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Magnesium in PDB 5oxt: Direct-Evolutioned Unspecific Peroxygenase From Agrocybe Aegerita, in Complex with Acetate

Enzymatic activity of Direct-Evolutioned Unspecific Peroxygenase From Agrocybe Aegerita, in Complex with Acetate

All present enzymatic activity of Direct-Evolutioned Unspecific Peroxygenase From Agrocybe Aegerita, in Complex with Acetate:
1.11.2.1;

Protein crystallography data

The structure of Direct-Evolutioned Unspecific Peroxygenase From Agrocybe Aegerita, in Complex with Acetate, PDB code: 5oxt was solved by M.Ramirez-Escudero, J.Sanz-Aparicio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.23 / 1.42
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.999, 99.151, 83.890, 90.00, 103.27, 90.00
R / Rfree (%) 15 / 16.4

Other elements in 5oxt:

The structure of Direct-Evolutioned Unspecific Peroxygenase From Agrocybe Aegerita, in Complex with Acetate also contains other interesting chemical elements:

Iron (Fe) 3 atoms
Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Direct-Evolutioned Unspecific Peroxygenase From Agrocybe Aegerita, in Complex with Acetate (pdb code 5oxt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Direct-Evolutioned Unspecific Peroxygenase From Agrocybe Aegerita, in Complex with Acetate, PDB code: 5oxt:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5oxt

Go back to Magnesium Binding Sites List in 5oxt
Magnesium binding site 1 out of 3 in the Direct-Evolutioned Unspecific Peroxygenase From Agrocybe Aegerita, in Complex with Acetate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Direct-Evolutioned Unspecific Peroxygenase From Agrocybe Aegerita, in Complex with Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:4.8
occ:1.00
 O A:HOH1293 2.1 6.9 1.0
OE2 A:GLU122 2.1 6.6 1.0
O A:GLY123 2.1 6.2 1.0
O A:HOH1221 2.1 6.2 1.0
OG A:SER126 2.1 6.3 1.0
O1A A:HEM1000 2.2 5.6 1.0
CD A:GLU122 3.1 6.6 1.0
CGA A:HEM1000 3.2 5.5 1.0
C A:GLY123 3.2 6.4 1.0
O2A A:HEM1000 3.3 5.8 1.0
CB A:SER126 3.4 6.5 1.0
N A:GLY123 3.6 6.3 1.0
CG A:GLU122 3.6 6.6 1.0
CA A:GLY123 3.9 6.4 1.0
O A:HOH1266 4.0 7.4 1.0
O A:HOH1253 4.1 6.0 1.0
OE1 A:GLU122 4.2 6.9 1.0
O A:HOH1110 4.2 6.3 1.0
N A:ASP124 4.3 6.5 1.0
O A:ASN137 4.3 8.0 1.0
NH2 A:ARG189 4.3 6.5 1.0
N A:SER126 4.4 6.5 1.0
CA A:SER126 4.4 6.7 1.0
CBA A:HEM1000 4.5 5.5 1.0
C A:GLU122 4.6 6.5 1.0
CA A:ASP124 4.6 6.8 1.0
O A:GLY130 4.7 7.2 1.0
CZ A:ARG189 4.8 6.5 1.0
C A:ASP124 4.8 6.8 1.0
CB A:ARG129 4.8 7.1 1.0
CB A:GLU122 4.8 6.5 1.0
CA A:GLU122 4.9 6.6 1.0
CAA A:HEM1000 4.9 5.5 1.0
O A:ASP124 5.0 6.7 1.0
CB A:ASN137 5.0 8.2 1.0

Magnesium binding site 2 out of 3 in 5oxt

Go back to Magnesium Binding Sites List in 5oxt
Magnesium binding site 2 out of 3 in the Direct-Evolutioned Unspecific Peroxygenase From Agrocybe Aegerita, in Complex with Acetate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Direct-Evolutioned Unspecific Peroxygenase From Agrocybe Aegerita, in Complex with Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:5.4
occ:1.00
 O B:HOH682 2.0 7.7 1.0
OE2 B:GLU122 2.1 7.4 1.0
O B:GLY123 2.1 6.8 1.0
O B:HOH569 2.1 6.8 1.0
OG B:SER126 2.1 6.8 1.0
O1A B:HEM402 2.3 6.2 1.0
CD B:GLU122 3.1 7.5 1.0
CGA B:HEM402 3.2 6.3 1.0
C B:GLY123 3.2 6.8 1.0
CB B:SER126 3.3 6.9 1.0
O2A B:HEM402 3.4 6.4 1.0
N B:GLY123 3.6 7.0 1.0
CG B:GLU122 3.6 7.4 1.0
CA B:GLY123 3.9 6.9 1.0
O B:HOH626 4.0 7.9 1.0
O B:HOH631 4.1 6.8 1.0
OE1 B:GLU122 4.2 7.6 1.0
O B:HOH505 4.2 7.2 1.0
O B:ASN137 4.3 9.5 1.0
N B:ASP124 4.3 6.9 1.0
NH2 B:ARG189 4.4 6.8 1.0
CA B:SER126 4.4 7.0 1.0
N B:SER126 4.4 6.9 1.0
CBA B:HEM402 4.6 6.2 1.0
C B:GLU122 4.6 7.2 1.0
CA B:ASP124 4.6 7.2 1.0
O B:GLY130 4.7 7.9 1.0
CB B:ARG129 4.8 8.0 1.0
CZ B:ARG189 4.8 6.9 1.0
C B:ASP124 4.8 7.1 1.0
CB B:GLU122 4.8 7.3 1.0
CA B:GLU122 4.9 7.3 1.0
CAA B:HEM402 5.0 6.2 1.0
O B:ASP124 5.0 7.1 1.0
CB B:ASN137 5.0 9.5 1.0

Magnesium binding site 3 out of 3 in 5oxt

Go back to Magnesium Binding Sites List in 5oxt
Magnesium binding site 3 out of 3 in the Direct-Evolutioned Unspecific Peroxygenase From Agrocybe Aegerita, in Complex with Acetate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Direct-Evolutioned Unspecific Peroxygenase From Agrocybe Aegerita, in Complex with Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1001

b:6.9
occ:1.00
 O C:HOH1272 2.0 8.4 1.0
OE2 C:GLU122 2.1 8.7 1.0
O C:HOH1194 2.1 8.7 1.0
O C:GLY123 2.1 8.2 1.0
OG C:SER126 2.1 8.7 1.0
O1A C:HEM1000 2.3 7.4 1.0
CD C:GLU122 3.1 8.8 1.0
CGA C:HEM1000 3.2 7.3 1.0
C C:GLY123 3.2 8.5 1.0
CB C:SER126 3.3 8.7 1.0
O2A C:HEM1000 3.4 7.4 1.0
CG C:GLU122 3.6 8.7 1.0
N C:GLY123 3.6 8.3 1.0
CA C:GLY123 4.0 8.4 1.0
O C:HOH1240 4.0 10.1 1.0
O C:HOH1275 4.1 7.6 1.0
OE1 C:GLU122 4.2 9.2 1.0
O C:HOH1105 4.2 9.4 1.0
O C:ASN137 4.3 11.6 1.0
N C:ASP124 4.3 8.8 1.0
NH2 C:ARG189 4.4 8.3 1.0
CA C:SER126 4.4 9.1 1.0
N C:SER126 4.4 8.9 1.0
CBA C:HEM1000 4.6 7.2 1.0
C C:GLU122 4.6 8.5 1.0
CA C:ASP124 4.6 9.4 1.0
O C:GLY130 4.7 10.0 1.0
CB C:ARG129 4.8 10.1 1.0
CZ C:ARG189 4.8 8.5 1.0
CB C:GLU122 4.8 8.6 1.0
C C:ASP124 4.8 9.2 1.0
CA C:GLU122 4.9 8.6 1.0
CAA C:HEM1000 4.9 7.2 1.0
CB C:ASN137 5.0 11.3 1.0
O C:ASP124 5.0 9.3 1.0

Reference:

M.Ramirez-Escudero, J.Sanz-Aparicio. Direct-Evolutioned Unspecific Peroxygenase From Agrocybe Aegerita, in Complex with Acetate To Be Published.
Page generated: Mon Sep 30 01:24:51 2024

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