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Iron in PDB 5ag1: Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) with Meso-Nitrated Heme

Enzymatic activity of Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) with Meso-Nitrated Heme

All present enzymatic activity of Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) with Meso-Nitrated Heme:
1.11.1.19;

Protein crystallography data

The structure of Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) with Meso-Nitrated Heme, PDB code: 5ag1 was solved by E.Strittmatter, K.Piontek, D.A.Plattner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.57 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.000, 46.780, 148.150, 90.00, 100.53, 90.00
R / Rfree (%) 17.451 / 21.547

Other elements in 5ag1:

The structure of Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) with Meso-Nitrated Heme also contains other interesting chemical elements:

Arsenic (As) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) with Meso-Nitrated Heme (pdb code 5ag1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) with Meso-Nitrated Heme, PDB code: 5ag1:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 5ag1

Go back to Iron Binding Sites List in 5ag1
Iron binding site 1 out of 2 in the Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) with Meso-Nitrated Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) with Meso-Nitrated Heme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1458

b:9.1
occ:1.00
FE A:N7H1458 0.0 9.1 1.0
NE2 A:HIS304 1.9 8.9 1.0
ND A:N7H1458 1.9 8.9 1.0
NA A:N7H1458 2.0 10.1 1.0
NC A:N7H1458 2.1 9.1 1.0
NB A:N7H1458 2.1 10.2 1.0
O1 A:NO21460 2.3 16.5 1.0
CE1 A:HIS304 2.8 8.9 1.0
C1D A:N7H1458 2.9 9.0 1.0
C4D A:N7H1458 2.9 9.2 1.0
CD2 A:HIS304 3.0 8.9 1.0
C1A A:N7H1458 3.0 10.1 1.0
C4A A:N7H1458 3.0 10.9 1.0
C4C A:N7H1458 3.1 9.0 1.0
C4B A:N7H1458 3.1 10.2 1.0
C1B A:N7H1458 3.1 10.8 1.0
C1C A:N7H1458 3.1 9.4 1.0
CHD A:N7H1458 3.4 8.9 1.0
CHA A:N7H1458 3.4 9.8 1.0
CHB A:N7H1458 3.5 12.2 1.0
CHC A:N7H1458 3.5 9.4 1.0
N A:NO21460 3.6 19.1 1.0
ND1 A:HIS304 3.9 8.8 1.0
CG A:HIS304 4.1 8.6 1.0
C2D A:N7H1458 4.2 9.1 1.0
C3D A:N7H1458 4.2 9.1 1.0
C2A A:N7H1458 4.2 10.8 1.0
C3A A:N7H1458 4.2 11.1 1.0
C3C A:N7H1458 4.3 9.4 1.0
C2C A:N7H1458 4.3 9.5 1.0
C2B A:N7H1458 4.3 11.2 1.0
NH1 A:ARG332 4.3 11.6 1.0
C3B A:N7H1458 4.3 10.5 1.0
O2 A:NO21460 4.5 26.4 1.0
CD A:ARG332 4.8 11.2 1.0
N1 A:N7H1458 4.8 14.2 1.0

Iron binding site 2 out of 2 in 5ag1

Go back to Iron Binding Sites List in 5ag1
Iron binding site 2 out of 2 in the Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) with Meso-Nitrated Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) with Meso-Nitrated Heme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1456

b:11.8
occ:1.00
FE B:N7H1456 0.0 11.8 1.0
NE2 B:HIS304 1.9 11.9 1.0
ND B:N7H1456 1.9 12.2 1.0
NA B:N7H1456 2.0 13.1 1.0
NC B:N7H1456 2.1 11.8 1.0
NB B:N7H1456 2.1 12.8 1.0
O1 B:NO21457 2.3 22.0 1.0
CE1 B:HIS304 2.8 11.7 1.0
C1D B:N7H1456 2.9 11.9 1.0
C4D B:N7H1456 2.9 11.8 1.0
CD2 B:HIS304 3.0 12.3 1.0
C1A B:N7H1456 3.0 13.3 1.0
C4A B:N7H1456 3.0 14.0 1.0
C4B B:N7H1456 3.1 11.9 1.0
C4C B:N7H1456 3.1 11.4 1.0
C1B B:N7H1456 3.1 13.4 1.0
C1C B:N7H1456 3.1 11.1 1.0
CHD B:N7H1456 3.4 11.7 1.0
CHA B:N7H1456 3.4 12.9 1.0
CHB B:N7H1456 3.5 14.5 1.0
CHC B:N7H1456 3.5 11.7 1.0
N B:NO21457 3.6 23.0 1.0
ND1 B:HIS304 3.9 12.1 1.0
CG B:HIS304 4.1 11.9 1.0
C2D B:N7H1456 4.2 12.0 1.0
C3D B:N7H1456 4.2 12.0 1.0
C2A B:N7H1456 4.2 14.2 1.0
C3A B:N7H1456 4.2 15.1 1.0
C3C B:N7H1456 4.3 11.3 1.0
C2C B:N7H1456 4.3 11.2 1.0
C2B B:N7H1456 4.3 13.0 1.0
C3B B:N7H1456 4.3 12.1 1.0
NH1 B:ARG332 4.3 13.4 1.0
O2 B:NO21457 4.6 28.1 1.0
CD B:ARG332 4.7 13.6 1.0
N1 B:N7H1456 4.8 17.4 1.0

Reference:

E.Strittmatter, K.Piontek, D.A.Plattner. Crystallographic Trapping of A Covalently Modified Heme in A Dye-Decolorizing Peroxidase To Be Published.
Page generated: Sun Dec 13 15:56:06 2020

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