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Chlorine in PDB 2yor: 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: 2yor 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) 47.51 / 2.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.290, 95.030, 127.200, 90.00, 90.00, 90.00
R / Rfree (%) 16.899 / 23.742

Other elements in 2yor:

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:

Magnesium (Mg) 2 atoms
Iron (Fe) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 2yor). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine 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: 2yor:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2yor

Go back to Chlorine Binding Sites List in 2yor
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1356

b:35.2
occ:1.00
 O A:HOH2008 3.0 21.3 1.0
N A:ASN71 3.1 9.0 1.0
O B:HOH2202 3.2 27.5 1.0
O A:HOH2092 3.4 15.2 1.0
CB A:ASN71 3.6 10.6 1.0
CB A:ASP70 3.7 18.7 1.0
CB A:PRO8 3.7 20.6 1.0
CB A:PRO238 3.7 8.3 1.0
CA A:ASP70 3.8 11.7 1.0
CD B:PRO238 3.8 12.9 1.0
C A:ASP70 3.9 10.9 1.0
CA A:ASN71 3.9 10.8 1.0
CB B:SER237 4.0 15.7 1.0
CG A:PRO238 4.1 8.3 1.0
O A:HOH2009 4.4 16.9 1.0
OG B:SER237 4.4 20.9 1.0
CA A:PRO8 4.5 22.4 1.0
CG B:PRO238 4.6 15.2 1.0
N B:PRO238 4.6 12.8 1.0
O A:HOH2090 4.7 11.1 1.0
CG A:PRO8 4.8 23.5 1.0
CG A:ASP70 4.8 29.9 1.0
O B:PRO238 4.9 13.9 1.0
OE1 A:GLN64 4.9 18.9 1.0
OD1 A:ASP70 5.0 34.2 1.0

Chlorine binding site 2 out of 4 in 2yor

Go back to Chlorine Binding Sites List in 2yor
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1356

b:34.1
occ:1.00
 O B:HOH2008 3.0 20.9 1.0
N B:ASN71 3.0 12.2 1.0
O A:HOH2247 3.2 32.0 1.0
O A:HOH2246 3.3 12.1 1.0
CB B:ASN71 3.5 11.7 1.0
CB B:ASP70 3.7 24.2 1.0
CB B:PRO238 3.7 12.8 1.0
CD A:PRO238 3.7 11.9 1.0
CA B:ASP70 3.7 18.1 1.0
CA B:ASN71 3.8 15.2 1.0
C B:ASP70 3.8 14.2 1.0
CB B:PRO8 3.9 23.9 1.0
CB A:SER237 4.0 18.0 1.0
CG B:PRO238 4.1 15.2 1.0
O A:HOH2018 4.4 21.1 1.0
OG A:SER237 4.5 20.6 1.0
CA B:PRO8 4.5 24.0 1.0
N A:PRO238 4.6 13.3 1.0
CG A:PRO238 4.7 8.3 1.0
O B:HOH2071 4.7 13.7 1.0
CG B:PRO8 4.8 28.9 1.0
CG B:ASP70 4.8 31.2 1.0
OE1 B:GLN64 4.8 24.0 1.0
O A:PRO238 4.8 9.0 1.0
CG B:ASN71 4.9 13.6 1.0
C B:ASN71 4.9 13.0 1.0
N B:GLN72 5.0 17.7 1.0
OD1 B:ASP70 5.0 37.5 1.0

Chlorine binding site 3 out of 4 in 2yor

Go back to Chlorine Binding Sites List in 2yor
Chlorine 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 Chlorine with other atoms in the Cl 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
B:Cl1358

b:68.4
occ:1.00
 O3 B:TRS1355 2.7 89.6 1.0
N B:GLY7 3.5 18.0 1.0
O B:HOH2003 3.6 40.5 1.0
CA B:PRO6 4.0 21.6 1.0
O B:HOH2005 4.1 21.6 1.0
C3 B:TRS1355 4.1 89.5 1.0
O B:HOH2007 4.1 26.9 1.0
O B:HOH2006 4.1 42.2 1.0
C B:PRO6 4.3 19.2 1.0
C1 B:TRS1355 4.3 89.5 1.0
CA B:GLY7 4.4 22.2 1.0
CB B:PRO6 4.5 19.9 1.0
O1 B:TRS1355 4.7 88.6 1.0
O B:GLY7 4.8 18.4 1.0
C B:TRS1355 4.9 90.0 1.0
C B:GLY7 4.9 22.3 1.0

Chlorine binding site 4 out of 4 in 2yor

Go back to Chlorine Binding Sites List in 2yor
Chlorine 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 Chlorine with other atoms in the Cl 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
B:Cl1361

b:51.7
occ:1.00
 OG1 B:THR143 3.4 27.3 1.0
O B:HOH2144 3.8 31.6 1.0
C3 B:NAG361 3.8 27.1 1.0
N2 B:NAG361 3.9 25.5 1.0
CB B:THR143 4.4 24.8 1.0
C2 B:NAG361 4.4 23.7 1.0
O3 B:NAG361 4.4 21.8 1.0
C1 B:NAG361 4.7 22.7 1.0
C4 B:NAG361 4.8 27.1 1.0
O4 B:NAG361 4.9 24.4 1.0
C7 B:NAG361 5.0 27.8 1.0
C8 B:NAG362 5.0 31.8 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: Sat Jul 20 15:15:33 2024

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