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Iron in PDB 5ag0: Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) Crystallized at pH 6.5

Enzymatic activity of Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) Crystallized at pH 6.5

All present enzymatic activity of Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) Crystallized at pH 6.5:
1.11.1.19;

Protein crystallography data

The structure of Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) Crystallized at pH 6.5, PDB code: 5ag0 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) 47.51 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.840, 46.570, 147.630, 90.00, 100.49, 90.00
R / Rfree (%) 18.737 / 22.225

Other elements in 5ag0:

The structure of Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) Crystallized at pH 6.5 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) Crystallized at pH 6.5 (pdb code 5ag0). 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) Crystallized at pH 6.5, PDB code: 5ag0:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 5ag0

Go back to Iron Binding Sites List in 5ag0
Iron binding site 1 out of 2 in the Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) Crystallized at pH 6.5


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) Crystallized at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1449

b:6.0
occ:1.00
FE A:HEM1449 0.0 6.0 1.0
ND A:HEM1449 1.9 6.0 1.0
NA A:HEM1449 2.0 6.0 1.0
O2 A:FMT1456 2.0 9.1 1.0
NC A:HEM1449 2.1 6.1 1.0
NB A:HEM1449 2.1 6.2 1.0
NE2 A:HIS304 2.1 6.1 1.0
C1D A:HEM1449 2.9 6.3 1.0
C4D A:HEM1449 2.9 6.0 1.0
C1A A:HEM1449 3.0 6.2 1.0
C4A A:HEM1449 3.0 6.1 1.0
C4B A:HEM1449 3.1 6.1 1.0
C4C A:HEM1449 3.1 6.2 1.0
C1B A:HEM1449 3.1 6.3 1.0
CE1 A:HIS304 3.1 5.8 1.0
C1C A:HEM1449 3.1 6.1 1.0
C A:FMT1456 3.1 9.3 1.0
CD2 A:HIS304 3.1 6.0 1.0
CHA A:HEM1449 3.4 5.9 1.0
CHD A:HEM1449 3.4 6.1 1.0
CHB A:HEM1449 3.4 6.3 1.0
CHC A:HEM1449 3.5 6.0 1.0
C2D A:HEM1449 4.2 6.1 1.0
C3D A:HEM1449 4.2 6.0 1.0
C2A A:HEM1449 4.2 6.3 1.0
O1 A:FMT1456 4.2 11.9 1.0
C3A A:HEM1449 4.2 6.2 1.0
NH1 A:ARG332 4.2 7.2 1.0
ND1 A:HIS304 4.2 6.0 1.0
C3C A:HEM1449 4.3 6.1 1.0
CG A:HIS304 4.3 5.8 1.0
C2C A:HEM1449 4.3 6.2 1.0
C2B A:HEM1449 4.3 6.1 1.0
C3B A:HEM1449 4.3 6.1 1.0
CD A:ARG332 4.8 7.2 1.0

Iron binding site 2 out of 2 in 5ag0

Go back to Iron Binding Sites List in 5ag0
Iron binding site 2 out of 2 in the Dyp-Type Peroxidase of Auricularia Auricula-Judae (Aaudypi) Crystallized at pH 6.5


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) Crystallized at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1449

b:12.7
occ:1.00
FE B:HEM1449 0.0 12.7 1.0
ND B:HEM1449 1.9 12.6 1.0
NA B:HEM1449 2.0 12.8 1.0
NC B:HEM1449 2.1 12.5 1.0
NB B:HEM1449 2.1 12.8 1.0
NE2 B:HIS304 2.1 13.0 1.0
O2 B:FMT1460 2.2 16.9 1.0
C1D B:HEM1449 2.9 12.2 1.0
C4D B:HEM1449 2.9 12.0 1.0
C1A B:HEM1449 3.0 13.1 1.0
C4A B:HEM1449 3.0 13.1 1.0
C1B B:HEM1449 3.1 13.1 1.0
C4C B:HEM1449 3.1 11.8 1.0
C4B B:HEM1449 3.1 12.1 1.0
CD2 B:HIS304 3.1 14.0 1.0
C1C B:HEM1449 3.1 11.6 1.0
C B:FMT1460 3.1 16.2 1.0
CE1 B:HIS304 3.1 13.0 1.0
CHD B:HEM1449 3.4 11.9 1.0
CHA B:HEM1449 3.4 12.6 1.0
CHB B:HEM1449 3.4 13.0 1.0
CHC B:HEM1449 3.5 11.9 1.0
NH1 B:ARG332 4.1 14.6 1.0
C2D B:HEM1449 4.2 12.5 1.0
C3D B:HEM1449 4.2 12.2 1.0
C2A B:HEM1449 4.2 13.5 1.0
C3A B:HEM1449 4.2 13.3 1.0
ND1 B:HIS304 4.2 14.0 1.0
CG B:HIS304 4.3 13.8 1.0
O1 B:FMT1460 4.3 17.2 1.0
C3C B:HEM1449 4.3 11.3 1.0
C2C B:HEM1449 4.3 11.1 1.0
C2B B:HEM1449 4.3 12.9 1.0
C3B B:HEM1449 4.3 12.4 1.0
CD B:ARG332 4.7 14.4 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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