Magnesium in PDB 7zbp: Unspecific Peroxygenase From Marasmius Rotula
Enzymatic activity of Unspecific Peroxygenase From Marasmius Rotula
All present enzymatic activity of Unspecific Peroxygenase From Marasmius Rotula:
1.11.2.1;
Protein crystallography data
The structure of Unspecific Peroxygenase From Marasmius Rotula, PDB code: 7zbp
was solved by
E.Santillana,
A.Romero,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
73.44 /
1.45
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
100.349,
107.44,
186.231,
90,
90,
90
|
R / Rfree (%)
|
15.8 /
18.4
|
Other elements in 7zbp:
The structure of Unspecific Peroxygenase From Marasmius Rotula also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Unspecific Peroxygenase From Marasmius Rotula
(pdb code 7zbp). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Unspecific Peroxygenase From Marasmius Rotula, PDB code: 7zbp:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7zbp
Go back to
Magnesium Binding Sites List in 7zbp
Magnesium binding site 1 out
of 4 in the Unspecific Peroxygenase From Marasmius Rotula
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Unspecific Peroxygenase From Marasmius Rotula within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg304
b:6.2
occ:1.00
|
OE2
|
A:GLU85
|
2.1
|
10.3
|
1.0
|
O
|
A:HOH529
|
2.1
|
9.5
|
1.0
|
O1D
|
A:HEM303
|
2.2
|
8.1
|
1.0
|
O
|
A:HOH501
|
2.2
|
10.6
|
1.0
|
O
|
A:HIS86
|
2.2
|
10.1
|
1.0
|
OG
|
A:SER89
|
2.2
|
10.1
|
1.0
|
CD
|
A:GLU85
|
3.1
|
10.0
|
1.0
|
CGD
|
A:HEM303
|
3.1
|
8.6
|
1.0
|
C
|
A:HIS86
|
3.3
|
9.1
|
1.0
|
CB
|
A:SER89
|
3.4
|
9.4
|
1.0
|
O2D
|
A:HEM303
|
3.5
|
8.8
|
1.0
|
N
|
A:HIS86
|
3.5
|
8.9
|
1.0
|
CG
|
A:GLU85
|
3.6
|
10.3
|
1.0
|
CA
|
A:HIS86
|
4.0
|
8.5
|
1.0
|
O
|
A:HOH475
|
4.1
|
11.4
|
1.0
|
O
|
A:HOH487
|
4.2
|
9.5
|
1.0
|
OE1
|
A:GLU85
|
4.2
|
10.8
|
1.0
|
ND1
|
A:HIS86
|
4.3
|
8.1
|
1.0
|
N
|
A:ASP87
|
4.3
|
9.4
|
1.0
|
O
|
A:HOH429
|
4.4
|
9.9
|
1.0
|
CA
|
A:SER89
|
4.5
|
8.4
|
1.0
|
CBD
|
A:HEM303
|
4.5
|
8.3
|
1.0
|
N
|
A:SER89
|
4.5
|
8.9
|
1.0
|
C
|
A:GLU85
|
4.5
|
8.4
|
1.0
|
CE1
|
A:HIS86
|
4.5
|
8.6
|
1.0
|
O
|
A:ASN100
|
4.5
|
9.3
|
1.0
|
CA
|
A:ASP87
|
4.6
|
9.3
|
1.0
|
CB
|
A:ARG92
|
4.6
|
9.1
|
1.0
|
CG
|
A:HIS86
|
4.6
|
8.1
|
1.0
|
O
|
A:GLU93
|
4.7
|
12.1
|
1.0
|
CA
|
A:GLU85
|
4.7
|
8.6
|
1.0
|
CB
|
A:ASN100
|
4.8
|
10.8
|
1.0
|
CB
|
A:GLU85
|
4.8
|
9.0
|
1.0
|
C
|
A:ASP87
|
4.8
|
9.6
|
1.0
|
CB
|
A:HIS86
|
5.0
|
8.2
|
1.0
|
CAD
|
A:HEM303
|
5.0
|
8.2
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7zbp
Go back to
Magnesium Binding Sites List in 7zbp
Magnesium binding site 2 out
of 4 in the Unspecific Peroxygenase From Marasmius Rotula
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Unspecific Peroxygenase From Marasmius Rotula within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg302
b:5.9
occ:1.00
|
OE2
|
B:GLU85
|
2.1
|
10.7
|
1.0
|
O1D
|
B:HEM301
|
2.1
|
8.2
|
1.0
|
O
|
B:HOH487
|
2.2
|
11.0
|
1.0
|
O
|
B:HIS86
|
2.2
|
9.5
|
1.0
|
O
|
B:HOH518
|
2.2
|
9.6
|
1.0
|
OG
|
B:SER89
|
2.2
|
9.9
|
1.0
|
CGD
|
B:HEM301
|
3.1
|
8.8
|
1.0
|
CD
|
B:GLU85
|
3.1
|
10.7
|
1.0
|
C
|
B:HIS86
|
3.3
|
9.9
|
1.0
|
O2D
|
B:HEM301
|
3.4
|
10.1
|
1.0
|
CB
|
B:SER89
|
3.5
|
9.6
|
1.0
|
N
|
B:HIS86
|
3.6
|
9.0
|
1.0
|
CG
|
B:GLU85
|
3.6
|
10.3
|
1.0
|
CA
|
B:HIS86
|
4.0
|
9.3
|
1.0
|
O
|
B:HOH526
|
4.1
|
12.8
|
1.0
|
O
|
B:HOH505
|
4.2
|
9.3
|
1.0
|
OE1
|
B:GLU85
|
4.2
|
11.6
|
1.0
|
ND1
|
B:HIS86
|
4.3
|
10.4
|
1.0
|
N
|
B:ASP87
|
4.4
|
10.4
|
1.0
|
O
|
B:HOH426
|
4.4
|
11.6
|
1.0
|
CBD
|
B:HEM301
|
4.4
|
8.3
|
1.0
|
CA
|
B:SER89
|
4.5
|
9.7
|
1.0
|
C
|
B:GLU85
|
4.5
|
8.7
|
1.0
|
CE1
|
B:HIS86
|
4.5
|
10.0
|
1.0
|
N
|
B:SER89
|
4.5
|
10.2
|
1.0
|
O
|
B:ASN100
|
4.6
|
11.0
|
1.0
|
CB
|
B:ARG92
|
4.6
|
10.4
|
1.0
|
CG
|
B:HIS86
|
4.7
|
8.9
|
1.0
|
O
|
B:GLU93
|
4.7
|
13.5
|
1.0
|
CA
|
B:ASP87
|
4.7
|
11.3
|
1.0
|
CA
|
B:GLU85
|
4.7
|
9.4
|
1.0
|
CB
|
B:ASN100
|
4.7
|
11.1
|
1.0
|
CB
|
B:GLU85
|
4.8
|
9.8
|
1.0
|
C
|
B:ASP87
|
4.9
|
11.6
|
1.0
|
CAD
|
B:HEM301
|
5.0
|
7.7
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7zbp
Go back to
Magnesium Binding Sites List in 7zbp
Magnesium binding site 3 out
of 4 in the Unspecific Peroxygenase From Marasmius Rotula
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Unspecific Peroxygenase From Marasmius Rotula within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg302
b:8.5
occ:1.00
|
OE2
|
C:GLU85
|
2.1
|
12.6
|
1.0
|
O1D
|
C:HEM301
|
2.1
|
10.3
|
1.0
|
O
|
C:HOH530
|
2.1
|
12.0
|
1.0
|
O
|
C:HIS86
|
2.2
|
10.4
|
1.0
|
O
|
C:HOH446
|
2.2
|
12.4
|
1.0
|
OG
|
C:SER89
|
2.2
|
10.6
|
1.0
|
CD
|
C:GLU85
|
3.1
|
11.9
|
1.0
|
CGD
|
C:HEM301
|
3.1
|
11.9
|
1.0
|
C
|
C:HIS86
|
3.3
|
12.1
|
1.0
|
CB
|
C:SER89
|
3.4
|
9.6
|
1.0
|
O2D
|
C:HEM301
|
3.4
|
11.5
|
1.0
|
N
|
C:HIS86
|
3.6
|
11.4
|
1.0
|
CG
|
C:GLU85
|
3.6
|
11.7
|
1.0
|
CA
|
C:HIS86
|
4.0
|
11.3
|
1.0
|
O
|
C:HOH496
|
4.1
|
12.3
|
1.0
|
O
|
C:HOH481
|
4.1
|
12.1
|
1.0
|
OE1
|
C:GLU85
|
4.2
|
15.0
|
1.0
|
ND1
|
C:HIS86
|
4.2
|
11.3
|
1.0
|
N
|
C:ASP87
|
4.4
|
12.2
|
1.0
|
O
|
C:HOH453
|
4.4
|
11.8
|
1.0
|
CBD
|
C:HEM301
|
4.4
|
10.2
|
1.0
|
CA
|
C:SER89
|
4.4
|
10.3
|
1.0
|
N
|
C:SER89
|
4.5
|
10.3
|
1.0
|
C
|
C:GLU85
|
4.5
|
12.4
|
1.0
|
CE1
|
C:HIS86
|
4.5
|
10.6
|
1.0
|
O
|
C:ASN100
|
4.6
|
11.7
|
1.0
|
CB
|
C:ARG92
|
4.6
|
11.3
|
1.0
|
O
|
C:GLU93
|
4.6
|
12.9
|
1.0
|
CG
|
C:HIS86
|
4.6
|
10.6
|
1.0
|
CA
|
C:ASP87
|
4.6
|
10.9
|
1.0
|
CB
|
C:ASN100
|
4.7
|
12.5
|
1.0
|
CA
|
C:GLU85
|
4.7
|
11.6
|
1.0
|
CB
|
C:GLU85
|
4.8
|
10.7
|
1.0
|
C
|
C:ASP87
|
4.9
|
10.2
|
1.0
|
CB
|
C:HIS86
|
5.0
|
11.2
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7zbp
Go back to
Magnesium Binding Sites List in 7zbp
Magnesium binding site 4 out
of 4 in the Unspecific Peroxygenase From Marasmius Rotula
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Unspecific Peroxygenase From Marasmius Rotula within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg302
b:12.9
occ:1.00
|
OE2
|
D:GLU85
|
2.1
|
17.0
|
1.0
|
O1D
|
D:HEM301
|
2.1
|
15.3
|
1.0
|
O
|
D:HOH520
|
2.1
|
18.2
|
1.0
|
O
|
D:HIS86
|
2.1
|
16.2
|
1.0
|
OG
|
D:SER89
|
2.2
|
15.6
|
1.0
|
O
|
D:HOH504
|
2.2
|
15.5
|
1.0
|
CGD
|
D:HEM301
|
3.1
|
14.8
|
1.0
|
CD
|
D:GLU85
|
3.1
|
18.3
|
1.0
|
C
|
D:HIS86
|
3.3
|
14.7
|
1.0
|
O2D
|
D:HEM301
|
3.4
|
16.9
|
1.0
|
CB
|
D:SER89
|
3.4
|
17.1
|
1.0
|
N
|
D:HIS86
|
3.5
|
15.3
|
1.0
|
CG
|
D:GLU85
|
3.6
|
16.6
|
1.0
|
O
|
D:HOH499
|
4.0
|
18.6
|
1.0
|
CA
|
D:HIS86
|
4.0
|
14.6
|
1.0
|
OE1
|
D:GLU85
|
4.1
|
19.5
|
1.0
|
O
|
D:HOH465
|
4.2
|
16.4
|
1.0
|
ND1
|
D:HIS86
|
4.3
|
15.2
|
1.0
|
N
|
D:ASP87
|
4.4
|
15.4
|
1.0
|
O
|
D:HOH437
|
4.4
|
16.7
|
1.0
|
CA
|
D:SER89
|
4.5
|
15.3
|
1.0
|
CBD
|
D:HEM301
|
4.5
|
14.3
|
1.0
|
C
|
D:GLU85
|
4.5
|
16.6
|
1.0
|
N
|
D:SER89
|
4.5
|
15.5
|
1.0
|
O
|
D:ASN100
|
4.5
|
20.3
|
1.0
|
CE1
|
D:HIS86
|
4.5
|
13.7
|
1.0
|
CB
|
D:ARG92
|
4.6
|
19.0
|
1.0
|
CG
|
D:HIS86
|
4.7
|
13.7
|
1.0
|
O
|
D:GLU93
|
4.7
|
20.7
|
1.0
|
CA
|
D:GLU85
|
4.7
|
15.2
|
1.0
|
CA
|
D:ASP87
|
4.7
|
16.5
|
1.0
|
CB
|
D:ASN100
|
4.8
|
22.8
|
1.0
|
CB
|
D:GLU85
|
4.8
|
16.3
|
1.0
|
C
|
D:ASP87
|
4.9
|
18.1
|
1.0
|
CB
|
D:HIS86
|
5.0
|
14.6
|
1.0
|
|
Reference:
D.Linde,
E.Santillana,
E.Fernandez-Fueyo,
A.Gonzalez-Benjumea,
J.Carro,
A.Gutierrez,
A.T.Martinez,
A.Romero.
Structural Characterization of Two Short Unspecific Peroxygenases: Two Different Dimeric Arrangements. Antioxidants V. 11 2022.
ISSN: ESSN 2076-3921
PubMed: 35624755
DOI: 10.3390/ANTIOX11050891
Page generated: Thu Oct 3 16:22:31 2024
|