Magnesium 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:

Iron

(Fe)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of A Dye-Decolorizing Peroxidase D143A Variant From Klebsiella Pneumoniae (Kpdyp), PDB code: 6fl2:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg402 b:21.8 occ:1.00 O A:HOH506 1.9 33.2 1.0 O A:HOH518 2.0 25.1 1.0 O A:HOH553 2.0 20.9 1.0 O A:HOH751 2.0 32.6 1.0 O A:HOH784 2.2 36.4 1.0 OD2 A:ASP220 2.2 19.9 1.0 CG A:ASP220 3.3 17.7 1.0 HZ1 A:LYS222 3.5 38.6 1.0 OD1 A:ASP220 3.6 18.8 1.0 O A:HOH522 3.8 25.4 1.0 O1D A:HEM401 4.0 13.2 1.0 O2D A:HEM401 4.0 13.4 1.0 O A:HOH802 4.1 42.9 1.0 NZ A:LYS222 4.2 32.2 1.0 OE1 A:GLU146 4.3 28.5 1.0 OE1 A:GLU204 4.3 23.7 1.0 CGD A:HEM401 4.4 11.9 1.0 HZ2 A:LYS222 4.4 38.6 1.0 HZ3 A:LYS222 4.4 38.6 1.0 HG3 A:GLU146 4.4 24.9 1.0 O A:HOH592 4.5 26.0 1.0 HZ1 A:LYS229 4.5 24.2 0.6 CB A:ASP220 4.6 14.5 1.0 HB2 A:ASP220 4.6 17.4 1.0 OE2 A:GLU204 4.6 17.5 1.0 O A:HOH823 4.6 43.9 1.0 HZ2 A:LYS229 4.7 24.2 0.6 O A:HOH803 4.8 45.4 1.0 CD A:GLU146 4.8 26.3 1.0 CD A:GLU204 4.8 17.7 1.0 O A:HOH503 4.9 40.8 1.0 HB3 A:ASP220 4.9 17.4 1.0 NZ A:LYS229 5.0 20.1 0.6

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg404 b:20.6 occ:1.00 O B:HOH852 1.8 30.1 1.0 O B:HOH505 2.0 32.7 1.0 O B:HOH592 2.0 18.4 1.0 O B:HOH517 2.1 21.9 1.0 O B:HOH741 2.1 27.7 1.0 OD2 B:ASP220 2.2 18.4 1.0 CG B:ASP220 3.2 15.9 1.0 HZ2 B:LYS222 3.5 38.9 1.0 OD1 B:ASP220 3.5 16.5 1.0 O B:HOH547 3.9 27.3 1.0 O B:HOH782 4.0 38.3 1.0 O2D B:HEM401 4.0 12.9 1.0 O1D B:HEM401 4.0 12.7 1.0 NZ B:LYS222 4.2 32.4 1.0 OE1 B:GLU204 4.2 24.2 1.0 HZ3 B:LYS222 4.3 38.9 1.0 HG3 B:GLU146 4.4 21.2 1.0 CGD B:HEM401 4.4 12.0 1.0 HZ2 B:LYS229 4.4 30.9 1.0 HZ1 B:LYS222 4.5 38.9 1.0 CB B:ASP220 4.5 13.8 1.0 HB2 B:ASP220 4.6 16.5 1.0 OE2 B:GLU204 4.6 21.3 1.0 OE1 B:GLU146 4.8 28.5 1.0 O B:HOH506 4.8 32.2 1.0 HZ1 B:LYS229 4.9 30.9 1.0 CD B:GLU204 4.9 20.5 1.0 O B:HOH504 4.9 42.8 1.0 HB3 B:ASP220 4.9 16.5 1.0 HZ3 B:LYS229 5.0 30.9 1.0 NZ B:LYS229 5.0 25.8 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