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Magnesium in PDB 9ifp: Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 2,6-Dimethoxyphenol

Enzymatic activity of Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 2,6-Dimethoxyphenol

All present enzymatic activity of Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 2,6-Dimethoxyphenol:
1.11.2.1;

Protein crystallography data

The structure of Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 2,6-Dimethoxyphenol, PDB code: 9ifp was solved by A.Fernandez-Garcia, J.Sanz-Aparicio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.93 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 271.298, 74.502, 106.15, 90, 111.8, 90
R / Rfree (%) 20 / 21.9

Other elements in 9ifp:

The structure of Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 2,6-Dimethoxyphenol also contains other interesting chemical elements:

Iron (Fe) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 2,6-Dimethoxyphenol (pdb code 9ifp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 2,6-Dimethoxyphenol, PDB code: 9ifp:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 9ifp

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Magnesium binding site 1 out of 3 in the Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 2,6-Dimethoxyphenol


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 Psathyrella Aberdarensis (Pabupo-II) in Complex with 2,6-Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg415

b:46.6
occ:1.00
 O1A A:HEM401 2.0 41.7 1.0
O A:HOH560 2.2 33.8 1.0
O A:HOH568 2.2 43.6 1.0
OE2 A:GLU138 2.2 43.5 1.0
O A:GLY139 2.2 33.7 1.0
CGA A:HEM401 3.0 41.5 1.0
CD A:GLU138 3.3 40.9 1.0
O2A A:HEM401 3.4 45.0 1.0
C A:GLY139 3.4 39.2 1.0
CG A:GLU138 3.8 41.7 1.0
O A:HOH533 3.8 44.0 1.0
N A:GLY139 3.8 35.5 1.0
O A:HOH608 4.0 33.1 1.0
O A:HOH611 4.1 30.6 1.0
O A:HOH548 4.1 32.1 1.0
CA A:GLY139 4.2 38.9 1.0
CBA A:HEM401 4.3 38.9 1.0
OE1 A:GLU138 4.4 40.3 1.0
N A:ASP140 4.5 39.6 1.0
NH2 A:ARG205 4.5 37.3 1.0
O A:ASN153 4.5 37.3 1.0
CAA A:HEM401 4.6 36.4 1.0
N A:GLY142 4.7 35.5 1.0
CA A:GLY142 4.7 36.9 1.0
CA A:ASP140 4.7 36.4 1.0
CZ A:ARG205 4.8 40.5 1.0
C A:GLU138 4.8 38.1 1.0
CB A:ARG145 4.8 40.0 1.0
C A:ASP140 4.9 35.8 1.0
CB A:GLU138 5.0 42.0 1.0
NE A:ARG205 5.0 40.6 1.0

Magnesium binding site 2 out of 3 in 9ifp

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Magnesium binding site 2 out of 3 in the Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 2,6-Dimethoxyphenol


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 Psathyrella Aberdarensis (Pabupo-II) in Complex with 2,6-Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg420

b:39.8
occ:1.00
 OE2 B:GLU138 1.9 46.0 1.0
O1A B:HEM401 2.0 42.8 1.0
O B:HOH575 2.1 38.5 1.0
O B:HOH564 2.1 39.8 1.0
O B:HOH595 2.2 40.1 1.0
O B:GLY139 2.2 37.6 1.0
CD B:GLU138 3.0 45.4 1.0
CGA B:HEM401 3.2 51.4 1.0
C B:GLY139 3.3 43.1 1.0
CG B:GLU138 3.6 44.6 1.0
O2A B:HEM401 3.6 49.1 1.0
N B:GLY139 3.7 42.5 1.0
O B:HOH542 4.0 30.7 1.0
CA B:GLY139 4.1 45.5 1.0
O B:HOH523 4.1 44.5 1.0
OE1 B:GLU138 4.1 49.4 1.0
O B:HOH524 4.1 36.5 1.0
O B:HOH561 4.2 32.9 1.0
N B:ASP140 4.4 40.4 1.0
O B:ASN153 4.4 41.5 1.0
CBA B:HEM401 4.5 44.3 1.0
C B:GLU138 4.6 43.9 1.0
CA B:ASP140 4.7 43.8 1.0
CAA B:HEM401 4.7 41.8 1.0
NH2 B:ARG205 4.8 46.0 1.0
CB B:GLU138 4.8 45.0 1.0
N B:GLY142 4.9 39.1 1.0
CB B:ARG145 4.9 40.6 1.0
CA B:GLU138 4.9 45.1 1.0
O B:ALA146 4.9 36.0 1.0
CZ B:ARG205 5.0 42.8 1.0
CB B:ASN153 5.0 41.1 1.0
CA B:GLY142 5.0 39.4 1.0

Magnesium binding site 3 out of 3 in 9ifp

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Magnesium binding site 3 out of 3 in the Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 2,6-Dimethoxyphenol


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 Psathyrella Aberdarensis (Pabupo-II) in Complex with 2,6-Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg413

b:45.0
occ:1.00
 O C:HOH585 2.0 51.3 1.0
O C:HOH542 2.1 46.3 1.0
OE2 C:GLU138 2.1 45.4 1.0
O C:HOH605 2.1 44.0 1.0
O1A C:HEM409 2.1 40.9 1.0
O C:GLY139 2.3 48.9 1.0
CD C:GLU138 3.2 51.1 1.0
CGA C:HEM409 3.2 42.6 1.0
C C:GLY139 3.5 49.2 1.0
O2A C:HEM409 3.6 43.6 1.0
CG C:GLU138 3.8 48.1 1.0
O C:HOH502 3.9 45.4 1.0
N C:GLY139 3.9 49.3 1.0
O C:HOH520 4.0 48.5 1.0
O C:HOH544 4.0 37.5 1.0
O C:HOH568 4.0 47.1 1.0
O C:ASN153 4.3 56.3 1.0
OE1 C:GLU138 4.3 49.3 1.0
CA C:GLY139 4.3 49.3 1.0
CBA C:HEM409 4.5 38.7 1.0
N C:ASP140 4.6 50.4 1.0
CB C:ARG145 4.6 46.1 1.0
CAA C:HEM409 4.7 37.8 1.0
NH2 C:ARG205 4.8 53.5 1.0
CA C:ASP140 4.8 51.5 1.0
N C:GLY142 4.8 50.6 1.0
O C:ALA146 4.9 48.5 1.0
C C:GLU138 4.9 48.2 1.0
CA C:GLY142 4.9 55.4 1.0
CB C:ASN153 4.9 48.0 1.0

Reference:

A.Fernandez-Garcia, J.Sanz-Aparicio. Unspecific Peroxygenase From Psathyrella Aberdarensis To Be Published.
Page generated: Sat Aug 23 06:02:50 2025

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