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Iron in PDB 8re3: Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans

Protein crystallography data

The structure of Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans, PDB code: 8re3 was solved by B.A.Salgueiro, K.Frade, C.Frazao, P.Matias, E.Moe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.74 / 1.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.09, 97.697, 116.037, 90, 90, 90
R / Rfree (%) 16.7 / 19.5

Other elements in 8re3:

The structure of Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans (pdb code 8re3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans, PDB code: 8re3:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 8re3

Go back to Iron Binding Sites List in 8re3
Iron binding site 1 out of 2 in the Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:16.1
occ:1.00
FE A:HEM501 0.0 16.1 1.0
ND A:HEM501 2.0 16.1 1.0
NA A:HEM501 2.0 17.7 1.0
NC A:HEM501 2.0 13.8 1.0
O A:OH502 2.0 20.5 1.0
NB A:HEM501 2.0 18.4 1.0
NE2 A:HIS324 2.1 17.5 1.0
C1C A:HEM501 3.0 14.8 1.0
C4B A:HEM501 3.0 16.4 1.0
C1A A:HEM501 3.0 18.0 1.0
C1D A:HEM501 3.0 17.9 1.0
C4D A:HEM501 3.0 18.5 1.0
C4A A:HEM501 3.1 21.8 1.0
C4C A:HEM501 3.1 17.0 1.0
CD2 A:HIS324 3.1 20.1 1.0
CE1 A:HIS324 3.1 20.9 1.0
C1B A:HEM501 3.1 19.2 1.0
HD2 A:HIS324 3.3 24.3 1.0
HE1 A:HIS324 3.3 25.3 1.0
CHC A:HEM501 3.4 16.6 1.0
CHA A:HEM501 3.4 17.7 1.0
CHD A:HEM501 3.4 16.7 1.0
CHB A:HEM501 3.5 16.4 1.0
HH11 A:ARG348 3.6 33.5 1.0
O A:OH503 3.7 26.4 1.0
HG3 A:MET328 4.0 25.6 1.0
NH1 A:ARG348 4.1 27.8 1.0
HD2 A:ARG348 4.1 30.3 1.0
ND1 A:HIS324 4.2 21.2 1.0
CG A:HIS324 4.2 19.1 1.0
HD3 A:ARG348 4.2 30.3 1.0
C2D A:HEM501 4.3 17.9 1.0
C3D A:HEM501 4.3 17.5 1.0
C3A A:HEM501 4.3 20.0 1.0
C2A A:HEM501 4.3 18.8 1.0
C2C A:HEM501 4.3 16.3 1.0
C3C A:HEM501 4.3 15.7 1.0
C3B A:HEM501 4.3 17.6 1.0
C2B A:HEM501 4.3 20.2 1.0
HHC A:HEM501 4.3 20.0 1.0
HHA A:HEM501 4.4 21.4 1.0
HHD A:HEM501 4.4 20.2 1.0
HH12 A:ARG348 4.4 33.5 1.0
HHB A:HEM501 4.5 19.8 1.0
CD A:ARG348 4.6 25.1 1.0
HZ A:PHE375 4.7 21.8 1.0
HE1 A:PHE375 4.7 24.1 1.0
CZ A:ARG348 4.8 24.8 1.0
NE A:ARG348 4.9 25.5 1.0
CZ A:PHE375 5.0 18.1 1.0
CG A:MET328 5.0 21.1 1.0
CE1 A:PHE375 5.0 19.9 1.0
HD1 A:HIS324 5.0 25.6 1.0

Iron binding site 2 out of 2 in 8re3

Go back to Iron Binding Sites List in 8re3
Iron binding site 2 out of 2 in the Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:14.7
occ:1.00
FE B:HEM501 0.0 14.7 1.0
NB B:HEM501 2.0 13.0 1.0
NA B:HEM501 2.0 17.0 1.0
NC B:HEM501 2.0 15.4 1.0
ND B:HEM501 2.0 15.4 1.0
NE2 B:HIS324 2.1 15.4 1.0
O B:OH502 2.1 19.4 1.0
C4B B:HEM501 3.0 14.0 1.0
C1C B:HEM501 3.0 15.4 1.0
C1A B:HEM501 3.0 17.6 1.0
CD2 B:HIS324 3.0 17.6 1.0
C1B B:HEM501 3.1 16.6 1.0
C4A B:HEM501 3.1 15.8 1.0
C4D B:HEM501 3.1 15.5 1.0
C4C B:HEM501 3.1 17.1 1.0
C1D B:HEM501 3.1 15.8 1.0
CE1 B:HIS324 3.1 18.2 1.0
HD2 B:HIS324 3.2 21.2 1.0
HE1 B:HIS324 3.3 22.0 1.0
CHC B:HEM501 3.4 14.7 1.0
CHA B:HEM501 3.4 18.4 1.0
CHD B:HEM501 3.5 13.2 1.0
CHB B:HEM501 3.5 15.0 1.0
O B:OH503 3.7 28.9 1.0
HH11 B:ARG348 3.7 34.5 1.0
HG3 B:MET328 4.0 24.6 1.0
HD2 B:ARG348 4.2 34.7 1.0
ND1 B:HIS324 4.2 20.7 1.0
CG B:HIS324 4.2 17.3 1.0
C3B B:HEM501 4.2 16.6 1.0
C2A B:HEM501 4.2 16.7 1.0
C2B B:HEM501 4.3 15.1 1.0
C3A B:HEM501 4.3 15.1 1.0
C2C B:HEM501 4.3 15.1 1.0
NH1 B:ARG348 4.3 28.6 1.0
C3C B:HEM501 4.3 15.8 1.0
HD3 B:ARG348 4.3 34.7 1.0
C2D B:HEM501 4.3 16.3 1.0
C3D B:HEM501 4.3 18.1 1.0
HHC B:HEM501 4.3 17.8 1.0
HHA B:HEM501 4.4 22.2 1.0
HHD B:HEM501 4.4 16.0 1.0
HHB B:HEM501 4.4 18.1 1.0
HE1 B:PHE375 4.6 24.8 1.0
HZ B:PHE375 4.6 21.4 1.0
HH12 B:ARG348 4.6 34.5 1.0
CD B:ARG348 4.6 28.8 1.0
CE1 B:PHE375 4.9 20.6 1.0
CZ B:PHE375 4.9 17.7 1.0
CG B:MET328 5.0 20.4 1.0
CZ B:ARG348 5.0 30.9 1.0
HD1 B:HIS324 5.0 25.0 1.0

Reference:

K.Frade, C.M.Silveira, B.A.Salgueiro, S.Mendes, L.O.Martins, C.Frazao, S.Todorovic, E.Moe. Biochemical, Biophysical, and Structural Analysis of An Unusual Dyp From the Extremophile Deinococcus Radiodurans. Molecules V. 29 2024.
ISSN: ESSN 1420-3049
PubMed: 38257271
DOI: 10.3390/MOLECULES29020358
Page generated: Thu Aug 7 22:00:15 2025

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