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Magnesium in PDB 2yp1: Crystallization of A 45 kDa Peroxygenase- Peroxidase From the Mushroom Agrocybe Aegerita and Structure Determination By Sad Utilizing Only the Haem Iron

Enzymatic activity of Crystallization of A 45 kDa Peroxygenase- Peroxidase From the Mushroom Agrocybe Aegerita and Structure Determination By Sad Utilizing Only the Haem Iron

All present enzymatic activity of Crystallization of A 45 kDa Peroxygenase- Peroxidase From the Mushroom Agrocybe Aegerita and Structure Determination By Sad Utilizing Only the Haem Iron:
1.11.2.1;

Protein crystallography data

The structure of Crystallization of A 45 kDa Peroxygenase- Peroxidase From the Mushroom Agrocybe Aegerita and Structure Determination By Sad Utilizing Only the Haem Iron, PDB code: 2yp1 was solved by K.Piontek, E.Strittmatter, R.Ullrich, D.A.Plattner, M.Hofrichter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.91 / 2.31
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 112.750, 144.880, 134.460, 90.00, 90.00, 90.00
R / Rfree (%) 17.74 / 23.039

Other elements in 2yp1:

The structure of Crystallization of A 45 kDa Peroxygenase- Peroxidase From the Mushroom Agrocybe Aegerita and Structure Determination By Sad Utilizing Only the Haem Iron also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystallization of A 45 kDa Peroxygenase- Peroxidase From the Mushroom Agrocybe Aegerita and Structure Determination By Sad Utilizing Only the Haem Iron (pdb code 2yp1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystallization of A 45 kDa Peroxygenase- Peroxidase From the Mushroom Agrocybe Aegerita and Structure Determination By Sad Utilizing Only the Haem Iron, PDB code: 2yp1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2yp1

Go back to Magnesium Binding Sites List in 2yp1
Magnesium binding site 1 out of 4 in the Crystallization of A 45 kDa Peroxygenase- Peroxidase From the Mushroom Agrocybe Aegerita and Structure Determination By Sad Utilizing Only the Haem Iron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystallization of A 45 kDa Peroxygenase- Peroxidase From the Mushroom Agrocybe Aegerita and Structure Determination By Sad Utilizing Only the Haem Iron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg353

b:18.5
occ:1.00
 OE2 A:GLU122 2.0 22.9 1.0
O A:HOH2123 2.0 18.2 1.0
O1A A:HEM350 2.0 20.7 1.0
O A:HOH2124 2.0 14.6 1.0
OG A:SER126 2.1 21.1 1.0
O A:GLY123 2.2 18.9 1.0
CGA A:HEM350 3.0 18.8 1.0
CD A:GLU122 3.1 26.5 1.0
C A:GLY123 3.3 21.3 1.0
CB A:SER126 3.3 18.3 1.0
O2A A:HEM350 3.4 19.7 1.0
N A:GLY123 3.7 22.3 1.0
CG A:GLU122 3.8 24.9 1.0
CA A:GLY123 4.0 20.8 1.0
OE1 A:GLU122 4.0 28.1 1.0
O A:HOH2115 4.1 22.4 1.0
O A:HOH2127 4.1 16.1 1.0
O A:HOH2041 4.2 20.6 1.0
O A:ASN137 4.3 22.6 1.0
CBA A:HEM350 4.4 19.1 1.0
N A:ASP124 4.4 15.3 1.0
NH2 A:ARG189 4.4 13.5 1.0
N A:SER126 4.4 16.2 1.0
CA A:SER126 4.4 20.7 1.0
CB A:ARG129 4.6 23.5 1.0
CA A:ASP124 4.6 19.3 1.0
O A:GLY130 4.7 21.1 1.0
C A:GLU122 4.7 24.0 1.0
C A:ASP124 4.8 20.5 1.0
CZ A:ARG189 4.8 16.3 1.0
CAA A:HEM350 4.9 17.5 1.0
O A:ARG129 4.9 19.6 1.0
CB A:GLU122 4.9 25.4 1.0
O A:ASP124 5.0 15.8 1.0
CA A:GLU122 5.0 23.4 1.0

Magnesium binding site 2 out of 4 in 2yp1

Go back to Magnesium Binding Sites List in 2yp1
Magnesium binding site 2 out of 4 in the Crystallization of A 45 kDa Peroxygenase- Peroxidase From the Mushroom Agrocybe Aegerita and Structure Determination By Sad Utilizing Only the Haem Iron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystallization of A 45 kDa Peroxygenase- Peroxidase From the Mushroom Agrocybe Aegerita and Structure Determination By Sad Utilizing Only the Haem Iron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg353

b:12.2
occ:1.00
 OE2 B:GLU122 2.0 16.2 1.0
O1A B:HEM350 2.0 15.9 1.0
O B:HOH2157 2.0 12.8 1.0
O B:HOH2158 2.1 17.1 1.0
OG B:SER126 2.1 14.3 1.0
O B:GLY123 2.2 14.1 1.0
CGA B:HEM350 3.0 16.1 1.0
CD B:GLU122 3.0 17.3 1.0
CB B:SER126 3.3 11.9 1.0
C B:GLY123 3.3 13.2 1.0
O2A B:HEM350 3.4 16.0 1.0
CG B:GLU122 3.5 14.5 1.0
N B:GLY123 3.7 11.7 1.0
O B:HOH2152 3.9 15.0 1.0
O B:HOH2058 4.0 13.0 1.0
CA B:GLY123 4.0 13.8 1.0
O B:HOH2161 4.1 15.4 1.0
OE1 B:GLU122 4.1 21.9 1.0
O B:ASN137 4.2 18.3 1.0
CA B:SER126 4.4 13.0 1.0
N B:ASP124 4.4 12.5 1.0
CBA B:HEM350 4.4 13.3 1.0
N B:SER126 4.4 13.1 1.0
CB B:ARG129 4.6 12.6 1.0
NH2 B:ARG189 4.6 12.4 1.0
O B:GLY130 4.7 13.5 1.0
CA B:ASP124 4.7 13.9 1.0
C B:GLU122 4.7 13.2 1.0
CB B:GLU122 4.8 14.9 1.0
C B:ASP124 4.9 14.4 1.0
CAA B:HEM350 4.9 12.2 1.0
CZ B:ARG189 4.9 15.2 1.0
CA B:GLU122 4.9 14.4 1.0

Magnesium binding site 3 out of 4 in 2yp1

Go back to Magnesium Binding Sites List in 2yp1
Magnesium binding site 3 out of 4 in the Crystallization of A 45 kDa Peroxygenase- Peroxidase From the Mushroom Agrocybe Aegerita and Structure Determination By Sad Utilizing Only the Haem Iron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystallization of A 45 kDa Peroxygenase- Peroxidase From the Mushroom Agrocybe Aegerita and Structure Determination By Sad Utilizing Only the Haem Iron within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg353

b:19.9
occ:1.00
 O1A C:HEM350 2.0 19.2 1.0
OE2 C:GLU122 2.0 23.0 1.0
O C:HOH2132 2.0 29.4 1.0
OG C:SER126 2.1 20.3 1.0
O C:HOH2131 2.2 17.9 1.0
O C:GLY123 2.2 19.0 1.0
CGA C:HEM350 2.9 18.9 1.0
CD C:GLU122 3.0 25.6 1.0
O2A C:HEM350 3.1 16.9 1.0
C C:GLY123 3.3 17.5 1.0
CB C:SER126 3.3 20.2 1.0
CG C:GLU122 3.4 17.8 1.0
N C:GLY123 3.5 16.5 1.0
CA C:GLY123 4.0 17.3 1.0
O C:HOH2120 4.1 18.0 1.0
OE1 C:GLU122 4.1 25.1 1.0
O C:HOH2045 4.2 22.5 1.0
CBA C:HEM350 4.3 15.2 1.0
O C:HOH2135 4.3 25.6 1.0
N C:SER126 4.3 21.5 1.0
CA C:SER126 4.4 21.2 1.0
N C:ASP124 4.4 18.2 1.0
O C:ASN137 4.5 20.6 1.0
NH2 C:ARG189 4.5 18.7 1.0
C C:GLU122 4.5 17.9 1.0
CB C:GLU122 4.6 17.7 1.0
CA C:ASP124 4.7 19.9 1.0
CA C:GLU122 4.7 19.0 1.0
CZ C:ARG189 4.7 19.9 1.0
CB C:ARG129 4.7 23.5 1.0
C C:ASP124 4.8 22.0 1.0
CAA C:HEM350 4.8 15.5 1.0
O C:GLY130 4.8 18.0 1.0
O C:ASP124 4.9 21.1 1.0

Magnesium binding site 4 out of 4 in 2yp1

Go back to Magnesium Binding Sites List in 2yp1
Magnesium binding site 4 out of 4 in the Crystallization of A 45 kDa Peroxygenase- Peroxidase From the Mushroom Agrocybe Aegerita and Structure Determination By Sad Utilizing Only the Haem Iron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystallization of A 45 kDa Peroxygenase- Peroxidase From the Mushroom Agrocybe Aegerita and Structure Determination By Sad Utilizing Only the Haem Iron within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg353

b:26.7
occ:1.00
 O D:HOH2084 1.7 25.3 1.0
O1A D:HEM350 2.0 32.0 1.0
O D:HOH2083 2.0 22.8 1.0
OE2 D:GLU122 2.0 25.1 1.0
OG D:SER126 2.1 29.5 1.0
O D:GLY123 2.2 23.9 1.0
CGA D:HEM350 3.0 32.4 1.0
CD D:GLU122 3.0 26.7 1.0
C D:GLY123 3.3 23.1 1.0
O2A D:HEM350 3.3 33.2 1.0
CB D:SER126 3.3 27.0 1.0
N D:GLY123 3.4 26.4 1.0
CG D:GLU122 3.5 24.8 1.0
O D:HOH2077 3.8 24.6 1.0
CA D:GLY123 3.9 23.0 1.0
OE1 D:GLU122 4.1 30.2 1.0
O D:HOH2029 4.2 36.3 1.0
O D:HOH2087 4.2 34.2 1.0
CBA D:HEM350 4.3 28.9 1.0
N D:ASP124 4.4 21.1 1.0
CA D:SER126 4.4 28.4 1.0
C D:GLU122 4.5 26.0 1.0
NH2 D:ARG189 4.5 21.4 1.0
N D:SER126 4.5 26.2 1.0
O D:ASN137 4.5 37.2 1.0
O D:GLY130 4.6 26.3 1.0
CA D:ASP124 4.7 25.2 1.0
CB D:GLU122 4.7 24.1 1.0
CA D:GLU122 4.8 24.3 1.0
CAA D:HEM350 4.8 24.6 1.0
CB D:ARG129 4.8 28.2 1.0
CZ D:ARG189 4.8 23.2 1.0
C D:ASP124 4.8 26.0 1.0
O D:ASP124 5.0 28.3 1.0

Reference:

K.Piontek, E.Strittmatter, R.Ullrichg.Groebe, M.Pecyna, M.Kluge, K.Scheibner, M.Hofrichter, D.A.Plattner. Structural Basis of Substrate Conversion in A New Aromatic Peroxygenase: P450 Functionality with Benefits J.Biol.Chem. V. 288 34767 2013.
ISSN: ISSN 0021-9258
PubMed: 24126915
DOI: 10.1074/JBC.M113.514521
Page generated: Wed Aug 14 07:38:49 2024

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