Magnesium in PDB 7a1a: 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae
Protein crystallography data
The structure of 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae, PDB code: 7a1a
was solved by
G.Hofer,
W.Keller,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.95 /
1.53
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
99.894,
99.894,
129.168,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.2 /
22.5
|
Other elements in 7a1a:
The structure of 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae
(pdb code 7a1a). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the
2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae, PDB code: 7a1a:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 7a1a
Go back to
Magnesium Binding Sites List in 7a1a
Magnesium binding site 1 out
of 2 in the 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg401
b:16.6
occ:1.00
|
O
|
A:HOH653
|
2.0
|
19.7
|
1.0
|
O
|
A:HOH656
|
2.0
|
20.1
|
1.0
|
O
|
A:HOH711
|
2.1
|
23.0
|
1.0
|
OD1
|
A:ASP293
|
2.2
|
16.3
|
1.0
|
OE2
|
A:GLU8
|
2.2
|
14.7
|
1.0
|
NE2
|
A:HIS167
|
2.3
|
12.6
|
1.0
|
CG
|
A:ASP293
|
3.0
|
23.2
|
1.0
|
HG2
|
A:GLU8
|
3.0
|
20.8
|
1.0
|
CE1
|
A:HIS167
|
3.2
|
9.8
|
1.0
|
CD
|
A:GLU8
|
3.2
|
14.6
|
1.0
|
OD2
|
A:ASP293
|
3.2
|
23.0
|
1.0
|
CD2
|
A:HIS167
|
3.3
|
11.4
|
1.0
|
HE1
|
A:HIS167
|
3.3
|
11.7
|
1.0
|
HD2
|
A:HIS167
|
3.4
|
13.7
|
1.0
|
CG
|
A:GLU8
|
3.6
|
17.4
|
1.0
|
O
|
A:HOH822
|
3.7
|
19.6
|
1.0
|
O
|
A:HOH725
|
3.9
|
17.2
|
1.0
|
HA
|
A:ASP293
|
4.0
|
12.8
|
1.0
|
O
|
A:HOH688
|
4.0
|
19.9
|
1.0
|
HE1
|
A:HIS222
|
4.2
|
18.1
|
1.0
|
HG3
|
A:GLU8
|
4.2
|
20.8
|
1.0
|
HD2
|
A:PHE296
|
4.2
|
14.5
|
1.0
|
OE1
|
A:GLU8
|
4.3
|
12.6
|
1.0
|
ND1
|
A:HIS167
|
4.3
|
11.4
|
1.0
|
CB
|
A:ASP293
|
4.3
|
12.7
|
1.0
|
O
|
A:GLU8
|
4.3
|
16.0
|
1.0
|
NE2
|
A:HIS222
|
4.3
|
12.8
|
1.0
|
CG
|
A:HIS167
|
4.4
|
13.6
|
1.0
|
HB3
|
A:GLU8
|
4.6
|
16.0
|
1.0
|
O
|
A:HOH760
|
4.6
|
25.7
|
1.0
|
HD2
|
A:PRO168
|
4.6
|
11.6
|
1.0
|
CE1
|
A:HIS222
|
4.6
|
15.1
|
1.0
|
CA
|
A:ASP293
|
4.6
|
10.7
|
1.0
|
CB
|
A:GLU8
|
4.7
|
13.3
|
1.0
|
HB2
|
A:ASP293
|
4.7
|
15.3
|
1.0
|
CD2
|
A:PHE296
|
4.8
|
12.1
|
1.0
|
HE2
|
A:PHE296
|
4.8
|
17.8
|
1.0
|
HB2
|
A:ALA10
|
4.8
|
17.7
|
1.0
|
O
|
A:HOH610
|
5.0
|
13.8
|
1.0
|
HB3
|
A:ASP293
|
5.0
|
15.3
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 7a1a
Go back to
Magnesium Binding Sites List in 7a1a
Magnesium binding site 2 out
of 2 in the 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of 2,3-Dihydroxybenzoate Decarboxylase of Aspergillus Oryzae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg401
b:16.1
occ:0.73
|
O
|
B:HOH720
|
2.1
|
24.2
|
1.0
|
O
|
B:HOH697
|
2.1
|
20.5
|
1.0
|
OD1
|
B:ASP293
|
2.2
|
21.9
|
1.0
|
OE2
|
B:GLU8
|
2.2
|
19.1
|
1.0
|
O
|
B:HOH756
|
2.2
|
37.6
|
1.0
|
NE2
|
B:HIS167
|
2.4
|
14.1
|
1.0
|
HG2
|
B:GLU8
|
3.0
|
20.6
|
1.0
|
CG
|
B:ASP293
|
3.1
|
27.6
|
1.0
|
CD
|
B:GLU8
|
3.2
|
17.3
|
1.0
|
CE1
|
B:HIS167
|
3.3
|
11.5
|
1.0
|
CD2
|
B:HIS167
|
3.3
|
14.0
|
1.0
|
OD2
|
B:ASP293
|
3.4
|
43.4
|
1.0
|
HE1
|
B:HIS167
|
3.4
|
13.8
|
1.0
|
HD2
|
B:HIS167
|
3.5
|
16.8
|
1.0
|
O
|
B:HOH812
|
3.6
|
22.8
|
1.0
|
CG
|
B:GLU8
|
3.6
|
17.1
|
1.0
|
O
|
B:HOH731
|
3.9
|
17.4
|
1.0
|
HA
|
B:ASP293
|
4.0
|
15.6
|
1.0
|
HD2
|
B:PHE296
|
4.1
|
19.1
|
1.0
|
O
|
B:HOH626
|
4.1
|
18.8
|
1.0
|
HG3
|
B:GLU8
|
4.2
|
20.6
|
1.0
|
HE1
|
B:HIS222
|
4.3
|
21.1
|
1.0
|
OE1
|
B:GLU8
|
4.3
|
15.8
|
1.0
|
CB
|
B:ASP293
|
4.3
|
14.6
|
1.0
|
O
|
B:GLU8
|
4.3
|
19.2
|
1.0
|
NE2
|
B:HIS222
|
4.4
|
16.0
|
1.0
|
O
|
B:HOH724
|
4.4
|
25.6
|
1.0
|
ND1
|
B:HIS167
|
4.4
|
13.2
|
1.0
|
O
|
B:HOH762
|
4.4
|
31.9
|
1.0
|
CG
|
B:HIS167
|
4.4
|
13.1
|
1.0
|
HE2
|
B:PHE296
|
4.6
|
20.7
|
1.0
|
HD2
|
B:PRO168
|
4.6
|
13.2
|
1.0
|
CD2
|
B:PHE296
|
4.6
|
15.9
|
1.0
|
HB3
|
B:GLU8
|
4.6
|
17.5
|
1.0
|
HB2
|
B:ASP293
|
4.6
|
17.5
|
1.0
|
CA
|
B:ASP293
|
4.6
|
13.0
|
1.0
|
CE1
|
B:HIS222
|
4.7
|
17.6
|
1.0
|
O
|
B:HOH686
|
4.7
|
23.0
|
1.0
|
CB
|
B:GLU8
|
4.8
|
14.6
|
1.0
|
CE2
|
B:PHE296
|
4.9
|
17.2
|
1.0
|
HB2
|
B:ALA10
|
5.0
|
20.0
|
1.0
|
|
Reference:
G.Hofer,
X.Sheng,
S.Braeuer,
S.E.Payer,
K.Plasch,
W.Goessler,
K.Faber,
W.Keller,
F.Himo,
S.M.Glueck.
Metal Ion Promiscuity and Structure of 2,3-Dihydroxybenzoic Acid Decarboxylase of Aspergillus Oryzae. Chembiochem 2020.
ISSN: ESSN 1439-7633
PubMed: 33090643
DOI: 10.1002/CBIC.202000600
Page generated: Tue Dec 15 03:19:31 2020
|