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

The structure of Crystal Structure of A Dye-Decolorizing Peroxidase From Klebsiella Pneumoniae (Kpdyp), PDB code: 6fks 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)	52.22 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.520, 75.850, 75.640, 90.00, 107.86, 90.00
R / Rfree (%)	12.8 / 16.7

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

Iron binding site 1 out of 2 in the Crystal Structure of A Dye-Decolorizing Peroxidase 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 From Klebsiella Pneumoniae (Kpdyp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:12.7 occ:1.00 FE A:HEM401 0.0 12.7 1.0 ND A:HEM401 2.0 12.6 1.0 NA A:HEM401 2.1 12.9 1.0 NB A:HEM401 2.1 12.0 1.0 NC A:HEM401 2.1 12.5 1.0 NE2 A:HIS215 2.2 12.6 1.0 C1D A:HEM401 3.0 13.4 1.0 C4D A:HEM401 3.0 13.0 1.0 C1A A:HEM401 3.1 12.1 1.0 C4A A:HEM401 3.1 12.1 1.0 C1B A:HEM401 3.1 13.9 1.0 C4C A:HEM401 3.1 12.2 1.0 C4B A:HEM401 3.1 13.3 1.0 C1C A:HEM401 3.1 12.6 1.0 CD2 A:HIS215 3.1 13.1 1.0 CE1 A:HIS215 3.2 13.5 1.0 HD2 A:HIS215 3.3 15.7 1.0 HE1 A:HIS215 3.4 16.2 1.0 CHD A:HEM401 3.4 13.1 1.0 CHA A:HEM401 3.4 13.1 1.0 CHB A:HEM401 3.4 13.7 1.0 CHC A:HEM401 3.5 13.2 1.0 HH11 A:ARG232 3.7 16.8 1.0 HG21 A:VAL219 3.8 16.0 1.0 HE1 A:PHE248 3.9 13.9 1.0 O A:HOH680 4.1 15.8 1.0 NH1 A:ARG232 4.2 14.0 1.0 HD3 A:ARG232 4.2 18.0 1.0 C2D A:HEM401 4.2 13.6 1.0 C3D A:HEM401 4.2 13.6 1.0 C3A A:HEM401 4.3 12.5 1.0 ND1 A:HIS215 4.3 12.9 1.0 C2A A:HEM401 4.3 12.8 1.0 CG A:HIS215 4.3 12.6 1.0 HE1 A:MET276 4.3 24.1 1.0 C3B A:HEM401 4.3 12.8 1.0 C2B A:HEM401 4.3 13.7 1.0 C2C A:HEM401 4.3 12.3 1.0 C3C A:HEM401 4.3 12.8 1.0 HD2 A:ARG232 4.3 18.0 1.0 HH12 A:ARG232 4.4 16.8 1.0 HHA A:HEM401 4.4 15.7 1.0 HHD A:HEM401 4.4 15.8 1.0 HHB A:HEM401 4.4 16.5 1.0 HHC A:HEM401 4.4 15.8 1.0 HG11 A:VAL219 4.6 18.4 1.0 CE1 A:PHE248 4.7 11.6 1.0 CD A:ARG232 4.7 15.0 1.0 CG2 A:VAL219 4.8 13.3 1.0 CZ A:ARG232 4.8 13.6 1.0 HD1 A:PHE248 4.9 14.2 1.0

Iron binding site 2 out of 2 in the Crystal Structure of A Dye-Decolorizing Peroxidase 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 From Klebsiella Pneumoniae (Kpdyp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:15.3 occ:1.00 FE B:HEM401 0.0 15.3 1.0 ND B:HEM401 2.0 15.2 1.0 NA B:HEM401 2.0 16.4 1.0 NB B:HEM401 2.1 15.4 1.0 NC B:HEM401 2.1 14.7 1.0 NE2 B:HIS215 2.2 15.7 1.0 C4D B:HEM401 3.0 15.1 1.0 C1A B:HEM401 3.0 16.4 1.0 C4A B:HEM401 3.1 16.1 1.0 C4B B:HEM401 3.1 14.8 1.0 C1D B:HEM401 3.1 14.7 1.0 C1B B:HEM401 3.1 15.7 1.0 C1C B:HEM401 3.1 13.2 1.0 C4C B:HEM401 3.1 14.3 1.0 CD2 B:HIS215 3.2 15.3 1.0 CE1 B:HIS215 3.2 16.3 1.0 HD2 B:HIS215 3.3 18.4 1.0 CHA B:HEM401 3.4 16.9 1.0 HE1 B:HIS215 3.4 19.6 1.0 CHC B:HEM401 3.5 13.5 1.0 CHB B:HEM401 3.5 16.4 1.0 CHD B:HEM401 3.5 14.2 1.0 HH11 B:ARG232 3.8 20.8 1.0 HG21 B:VAL219 3.8 19.5 1.0 HE1 B:PHE248 3.9 16.9 1.0 NH1 B:ARG232 4.2 17.3 1.0 O B:HOH655 4.2 16.4 1.0 C3D B:HEM401 4.2 15.3 1.0 C2A B:HEM401 4.2 16.9 1.0 HD3 B:ARG232 4.3 18.0 1.0 C3A B:HEM401 4.3 15.9 1.0 C2D B:HEM401 4.3 15.0 1.0 HE1 B:MET276 4.3 27.9 1.0 C3B B:HEM401 4.3 15.5 1.0 ND1 B:HIS215 4.3 15.7 1.0 C2B B:HEM401 4.3 16.1 1.0 CG B:HIS215 4.3 15.1 1.0 C2C B:HEM401 4.3 13.3 1.0 HHA B:HEM401 4.3 20.3 1.0 C3C B:HEM401 4.3 14.2 1.0 HH12 B:ARG232 4.3 20.8 1.0 HHB B:HEM401 4.4 19.6 1.0 HHC B:HEM401 4.4 16.2 1.0 HHD B:HEM401 4.5 17.0 1.0 HD2 B:ARG232 4.5 18.0 1.0 HG11 B:VAL219 4.6 20.1 1.0 CE1 B:PHE248 4.6 14.1 1.0 CD B:ARG232 4.8 15.0 1.0 CG2 B:VAL219 4.8 16.2 1.0 CZ B:ARG232 4.9 15.9 1.0 HD1 B:PHE248 4.9 16.9 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