Magnesium 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:

Iron

(Fe)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of A Dye-Decolorizing Peroxidase From Klebsiella Pneumoniae (Kpdyp), PDB code: 6fks:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg405 b:23.7 occ:1.00 O A:HOH751 2.0 31.1 1.0 O A:HOH662 2.0 29.9 1.0 O A:HOH546 2.0 20.4 1.0 O A:HOH529 2.0 22.1 1.0 O A:HOH649 2.1 32.8 1.0 OD2 A:ASP220 2.2 22.1 1.0 CG A:ASP220 3.2 20.5 1.0 OD1 A:ASP220 3.6 20.8 1.0 O A:HOH506 3.7 35.2 1.0 O2D A:HEM401 4.0 17.6 1.0 O1D A:HEM401 4.0 17.4 1.0 OE1 A:GLU204 4.2 30.6 1.0 O A:HOH711 4.2 44.1 1.0 OE2 A:GLU204 4.3 29.1 1.0 CGD A:HEM401 4.4 16.2 1.0 HG3 A:GLU146 4.4 28.4 1.0 HZ3 A:LYS229 4.5 36.5 1.0 CB A:ASP220 4.5 18.4 1.0 HB2 A:ASP220 4.5 22.1 1.0 CD A:GLU204 4.7 28.0 1.0 HE3 A:LYS222 4.7 48.0 1.0 OE1 A:GLU146 4.8 31.6 1.0 HB3 A:ASP220 4.9 22.1 1.0 HZ1 A:LYS229 4.9 36.5 1.0 HZ2 A:LYS229 5.0 36.5 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg403 b:24.5 occ:1.00 O B:HOH562 1.9 21.6 1.0 O B:HOH510 2.0 34.8 1.0 O B:HOH709 2.1 31.6 1.0 O B:HOH631 2.1 30.4 1.0 OD2 B:ASP220 2.1 23.3 1.0 O B:HOH523 2.1 24.5 1.0 CG B:ASP220 3.2 21.9 1.0 OD1 B:ASP220 3.6 21.4 1.0 HZ1 B:LYS222 3.6 46.4 1.0 O B:HOH530 3.8 33.3 1.0 O2D B:HEM401 3.9 18.6 1.0 O1D B:HEM401 3.9 18.2 1.0 O B:HOH724 4.1 47.7 1.0 OE1 B:GLU204 4.3 30.2 1.0 HG3 B:GLU146 4.3 30.7 1.0 CGD B:HEM401 4.3 18.0 1.0 NZ B:LYS222 4.4 38.7 1.0 OE2 B:GLU204 4.4 24.7 1.0 HZ3 B:LYS222 4.4 46.4 1.0 OE1 B:GLU146 4.4 33.6 1.0 CB B:ASP220 4.4 20.1 1.0 HB2 B:ASP220 4.5 24.2 1.0 HZ2 B:LYS222 4.5 46.4 1.0 O B:HOH580 4.7 33.8 1.0 CD B:GLU204 4.7 25.4 1.0 O B:HOH725 4.8 53.9 1.0 HB3 B:ASP220 4.8 24.2 1.0 CD B:GLU146 4.8 30.8 1.0 CG B:GLU146 5.0 25.6 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