Magnesium 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:

Iron

(Fe)

2 atoms

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

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg404 b:20.9 occ:1.00 O A:HOH520 1.9 32.1 1.0 O A:HOH553 2.0 19.8 1.0 O A:HOH516 2.1 24.3 1.0 O A:HOH747 2.1 30.8 1.0 O A:HOH804 2.1 32.8 1.0 OD2 A:ASP220 2.2 19.1 1.0 CG A:ASP220 3.2 15.7 1.0 HZ1 A:LYS222 3.4 37.8 1.0 OD1 A:ASP220 3.6 17.9 1.0 O A:HOH508 3.6 45.2 1.0 O A:HOH533 3.8 26.2 1.0 O1D A:HEM401 3.9 13.9 1.0 O2D A:HEM401 3.9 13.4 1.0 O A:HOH838 4.3 39.8 1.0 NZ A:LYS222 4.3 31.5 1.0 CGD A:HEM401 4.3 12.8 1.0 OE1 A:GLU204 4.3 24.0 1.0 HZ2 A:LYS229 4.4 33.8 1.0 HG3 A:GLU146 4.4 22.0 1.0 HZ2 A:LYS222 4.4 37.8 1.0 CB A:ASP220 4.5 13.2 1.0 HB2 A:ASP220 4.5 15.8 1.0 O A:HOH661 4.5 25.2 1.0 OE1 A:GLU146 4.5 25.1 1.0 HZ3 A:LYS222 4.6 37.8 1.0 OE2 A:GLU204 4.6 16.8 1.0 HZ1 A:LYS229 4.8 33.8 1.0 CD A:GLU204 4.8 18.2 1.0 HB3 A:ASP220 4.9 15.8 1.0 CD A:GLU146 4.9 23.1 1.0 NZ A:LYS229 4.9 28.2 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg404 b:17.9 occ:1.00 O B:HOH830 2.0 24.6 1.0 O B:HOH514 2.0 28.5 1.0 O B:HOH742 2.0 25.3 1.0 O B:HOH576 2.0 16.6 1.0 O B:HOH520 2.1 17.8 1.0 OD2 B:ASP220 2.1 16.4 1.0 CG B:ASP220 3.2 13.6 1.0 HZ3 B:LYS222 3.4 39.0 1.0 OD1 B:ASP220 3.5 14.7 1.0 O B:HOH546 3.9 24.1 1.0 O2D B:HEM401 3.9 12.8 1.0 O1D B:HEM401 4.0 12.7 1.0 O B:HOH776 4.1 31.0 1.0 OE1 B:GLU204 4.2 23.4 1.0 NZ B:LYS222 4.3 32.5 1.0 CGD B:HEM401 4.3 11.0 1.0 HG3 B:GLU146 4.4 17.3 1.0 HZ1 B:LYS222 4.5 39.0 1.0 CB B:ASP220 4.5 11.9 1.0 HB2 B:ASP220 4.5 14.3 1.0 HZ2 B:LYS222 4.5 39.0 1.0 OE2 B:GLU204 4.5 19.5 1.0 OE1 B:GLU146 4.5 23.1 1.0 HZ1 B:LYS229 4.5 25.8 1.0 O B:HOH510 4.7 31.4 1.0 CD B:GLU204 4.8 19.4 1.0 HB3 B:ASP220 4.8 14.3 1.0 CD B:GLU146 4.9 19.8 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