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Magnesium in PDB 7wjr: Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant A63S From Aspergillus Oryzae in Complex with Catechol

Enzymatic activity of Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant A63S From Aspergillus Oryzae in Complex with Catechol

All present enzymatic activity of Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant A63S From Aspergillus Oryzae in Complex with Catechol:
4.1.1.46;

Protein crystallography data

The structure of Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant A63S From Aspergillus Oryzae in Complex with Catechol, PDB code: 7wjr was solved by F.Yan, X.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.68 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.932, 105.842, 181.689, 90, 90, 90
R / Rfree (%) 14.4 / 17.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant A63S From Aspergillus Oryzae in Complex with Catechol (pdb code 7wjr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant A63S From Aspergillus Oryzae in Complex with Catechol, PDB code: 7wjr:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7wjr

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Magnesium binding site 1 out of 4 in the Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant A63S From Aspergillus Oryzae in Complex with Catechol


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 Dihydroxybenzoate Decarboxylase Mutant A63S From Aspergillus Oryzae in Complex with Catechol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg400

b:38.0
occ:1.00
 NE2 A:HIS167 2.0 14.7 1.0
O A:HOH766 2.1 18.6 1.0
O4 A:CAQ401 2.3 17.0 1.0
OD1 A:ASP293 2.3 23.0 1.0
OE2 A:GLU8 2.3 16.9 1.0
CE1 A:HIS167 2.9 16.6 1.0
CD2 A:HIS167 3.0 16.4 1.0
CG A:ASP293 3.2 21.3 1.0
CD A:GLU8 3.3 14.5 1.0
O A:HOH637 3.4 19.7 1.0
OD2 A:ASP293 3.6 18.8 1.0
C4 A:CAQ401 3.6 25.6 1.0
CG A:GLU8 3.6 13.4 1.0
O A:HOH687 3.8 16.2 1.0
ND1 A:HIS167 4.0 16.3 1.0
CG A:HIS167 4.1 14.8 1.0
O A:GLU8 4.3 15.2 1.0
O A:HOH654 4.3 20.2 1.0
C5 A:CAQ401 4.3 17.4 1.0
NE2 A:HIS222 4.4 15.3 1.0
OE1 A:GLU8 4.4 15.2 1.0
CB A:ASP293 4.5 16.3 1.0
O3 A:CAQ401 4.5 19.0 1.0
C3 A:CAQ401 4.5 21.6 1.0
CE1 A:HIS222 4.6 13.7 1.0
CA A:ASP293 4.7 15.7 1.0
O A:HOH606 4.7 15.7 1.0
CB A:GLU8 4.8 15.5 1.0
CD2 A:PHE296 4.9 18.9 1.0

Magnesium binding site 2 out of 4 in 7wjr

Go back to Magnesium Binding Sites List in 7wjr
Magnesium binding site 2 out of 4 in the Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant A63S From Aspergillus Oryzae in Complex with Catechol


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 Dihydroxybenzoate Decarboxylase Mutant A63S From Aspergillus Oryzae in Complex with Catechol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg400

b:35.5
occ:1.00
 OD1 B:ASP293 2.1 16.4 1.0
O3 B:CAQ401 2.1 17.6 1.0
NE2 B:HIS167 2.1 15.1 1.0
O B:HOH735 2.1 13.8 1.0
OE2 B:GLU8 2.4 17.2 1.0
CE1 B:HIS167 3.0 13.8 1.0
CG B:ASP293 3.0 18.4 1.0
CD2 B:HIS167 3.2 14.3 1.0
C3 B:CAQ401 3.4 22.5 1.0
CD B:GLU8 3.4 15.3 1.0
OD2 B:ASP293 3.4 15.8 1.0
O B:HOH749 3.6 17.9 1.0
CG B:GLU8 3.7 13.9 1.0
C2 B:CAQ401 3.9 18.1 1.0
O B:HOH660 4.0 16.3 1.0
ND1 B:HIS167 4.1 15.5 1.0
CG B:HIS167 4.3 17.1 1.0
CB B:ASP293 4.3 15.2 1.0
O B:GLU8 4.3 16.1 1.0
NE2 B:HIS222 4.4 14.6 1.0
C4 B:CAQ401 4.4 19.3 1.0
CA B:ASP293 4.5 15.9 1.0
OE1 B:GLU8 4.5 14.1 1.0
O4 B:CAQ401 4.6 17.6 1.0
CE1 B:HIS222 4.7 15.2 1.0
CD2 B:PHE296 4.7 20.5 1.0
O B:HOH705 4.8 13.4 1.0
CB B:GLU8 4.8 16.7 1.0

Magnesium binding site 3 out of 4 in 7wjr

Go back to Magnesium Binding Sites List in 7wjr
Magnesium binding site 3 out of 4 in the Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant A63S From Aspergillus Oryzae in Complex with Catechol


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 Dihydroxybenzoate Decarboxylase Mutant A63S From Aspergillus Oryzae in Complex with Catechol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg400

b:34.2
occ:1.00
 OE2 C:GLU8 2.0 15.6 1.0
NE2 C:HIS167 2.0 14.7 1.0
OD1 C:ASP293 2.2 17.4 1.0
O C:HOH758 2.2 13.7 1.0
O3 C:CAQ401 2.5 22.0 1.0
CD2 C:HIS167 3.0 13.4 1.0
CD C:GLU8 3.0 15.8 1.0
CG C:ASP293 3.0 17.5 1.0
CE1 C:HIS167 3.0 14.7 1.0
OD2 C:ASP293 3.4 18.9 1.0
CG C:GLU8 3.4 12.3 1.0
C3 C:CAQ401 3.8 22.1 1.0
O C:HOH775 3.8 15.5 1.0
O C:HOH716 3.9 17.1 1.0
ND1 C:HIS167 4.1 15.3 1.0
OE1 C:GLU8 4.1 12.1 1.0
NE2 C:HIS222 4.1 14.9 1.0
CG C:HIS167 4.1 13.6 1.0
O C:GLU8 4.2 17.6 1.0
CB C:ASP293 4.2 15.1 1.0
O C:HOH648 4.3 20.7 1.0
C2 C:CAQ401 4.4 20.1 1.0
CE1 C:HIS222 4.4 15.8 1.0
CA C:ASP293 4.5 14.6 1.0
CB C:GLU8 4.5 12.0 1.0
C4 C:CAQ401 4.8 19.5 1.0
O C:HOH681 4.9 16.6 1.0
O4 C:CAQ401 4.9 19.8 1.0
C C:GLU8 4.9 13.3 1.0
CD2 C:PHE296 5.0 23.0 1.0

Magnesium binding site 4 out of 4 in 7wjr

Go back to Magnesium Binding Sites List in 7wjr
Magnesium binding site 4 out of 4 in the Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant A63S From Aspergillus Oryzae in Complex with Catechol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Dihydroxybenzoate Decarboxylase Mutant A63S From Aspergillus Oryzae in Complex with Catechol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg400

b:31.2
occ:1.00
 OE2 D:GLU8 2.0 12.9 1.0
NE2 D:HIS167 2.1 13.7 1.0
OD1 D:ASP293 2.2 16.6 1.0
O D:HOH699 2.3 11.6 1.0
O4 D:CAQ401 2.5 19.4 1.0
CG D:ASP293 3.0 16.4 1.0
CD D:GLU8 3.0 14.1 1.0
CD2 D:HIS167 3.0 10.8 1.0
CE1 D:HIS167 3.1 16.1 1.0
OD2 D:ASP293 3.3 16.6 1.0
CG D:GLU8 3.4 15.2 1.0
O D:HOH714 3.8 14.5 1.0
C4 D:CAQ401 3.8 20.1 1.0
O D:HOH670 4.1 13.9 1.0
OE1 D:GLU8 4.1 12.6 1.0
NE2 D:HIS222 4.1 16.4 1.0
CG D:HIS167 4.2 13.7 1.0
ND1 D:HIS167 4.2 13.4 1.0
O D:GLU8 4.2 12.8 1.0
CB D:ASP293 4.2 13.4 1.0
O D:HOH678 4.3 15.6 1.0
CE1 D:HIS222 4.4 15.0 1.0
CA D:ASP293 4.5 16.3 1.0
C5 D:CAQ401 4.5 17.1 1.0
CB D:GLU8 4.5 16.4 1.0
C3 D:CAQ401 4.8 19.5 1.0
O3 D:CAQ401 4.9 17.3 1.0
C D:GLU8 4.9 14.6 1.0
O D:HOH658 4.9 13.9 1.0

Reference:

F.Yan, X.Song. Molecular Mechanism of Reversible Decarboxylase with Efficient CO2 Fixation To Be Published.
Page generated: Thu Oct 3 11:19:07 2024

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