Magnesium in PDB 6yrj: Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferric State

The structure of Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferric State, PDB code: 6yrj was solved by M.Lucic, D.A.Axford, R.L.Owen, J.A.R.Worrall, M.A.Hough, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	13.00 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86, 120.4, 197.5, 90, 90, 90
R / Rfree (%)	15.9 / 19.2

The structure of Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferric State also contains other interesting chemical elements:

Iron

(Fe)

6 atoms

The binding sites of Magnesium atom in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferric State (pdb code 6yrj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferric State, PDB code: 6yrj:

Magnesium binding site 1 out of 1 in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferric State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferric State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:25.4 occ:1.00 OD2 A:ASP191 2.0 25.7 1.0 O A:HOH510 2.1 24.2 1.0 O A:HOH501 2.1 30.4 1.0 CG A:ASP191 3.1 29.5 1.0 CB A:ASP191 3.6 26.8 1.0 OE1 A:GLU254 3.9 33.7 1.0 OD1 A:ASP189 3.9 27.1 1.0 O A:HOH628 4.1 30.3 1.0 NH1 C:ARG127 4.1 37.9 1.0 OD1 A:ASP191 4.1 30.7 1.0 O A:HOH636 4.1 36.4 1.0 O A:HOH556 4.3 36.0 1.0 N A:ASP191 4.5 24.2 1.0 CA A:ASP191 4.7 27.2 1.0 CG A:ASP189 5.0 28.6 1.0

M.Lucic, D.A.Svistunenko, M.T.Wilson, A.K.Chaplin, B.Davy, A.Ebrahim, D.Axford, T.Tosha, H.Sugimoto, S.Owada, F.S.N.Dworkowski, I.Tews, R.L.Owen, M.A.Hough, J.A.R.Worrall. Serial Femtosecond Zero Dose Crystallography Captures A Water-Free Distal Heme Site in A Dye-Decolorising Peroxidase to Reveal A Catalytic Role For An Arginine in Fe IV =O Formation. Angew.Chem.Int.Ed.Engl. V. 59 21656 2020.
ISSN: ESSN 1521-3773
PubMed: 32780931
DOI: 10.1002/ANIE.202008622