.0
O B:HOH2199 4.6 55.7 1.0
C2 B:LAF1338 4.7 68.7 0.3
CZ B:PHE214 4.7 19.1 1.0
CE1 B:PHE214 4.8 19.0 1.0
CE1 B:PHE86 4.8 19.7 1.0
C4 B:LAF1337 4.8 25.9 1.0
C B:SER175 4.8 30.4 1.0
CA B:SER175 4.8 30.0 1.0
C1 B:LAF1338 4.8 34.4 0.3
CG B:ASP131 4.9 42.0 0.5
C1 B:LAF1338 4.9 71.0 0.3

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: Tue Dec 15 05:25:08 2020

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