Zinc in PDB 7oo5: Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades

Enzymatic activity of Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades

All present enzymatic activity of Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades:
1.11.1.14;

Protein crystallography data

The structure of Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades, PDB code: 7oo5 was solved by A.Romero, F.J.Ruiz-Duenas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.56 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.126, 74.95, 82.768, 90, 90, 90
R / Rfree (%) 23.2 / 26.9

Other elements in 7oo5:

The structure of Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Iron (Fe) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades (pdb code 7oo5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades, PDB code: 7oo5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7oo5

Go back to Zinc Binding Sites List in 7oo5
Zinc binding site 1 out of 2 in the Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:58.2
occ:1.00
OE2 A:GLU220 1.9 48.9 1.0
OD2 A:ASP180 2.4 57.2 1.0
ND1 A:HIS217 2.6 56.3 1.0
CD A:GLU220 2.7 49.1 1.0
OE1 A:GLU220 2.9 44.0 1.0
CG A:ASP180 3.1 62.0 1.0
O A:GLY215 3.5 50.1 1.0
CE1 A:HIS217 3.5 60.6 1.0
CG A:HIS217 3.6 54.0 1.0
O A:PRO211 3.6 60.0 1.0
CB A:ASP180 3.8 54.4 1.0
CB A:HIS217 3.8 50.9 1.0
OD1 A:ASP180 3.8 59.0 1.0
CG A:GLU220 4.1 48.2 1.0
N A:HIS217 4.3 54.6 1.0
CE A:MET229 4.3 46.6 1.0
CG A:PRO211 4.5 53.9 1.0
CD A:PRO211 4.5 54.4 1.0
CA A:ASP180 4.5 54.7 1.0
C A:PRO211 4.6 58.7 1.0
C A:GLY215 4.6 51.3 1.0
CA A:HIS217 4.7 52.9 1.0
NE2 A:HIS217 4.7 56.7 1.0
CD2 A:HIS217 4.7 59.3 1.0
CG2 A:ILE179 4.9 47.2 1.0
N A:PRO211 4.9 59.4 1.0
OD1 A:ASP213 5.0 54.0 1.0

Zinc binding site 2 out of 2 in 7oo5

Go back to Zinc Binding Sites List in 7oo5
Zinc binding site 2 out of 2 in the Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Lignin Peroxidase (Apelip) From Agrocybe Pediades within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:48.4
occ:1.00
NE2 A:HIS71 2.1 52.9 1.0
OE1 A:GLU84 2.1 46.8 1.0
O A:HOH526 2.3 25.2 1.0
OE2 A:GLU84 2.4 43.9 1.0
CD A:GLU84 2.6 48.8 1.0
CD2 A:HIS71 2.8 49.0 1.0
CE1 A:HIS71 3.2 50.6 1.0
CG A:HIS71 3.9 46.0 1.0
ND1 A:HIS71 4.1 47.8 1.0
CG A:GLU84 4.1 43.9 1.0
OG1 A:THR88 4.2 39.9 1.0
CG2 A:ILE87 4.7 47.5 1.0
OG1 A:THR75 4.9 55.4 1.0
O A:GLU84 5.0 40.1 1.0

Reference:

M.I.Sanchez-Ruiz, I.Ayuso-Fernandez, J.Rencoret, A.M.Gonzalez-Ramirez, D.Linde, I.Davo-Siguero, A.Romero, A.Gutierrez, A.T.Martinez, F.J.Ruiz-Duenas. Agaricales Mushroom Lignin Peroxidase: From Structure-Function to Degradative Capabilities. Antioxidants V. 10 2021.
ISSN: ESSN 2076-3921
PubMed: 34573078
DOI: 10.3390/ANTIOX10091446
Page generated: Fri Nov 5 16:55:58 2021

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