Iron in PDB 6fiy: Crystal Structure of A Dye-Decolorizing Peroxidase D143AR232A Variant From Klebsiella Pneumoniae (Kpdyp)

The structure of Crystal Structure of A Dye-Decolorizing Peroxidase D143AR232A Variant From Klebsiella Pneumoniae (Kpdyp), PDB code: 6fiy was solved by V.Pfanzagl, S.Hofbauer, G.Mlynek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.47 / 1.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.620, 76.310, 75.940, 90.00, 107.92, 90.00
R / Rfree (%)	12.5 / 15

The structure of Crystal Structure of A Dye-Decolorizing Peroxidase D143AR232A Variant From Klebsiella Pneumoniae (Kpdyp) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Iron atom in the Crystal Structure of A Dye-Decolorizing Peroxidase D143AR232A Variant From Klebsiella Pneumoniae (Kpdyp) (pdb code 6fiy). 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 of A Dye-Decolorizing Peroxidase D143AR232A Variant From Klebsiella Pneumoniae (Kpdyp), PDB code: 6fiy:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of A Dye-Decolorizing Peroxidase D143AR232A Variant From Klebsiella Pneumoniae (Kpdyp)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of A Dye-Decolorizing Peroxidase D143AR232A Variant From Klebsiella Pneumoniae (Kpdyp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:8.9 occ:1.00 FE A:HEM401 0.0 8.9 1.0 NC A:HEM401 2.0 8.9 1.0 ND A:HEM401 2.0 9.6 1.0 NA A:HEM401 2.0 9.1 1.0 NB A:HEM401 2.0 9.1 1.0 NE2 A:HIS215 2.1 9.3 1.0 O A:HOH665 2.2 15.3 1.0 C1C A:HEM401 3.0 9.1 1.0 C4B A:HEM401 3.0 8.5 1.0 C4D A:HEM401 3.0 9.3 1.0 C1D A:HEM401 3.1 9.3 1.0 CE1 A:HIS215 3.1 9.2 1.0 C1B A:HEM401 3.1 9.1 1.0 C1A A:HEM401 3.1 9.5 1.0 CD2 A:HIS215 3.1 8.7 1.0 C4A A:HEM401 3.1 9.1 1.0 C4C A:HEM401 3.1 8.7 1.0 HE1 A:HIS215 3.2 11.0 1.0 HD2 A:HIS215 3.2 10.4 1.0 CHA A:HEM401 3.4 9.8 1.0 CHC A:HEM401 3.4 8.7 1.0 CHD A:HEM401 3.4 9.1 1.0 CHB A:HEM401 3.4 9.7 1.0 O A:HOH777 3.7 33.0 1.0 HG21 A:VAL219 3.8 12.2 1.0 HO2 A:GOL402 3.8 18.6 1.0 HE1 A:PHE248 3.9 12.4 1.0 ND1 A:HIS215 4.2 9.1 1.0 CG A:HIS215 4.2 9.1 1.0 HE1 A:MET276 4.2 16.2 1.0 O A:HOH654 4.2 18.6 1.0 C3B A:HEM401 4.2 9.0 1.0 C2B A:HEM401 4.3 9.1 1.0 C2C A:HEM401 4.3 9.3 1.0 C3D A:HEM401 4.3 9.6 1.0 C2A A:HEM401 4.3 10.0 1.0 C2D A:HEM401 4.3 9.2 1.0 C3C A:HEM401 4.3 9.3 1.0 C3A A:HEM401 4.3 9.9 1.0 HHA A:HEM401 4.4 11.7 1.0 HHC A:HEM401 4.4 10.5 1.0 HHD A:HEM401 4.4 11.0 1.0 HHB A:HEM401 4.4 11.6 1.0 HG11 A:VAL219 4.6 12.6 1.0 O2 A:GOL402 4.7 15.5 1.0 CE1 A:PHE248 4.7 10.3 1.0 CG2 A:VAL219 4.8 10.2 1.0 O A:HOH601 4.9 18.5 1.0 HD1 A:PHE248 4.9 11.2 1.0 HD1 A:HIS215 4.9 10.9 1.0 HE2 A:MET276 5.0 16.2 1.0

Iron binding site 2 out of 2 in the Crystal Structure of A Dye-Decolorizing Peroxidase D143AR232A Variant From Klebsiella Pneumoniae (Kpdyp)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of A Dye-Decolorizing Peroxidase D143AR232A Variant From Klebsiella Pneumoniae (Kpdyp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:7.9 occ:1.00 FE B:HEM401 0.0 7.9 1.0 ND B:HEM401 2.0 8.5 1.0 NC B:HEM401 2.0 7.7 1.0 NB B:HEM401 2.0 8.4 1.0 NA B:HEM401 2.0 8.7 1.0 NE2 B:HIS215 2.1 8.2 1.0 O B:HOH672 2.2 12.9 1.0 CE1 B:HIS215 3.0 7.8 1.0 C1D B:HEM401 3.0 8.6 1.0 C4C B:HEM401 3.0 8.1 1.0 C4D B:HEM401 3.0 8.7 1.0 C1C B:HEM401 3.1 7.7 1.0 C4B B:HEM401 3.1 7.9 1.0 C4A B:HEM401 3.1 8.7 1.0 C1B B:HEM401 3.1 8.1 1.0 C1A B:HEM401 3.1 8.9 1.0 CD2 B:HIS215 3.1 8.3 1.0 HE1 B:HIS215 3.2 9.4 1.0 HD2 B:HIS215 3.3 9.9 1.0 CHD B:HEM401 3.4 8.3 1.0 CHA B:HEM401 3.4 8.9 1.0 CHB B:HEM401 3.4 9.2 1.0 CHC B:HEM401 3.4 7.9 1.0 HO2 B:GOL402 3.7 16.4 1.0 O B:HOH794 3.7 33.3 1.0 HG21 B:VAL219 3.9 11.5 1.0 HE1 B:PHE248 3.9 12.2 1.0 HE1 B:MET276 4.1 14.2 1.0 ND1 B:HIS215 4.2 8.4 1.0 O B:HOH686 4.2 15.0 1.0 CG B:HIS215 4.2 8.3 1.0 C2C B:HEM401 4.2 8.1 1.0 C3C B:HEM401 4.3 8.3 1.0 C2B B:HEM401 4.3 8.4 1.0 C3D B:HEM401 4.3 9.0 1.0 C2D B:HEM401 4.3 8.9 1.0 C3B B:HEM401 4.3 7.7 1.0 C3A B:HEM401 4.3 8.8 1.0 C2A B:HEM401 4.3 9.1 1.0 HHD B:HEM401 4.4 10.0 1.0 HHA B:HEM401 4.4 10.6 1.0 HHB B:HEM401 4.4 11.1 1.0 HHC B:HEM401 4.4 9.4 1.0 O2 B:GOL402 4.6 13.7 1.0 CE1 B:PHE248 4.6 10.2 1.0 HG11 B:VAL219 4.7 12.3 1.0 CG2 B:VAL219 4.8 9.6 1.0 O B:HOH593 4.9 18.7 1.0 CE B:MET276 4.9 11.8 1.0 HD1 B:PHE248 4.9 11.0 1.0 HE2 B:MET276 4.9 14.2 1.0 HD1 B:HIS215 5.0 10.0 1.0 H32 B:GOL402 5.0 14.4 1.0

V.Pfanzagl, K.Nys, M.Bellei, H.Michlits, G.Mlynek, G.Battistuzzi, K.Djinovic-Carugo, S.Van Doorslaer, P.G.Furtmuller, S.Hofbauer, C.Obinger. Roles of Distal Aspartate and Arginine of B-Class Dye-Decolorizing Peroxidase in Heterolytic Hydrogen Peroxide Cleavage. J. Biol. Chem. V. 293 14823 2018.
ISSN: ESSN 1083-351X
PubMed: 30072383
DOI: 10.1074/JBC.RA118.004773