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Iron in PDB 1b85: Lignin Peroxidase

Enzymatic activity of Lignin Peroxidase

All present enzymatic activity of Lignin Peroxidase:
1.11.1.14;

Protein crystallography data

The structure of Lignin Peroxidase, PDB code: 1b85 was solved by W.Blodig, W.A.Doyle, A.T.Smith, K.Piontek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 1.85
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 73.400, 94.400, 230.990, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 18.1

Other elements in 1b85:

The structure of Lignin Peroxidase also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Lignin Peroxidase (pdb code 1b85). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Lignin Peroxidase, PDB code: 1b85:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 1b85

Go back to Iron Binding Sites List in 1b85
Iron binding site 1 out of 2 in the Lignin Peroxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Lignin Peroxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe350

b:12.0
occ:1.00
FE A:HEM350 0.0 12.0 1.0
ND A:HEM350 2.0 11.7 1.0
NA A:HEM350 2.0 11.9 1.0
NB A:HEM350 2.0 14.8 1.0
NC A:HEM350 2.0 11.3 1.0
O A:HOH362 2.2 16.8 1.0
NE2 A:HIS176 2.2 11.8 1.0
C1D A:HEM350 3.0 11.9 1.0
C1A A:HEM350 3.0 11.8 1.0
C4C A:HEM350 3.0 12.1 1.0
C4A A:HEM350 3.0 11.6 1.0
C4D A:HEM350 3.0 11.3 1.0
C1C A:HEM350 3.1 12.7 1.0
C4B A:HEM350 3.1 13.3 1.0
C1B A:HEM350 3.1 13.2 1.0
CE1 A:HIS176 3.2 12.1 1.0
CD2 A:HIS176 3.2 13.0 1.0
CHD A:HEM350 3.4 11.3 1.0
CHA A:HEM350 3.4 11.9 1.0
CHB A:HEM350 3.4 14.2 1.0
CHC A:HEM350 3.5 13.5 1.0
C2D A:HEM350 4.2 10.9 1.0
C3D A:HEM350 4.2 12.4 1.0
C3A A:HEM350 4.3 11.5 1.0
C2C A:HEM350 4.3 12.1 1.0
C2A A:HEM350 4.3 11.6 1.0
ND1 A:HIS176 4.3 10.8 1.0
C3C A:HEM350 4.3 11.4 1.0
C2B A:HEM350 4.3 11.1 1.0
C3B A:HEM350 4.3 13.1 1.0
CG A:HIS176 4.3 10.5 1.0
O A:HOH430 4.5 17.8 1.0
O A:HOH519 4.6 30.5 1.0

Iron binding site 2 out of 2 in 1b85

Go back to Iron Binding Sites List in 1b85
Iron binding site 2 out of 2 in the Lignin Peroxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Lignin Peroxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe350

b:11.7
occ:1.00
FE B:HEM350 0.0 11.7 1.0
NA B:HEM350 2.0 12.5 1.0
NC B:HEM350 2.0 10.6 1.0
NB B:HEM350 2.0 10.7 1.0
ND B:HEM350 2.0 9.5 1.0
O B:HOH361 2.1 13.8 1.0
NE2 B:HIS176 2.1 11.0 1.0
C1A B:HEM350 3.0 11.6 1.0
C1C B:HEM350 3.0 12.1 1.0
C1B B:HEM350 3.0 12.2 1.0
C4B B:HEM350 3.0 12.3 1.0
C4C B:HEM350 3.0 9.2 1.0
C4A B:HEM350 3.1 11.2 1.0
C1D B:HEM350 3.1 9.8 1.0
C4D B:HEM350 3.1 10.9 1.0
CE1 B:HIS176 3.1 11.6 1.0
CD2 B:HIS176 3.1 11.9 1.0
CHD B:HEM350 3.4 11.8 1.0
CHC B:HEM350 3.4 11.8 1.0
CHA B:HEM350 3.4 11.3 1.0
CHB B:HEM350 3.5 12.4 1.0
C2A B:HEM350 4.2 11.7 1.0
ND1 B:HIS176 4.3 12.1 1.0
C3A B:HEM350 4.3 11.6 1.0
C2C B:HEM350 4.3 12.0 1.0
C3C B:HEM350 4.3 10.9 1.0
C2D B:HEM350 4.3 9.9 1.0
C3B B:HEM350 4.3 12.7 1.0
C2B B:HEM350 4.3 13.3 1.0
C3D B:HEM350 4.3 10.7 1.0
CG B:HIS176 4.3 10.7 1.0
O B:HOH455 4.5 16.7 1.0
O B:HOH486 4.6 32.2 1.0

Reference:

W.Blodig, A.T.Smith, W.A.Doyle, K.Piontek. Crystal Structures of Pristine and Oxidatively Processed Lignin Peroxidase Expressed in Escherichia Coli and of the W171F Variant That Eliminates the Redox Active Tryptophan 171. Implications For the Reaction Mechanism. J.Mol.Biol. V. 305 851 2001.
ISSN: ISSN 0022-2836
PubMed: 11162097
DOI: 10.1006/JMBI.2000.4346
Page generated: Sun Dec 13 14:07:35 2020

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