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

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 1gzg

Go back to Magnesium Binding Sites List in 1gzg
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1338

b:15.3
occ:1.00
OE1 A:GLU245 2.0 15.7 1.0
O A:HOH2298 2.0 16.2 1.0
O A:HOH2243 2.1 17.6 1.0
O A:HOH2296 2.1 16.0 1.0
O A:HOH2242 2.1 15.3 1.0
O A:HOH2297 2.1 14.7 1.0
CD A:GLU245 3.1 14.6 1.0
OE2 A:GLU245 3.4 15.6 1.0
NH1 A:ARG181 3.7 16.4 1.0
OD1 A:ASP249 3.8 13.8 1.0
O A:HOH2241 4.0 18.2 1.0
O A:HOH2301 4.1 16.2 1.0
O A:HOH2302 4.2 15.1 1.0
OD2 A:ASP249 4.2 13.8 1.0
O A:MET178 4.3 17.0 1.0
CG A:GLU245 4.4 13.9 1.0
CG A:ASP249 4.5 14.8 1.0
O A:SER203 4.5 14.5 1.0
OD1 A:ASP179 4.5 18.0 1.0
O A:GLU245 4.5 14.0 1.0
CB A:GLU245 4.6 14.3 1.0
CA A:GLU245 4.7 14.5 1.0
CA A:ASP179 4.7 15.5 1.0
O B:HOH2032 4.8 21.7 1.0
SD A:MET177 4.8 16.2 1.0
CE A:MET177 4.9 17.0 1.0
CZ A:ARG181 5.0 17.3 1.0

Magnesium binding site 2 out of 2 in 1gzg

Go back to Magnesium Binding Sites List in 1gzg
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1341

b:15.2
occ:0.50
O B:HOH2261 1.8 28.5 1.0
O B:HOH2258 2.0 25.4 1.0
O B:HOH2260 2.0 32.4 1.0
O B:HOH2219 2.1 31.1 1.0
OE1 B:GLU245 2.1 24.5 1.0
O B:HOH2259 2.1 35.2 1.0
CD B:GLU245 3.2 23.3 1.0
OD1 B:ASP249 3.7 21.5 1.0
OE2 B:GLU245 3.7 25.8 1.0
NH1 B:ARG181 3.7 33.1 1.0
O B:HOH2264 4.1 32.6 1.0
O B:HOH2218 4.1 39.3 1.0
OD2 B:ASP249 4.1 19.7 1.0
O B:MET178 4.3 31.7 1.0
O B:HOH2262 4.3 34.3 1.0
CG B:ASP249 4.3 20.6 1.0
O B:GLU245 4.4 18.7 1.0
CG B:GLU245 4.4 20.6 1.0
O B:SER203 4.5 19.9 1.0
OD1 B:ASP179 4.5 33.2 1.0
CB B:GLU245 4.5 19.0 1.0
O B:HOH2221 4.5 39.5 1.0
CA B:GLU245 4.7 18.6 1.0
SD B:MET177 4.7 29.4 0.3
CA B:ASP179 4.8 32.2 1.0
SD B:MET177 4.8 32.3 0.7
CE B:MET177 4.9 28.8 0.3
C B:GLU245 4.9 18.4 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: Mon Dec 14 05:58:29 2020

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