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

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

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

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 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 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

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