Iron in PDB 6fl2: Crystal Structure of A Dye-Decolorizing Peroxidase D143A Variant From Klebsiella Pneumoniae (Kpdyp)

The structure of Crystal Structure of A Dye-Decolorizing Peroxidase D143A Variant From Klebsiella Pneumoniae (Kpdyp), PDB code: 6fl2 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)	52.68 / 1.27
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.760, 76.690, 76.140, 90.00, 107.79, 90.00
R / Rfree (%)	11.4 / 14.1

The structure of Crystal Structure of A Dye-Decolorizing Peroxidase D143A 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 D143A Variant From Klebsiella Pneumoniae (Kpdyp) (pdb code 6fl2). 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 D143A Variant From Klebsiella Pneumoniae (Kpdyp), PDB code: 6fl2:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of A Dye-Decolorizing Peroxidase D143A 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 D143A Variant From Klebsiella Pneumoniae (Kpdyp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:10.2 occ:1.00 FE A:HEM401 0.0 10.2 1.0 NB A:HEM401 2.0 10.3 1.0 ND A:HEM401 2.0 11.2 1.0 NA A:HEM401 2.0 10.5 1.0 NC A:HEM401 2.0 9.9 1.0 O2 A:NO2403 2.1 13.2 0.9 NE2 A:HIS215 2.1 10.7 1.0 C1B A:HEM401 3.0 10.6 1.0 C1A A:HEM401 3.1 10.8 1.0 C4A A:HEM401 3.1 10.4 1.0 C4D A:HEM401 3.1 10.2 1.0 C1D A:HEM401 3.1 10.2 1.0 C1C A:HEM401 3.1 10.6 1.0 CE1 A:HIS215 3.1 11.5 1.0 C4B A:HEM401 3.1 10.3 1.0 C4C A:HEM401 3.1 9.8 1.0 N A:NO2403 3.1 15.5 0.9 CD2 A:HIS215 3.1 11.2 1.0 HE1 A:HIS215 3.2 13.8 1.0 HD2 A:HIS215 3.3 13.4 1.0 CHA A:HEM401 3.4 10.9 1.0 CHB A:HEM401 3.4 11.1 1.0 CHC A:HEM401 3.4 10.1 1.0 CHD A:HEM401 3.4 9.8 1.0 HH11 A:ARG232 3.7 13.3 1.0 HG21 A:VAL219 3.9 13.9 1.0 HE1 A:PHE248 4.0 12.7 1.0 NH1 A:ARG232 4.2 11.1 1.0 ND1 A:HIS215 4.2 10.4 1.0 HE1 A:MET276 4.2 17.1 1.0 CG A:HIS215 4.2 10.6 1.0 C2A A:HEM401 4.3 11.2 1.0 C2C A:HEM401 4.3 9.9 1.0 C2B A:HEM401 4.3 10.4 1.0 C3A A:HEM401 4.3 11.4 1.0 C3B A:HEM401 4.3 10.9 1.0 C3D A:HEM401 4.3 10.0 1.0 C3C A:HEM401 4.3 10.1 1.0 C2D A:HEM401 4.3 10.2 1.0 HD3 A:ARG232 4.3 13.3 1.0 O1 A:NO2403 4.3 12.3 0.9 HH12 A:ARG232 4.4 13.3 1.0 HHB A:HEM401 4.4 13.3 1.0 HHA A:HEM401 4.4 13.0 1.0 HD2 A:ARG232 4.4 13.3 1.0 HHC A:HEM401 4.4 12.1 1.0 HHD A:HEM401 4.4 11.8 1.0 HG11 A:VAL219 4.7 14.1 1.0 CE1 A:PHE248 4.7 10.6 1.0 CD A:ARG232 4.8 11.1 1.0 CG2 A:VAL219 4.9 11.6 1.0 HD1 A:PHE248 4.9 11.8 1.0 CZ A:ARG232 4.9 10.6 1.0 HD1 A:HIS215 5.0 12.5 1.0

Iron binding site 2 out of 2 in the Crystal Structure of A Dye-Decolorizing Peroxidase D143A 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 D143A Variant From Klebsiella Pneumoniae (Kpdyp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:8.9 occ:1.00 FE B:HEM401 0.0 8.9 1.0 NB B:HEM401 2.0 9.4 1.0 NC B:HEM401 2.0 8.7 1.0 NA B:HEM401 2.1 9.1 1.0 ND B:HEM401 2.1 9.0 1.0 NE2 B:HIS215 2.1 9.6 1.0 O2 B:NO2405 2.1 11.8 0.9 C1B B:HEM401 3.1 9.4 1.0 C1D B:HEM401 3.1 9.2 1.0 C1C B:HEM401 3.1 7.8 1.0 C4C B:HEM401 3.1 8.6 1.0 C4B B:HEM401 3.1 8.6 1.0 C1A B:HEM401 3.1 9.1 1.0 C4A B:HEM401 3.1 9.4 1.0 N B:NO2405 3.1 15.2 0.9 CE1 B:HIS215 3.1 8.5 1.0 C4D B:HEM401 3.1 8.8 1.0 CD2 B:HIS215 3.1 9.6 1.0 HE1 B:HIS215 3.3 10.2 1.0 HD2 B:HIS215 3.3 11.5 1.0 CHD B:HEM401 3.4 9.1 1.0 CHB B:HEM401 3.4 9.7 1.0 CHC B:HEM401 3.4 8.9 1.0 CHA B:HEM401 3.4 9.0 1.0 HH11 B:ARG232 3.7 11.5 1.0 HE1 B:PHE248 3.9 12.9 1.0 HG21 B:VAL219 4.0 13.4 1.0 NH1 B:ARG232 4.2 9.6 1.0 HE1 B:MET276 4.2 14.9 1.0 ND1 B:HIS215 4.2 9.3 1.0 CG B:HIS215 4.3 9.4 1.0 HD3 B:ARG232 4.3 12.2 1.0 C3B B:HEM401 4.3 8.9 1.0 C2C B:HEM401 4.3 9.1 1.0 C3C B:HEM401 4.3 9.2 1.0 C2D B:HEM401 4.3 9.0 1.0 C2B B:HEM401 4.3 8.6 1.0 C2A B:HEM401 4.3 9.5 1.0 C3A B:HEM401 4.3 9.8 1.0 C3D B:HEM401 4.3 9.3 1.0 O1 B:NO2405 4.3 11.0 0.9 HD2 B:ARG232 4.4 12.2 1.0 HH12 B:ARG232 4.4 11.5 1.0 HHD B:HEM401 4.4 10.8 1.0 HHB B:HEM401 4.4 11.7 1.0 HHC B:HEM401 4.4 10.7 1.0 HHA B:HEM401 4.4 10.8 1.0 CD B:ARG232 4.7 10.2 1.0 HG11 B:VAL219 4.7 12.6 1.0 CE1 B:PHE248 4.7 10.7 1.0 CZ B:ARG232 4.9 9.1 1.0 HD1 B:PHE248 4.9 11.8 1.0 CG2 B:VAL219 4.9 11.2 1.0 HD1 B:HIS215 5.0 11.2 1.0 CE B:MET276 5.0 12.4 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