Atomistry » Sodium » PDB 1ghy-1hn1 » 1gzg
Atomistry »
  Sodium »
    PDB 1ghy-1hn1 »
      1gzg »

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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy