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Magnesium in PDB 3r75: Crystal Structure of 2-Amino-2-Desoxyisochorismate Synthase (Adic) Synthase Phze From Burkholderia Lata 383 in Complex with Benzoate, Pyruvate, Glutamine and Contaminating ZN2+

Enzymatic activity of Crystal Structure of 2-Amino-2-Desoxyisochorismate Synthase (Adic) Synthase Phze From Burkholderia Lata 383 in Complex with Benzoate, Pyruvate, Glutamine and Contaminating ZN2+

All present enzymatic activity of Crystal Structure of 2-Amino-2-Desoxyisochorismate Synthase (Adic) Synthase Phze From Burkholderia Lata 383 in Complex with Benzoate, Pyruvate, Glutamine and Contaminating ZN2+:
4.1.3.27;

Protein crystallography data

The structure of Crystal Structure of 2-Amino-2-Desoxyisochorismate Synthase (Adic) Synthase Phze From Burkholderia Lata 383 in Complex with Benzoate, Pyruvate, Glutamine and Contaminating ZN2+, PDB code: 3r75 was solved by Q.A.Li, D.V.Mavrodi, L.S.Thomashow, M.Roessle, W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.62 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 259.710, 94.512, 53.546, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 20

Other elements in 3r75:

The structure of Crystal Structure of 2-Amino-2-Desoxyisochorismate Synthase (Adic) Synthase Phze From Burkholderia Lata 383 in Complex with Benzoate, Pyruvate, Glutamine and Contaminating ZN2+ also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 2-Amino-2-Desoxyisochorismate Synthase (Adic) Synthase Phze From Burkholderia Lata 383 in Complex with Benzoate, Pyruvate, Glutamine and Contaminating ZN2+ (pdb code 3r75). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of 2-Amino-2-Desoxyisochorismate Synthase (Adic) Synthase Phze From Burkholderia Lata 383 in Complex with Benzoate, Pyruvate, Glutamine and Contaminating ZN2+, PDB code: 3r75:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3r75

Go back to Magnesium Binding Sites List in 3r75
Magnesium binding site 1 out of 3 in the Crystal Structure of 2-Amino-2-Desoxyisochorismate Synthase (Adic) Synthase Phze From Burkholderia Lata 383 in Complex with Benzoate, Pyruvate, Glutamine and Contaminating ZN2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of 2-Amino-2-Desoxyisochorismate Synthase (Adic) Synthase Phze From Burkholderia Lata 383 in Complex with Benzoate, Pyruvate, Glutamine and Contaminating ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg700

b:26.2
occ:1.00
 O A:HOH791 1.9 33.6 1.0
O A:HOH774 2.1 33.5 1.0
OE1 A:GLU244 2.1 27.3 1.0
O2 A:BEZ701 2.1 27.8 1.0
OE2 A:GLU382 2.1 27.4 1.0
O1 A:BEZ701 2.1 24.0 1.0
C A:BEZ701 2.5 30.9 1.0
CD A:GLU382 3.0 31.2 1.0
CD A:GLU244 3.0 35.5 1.0
OE1 A:GLU382 3.2 31.5 1.0
OE2 A:GLU244 3.3 35.9 1.0
NZ A:LYS240 3.9 30.6 1.0
N A:GLY218 3.9 24.4 1.0
C1 A:BEZ701 4.0 25.2 1.0
N A:THR369 4.1 30.0 1.0
OG A:SER217 4.2 39.3 1.0
OG1 A:THR219 4.2 25.4 1.0
O A:THR369 4.2 28.9 1.0
CA A:GLY218 4.2 22.5 1.0
OE1 A:GLU241 4.4 34.8 1.0
OE1 A:GLU379 4.4 32.9 1.0
N A:THR219 4.4 26.3 1.0
CB A:THR369 4.4 27.9 1.0
CG A:GLU244 4.4 35.7 1.0
CG A:GLU382 4.5 29.4 1.0
CB A:SER368 4.5 38.8 1.0
NZ A:LYS386 4.5 35.0 1.0
CB A:THR219 4.6 24.8 1.0
C A:GLY218 4.6 25.8 1.0
CA A:THR369 4.7 28.6 1.0
C2 A:BEZ701 4.8 29.7 1.0
C6 A:BEZ701 4.9 29.6 1.0
C A:THR369 4.9 28.5 1.0
CA A:SER368 5.0 33.4 1.0
C A:SER368 5.0 28.6 1.0
OE2 A:GLU379 5.0 31.9 1.0

Magnesium binding site 2 out of 3 in 3r75

Go back to Magnesium Binding Sites List in 3r75
Magnesium binding site 2 out of 3 in the Crystal Structure of 2-Amino-2-Desoxyisochorismate Synthase (Adic) Synthase Phze From Burkholderia Lata 383 in Complex with Benzoate, Pyruvate, Glutamine and Contaminating ZN2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of 2-Amino-2-Desoxyisochorismate Synthase (Adic) Synthase Phze From Burkholderia Lata 383 in Complex with Benzoate, Pyruvate, Glutamine and Contaminating ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg700

b:28.5
occ:1.00
 O B:HOH793 2.0 36.3 1.0
O1 B:BEZ701 2.1 28.8 1.0
OE1 B:GLU244 2.1 28.3 1.0
OE2 B:GLU382 2.1 28.4 1.0
O B:HOH795 2.1 37.9 1.0
O2 B:BEZ701 2.2 30.9 1.0
C B:BEZ701 2.4 35.4 1.0
CD B:GLU382 3.0 34.3 1.0
CD B:GLU244 3.1 31.4 1.0
OE1 B:GLU382 3.3 28.9 1.0
OE2 B:GLU244 3.4 35.2 1.0
C1 B:BEZ701 4.0 33.1 1.0
N B:GLY218 4.0 28.9 1.0
N B:THR369 4.0 31.8 1.0
NZ B:LYS240 4.1 30.3 1.0
OG1 B:THR219 4.2 28.4 1.0
OG B:SER217 4.2 39.9 1.0
O B:THR369 4.2 30.1 1.0
CA B:GLY218 4.3 28.6 1.0
OE1 B:GLU379 4.4 33.7 1.0
CG B:GLU244 4.4 35.4 1.0
CB B:SER368 4.4 42.8 1.0
CB B:THR369 4.4 30.3 1.0
N B:THR219 4.5 27.1 1.0
CG B:GLU382 4.5 32.1 1.0
OE1 B:GLU241 4.5 35.1 1.0
NZ B:LYS386 4.5 33.6 1.0
CB B:THR219 4.6 26.5 1.0
CA B:THR369 4.7 27.0 1.0
C B:GLY218 4.7 28.9 1.0
C6 B:BEZ701 4.8 30.5 1.0
C2 B:BEZ701 4.9 31.3 1.0
C B:THR369 4.9 31.4 1.0
C B:SER368 4.9 32.9 1.0
CA B:SER368 4.9 37.0 1.0

Magnesium binding site 3 out of 3 in 3r75

Go back to Magnesium Binding Sites List in 3r75
Magnesium binding site 3 out of 3 in the Crystal Structure of 2-Amino-2-Desoxyisochorismate Synthase (Adic) Synthase Phze From Burkholderia Lata 383 in Complex with Benzoate, Pyruvate, Glutamine and Contaminating ZN2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of 2-Amino-2-Desoxyisochorismate Synthase (Adic) Synthase Phze From Burkholderia Lata 383 in Complex with Benzoate, Pyruvate, Glutamine and Contaminating ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg644

b:74.2
occ:1.00
 CD B:ARG136 4.0 60.8 1.0
OD2 B:ASP140 4.0 52.1 1.0
CG B:ARG136 4.3 54.9 1.0
NH1 B:ARG136 4.4 71.6 1.0

Reference:

Q.A.Li, D.V.Mavrodi, L.S.Thomashow, M.Roessle, W.Blankenfeldt. Ligand Binding Induces An Ammonia Channel in 2-Amino-2-Desoxyisochorismate (Adic) Synthase Phze. J.Biol.Chem. V. 286 18213 2011.
ISSN: ISSN 0021-9258
PubMed: 21454481
DOI: 10.1074/JBC.M110.183418
Page generated: Mon Dec 14 08:44:11 2020

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