Iron in PDB 6fkt: Crystal Structure of A Dye-Decolorizing Peroxidase R232A Variant From Klebsiella Pneumoniae (Kpdyp)

The structure of Crystal Structure of A Dye-Decolorizing Peroxidase R232A Variant From Klebsiella Pneumoniae (Kpdyp), PDB code: 6fkt 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)	75.22 / 1.86
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.160, 91.160, 247.820, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 20.7

The structure of Crystal Structure of A Dye-Decolorizing Peroxidase R232A Variant From Klebsiella Pneumoniae (Kpdyp) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Iron atom in the Crystal Structure of A Dye-Decolorizing Peroxidase R232A Variant From Klebsiella Pneumoniae (Kpdyp) (pdb code 6fkt). 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 R232A Variant From Klebsiella Pneumoniae (Kpdyp), PDB code: 6fkt:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of A Dye-Decolorizing Peroxidase R232A 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 R232A Variant From Klebsiella Pneumoniae (Kpdyp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:25.1 occ:1.00 FE A:HEM500 0.0 25.1 1.0 NB A:HEM500 2.0 19.3 1.0 ND A:HEM500 2.0 20.0 1.0 NC A:HEM500 2.0 22.2 1.0 NA A:HEM500 2.1 24.1 1.0 NE2 A:HIS215 2.3 21.8 1.0 C1D A:HEM500 3.0 22.6 1.0 C1B A:HEM500 3.0 23.6 1.0 C4A A:HEM500 3.0 26.4 1.0 C4C A:HEM500 3.0 22.7 1.0 C4B A:HEM500 3.1 20.9 1.0 C1A A:HEM500 3.1 24.3 1.0 C1C A:HEM500 3.1 21.5 1.0 C4D A:HEM500 3.1 23.8 1.0 CD2 A:HIS215 3.2 24.8 1.0 HD2 A:HIS215 3.3 29.8 1.0 CE1 A:HIS215 3.3 26.1 1.0 CHD A:HEM500 3.4 20.1 1.0 CHB A:HEM500 3.4 24.1 1.0 CHC A:HEM500 3.4 19.4 1.0 CHA A:HEM500 3.5 22.6 1.0 HE1 A:HIS215 3.5 31.3 1.0 HG21 A:VAL219 3.9 32.1 1.0 HE1 A:PHE248 3.9 27.1 1.0 C3A A:HEM500 4.3 30.1 1.0 C2A A:HEM500 4.3 27.2 1.0 C2B A:HEM500 4.3 22.2 1.0 C2D A:HEM500 4.3 22.1 1.0 C3B A:HEM500 4.3 19.9 1.0 C3C A:HEM500 4.3 23.6 1.0 C3D A:HEM500 4.3 24.8 1.0 C2C A:HEM500 4.3 21.6 1.0 CG A:HIS215 4.4 27.1 1.0 HHD A:HEM500 4.4 24.1 1.0 HHB A:HEM500 4.4 28.9 1.0 ND1 A:HIS215 4.4 24.6 1.0 HHC A:HEM500 4.4 23.2 1.0 HHA A:HEM500 4.4 27.2 1.0 HE1 A:MET276 4.4 31.9 1.0 HA3 A:GLY144 4.5 66.3 1.0 HG11 A:VAL219 4.6 31.7 1.0 CE1 A:PHE248 4.7 22.6 1.0 CG2 A:VAL219 4.8 26.7 1.0

Iron binding site 2 out of 2 in the Crystal Structure of A Dye-Decolorizing Peroxidase R232A 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 R232A Variant From Klebsiella Pneumoniae (Kpdyp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:23.7 occ:1.00 FE B:HEM401 0.0 23.7 1.0 NA B:HEM401 2.0 25.2 1.0 NB B:HEM401 2.0 25.5 1.0 NC B:HEM401 2.1 22.0 1.0 ND B:HEM401 2.1 24.5 1.0 NE2 B:HIS215 2.3 26.4 1.0 C4A B:HEM401 3.0 26.0 1.0 C1B B:HEM401 3.0 28.8 1.0 C1A B:HEM401 3.0 25.7 1.0 C4B B:HEM401 3.1 27.0 1.0 C4C B:HEM401 3.1 22.4 1.0 C1C B:HEM401 3.1 22.5 1.0 C4D B:HEM401 3.1 27.8 1.0 C1D B:HEM401 3.1 24.9 1.0 CD2 B:HIS215 3.2 27.8 1.0 HD2 B:HIS215 3.3 33.3 1.0 CE1 B:HIS215 3.3 26.6 1.0 CHB B:HEM401 3.4 28.3 1.0 CHC B:HEM401 3.4 22.0 1.0 CHA B:HEM401 3.4 28.7 1.0 CHD B:HEM401 3.5 24.9 1.0 HE1 B:HIS215 3.5 31.9 1.0 HE1 B:PHE248 3.7 32.7 1.0 HG21 B:VAL219 3.8 34.6 1.0 O B:HOH521 4.1 39.7 1.0 C3A B:HEM401 4.2 27.4 1.0 C2A B:HEM401 4.2 29.7 1.0 C2B B:HEM401 4.3 35.5 1.0 C3B B:HEM401 4.3 34.0 1.0 C3C B:HEM401 4.3 22.6 1.0 C2C B:HEM401 4.3 23.9 1.0 C3D B:HEM401 4.3 27.1 1.0 C2D B:HEM401 4.3 28.7 1.0 CG B:HIS215 4.3 23.7 1.0 HHB B:HEM401 4.4 34.0 1.0 ND1 B:HIS215 4.4 26.9 1.0 HHA B:HEM401 4.4 34.5 1.0 HHC B:HEM401 4.4 26.4 1.0 HHD B:HEM401 4.4 29.9 1.0 HA3 B:GLY144 4.5 41.8 1.0 CE1 B:PHE248 4.5 27.2 1.0 HG11 B:VAL219 4.6 37.2 1.0 HE1 B:MET276 4.6 42.1 1.0 CG2 B:VAL219 4.8 28.9 1.0 HD1 B:PHE248 5.0 27.0 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