Magnesium in PDB 6yr4: Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure

The structure of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure, PDB code: 6yr4 was solved by M.Lucic, F.S.N.Dworkowski, 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)	47.61 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.35, 119.91, 194.15, 90, 90, 90
R / Rfree (%)	18.8 / 23.2

The structure of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure also contains other interesting chemical elements:

Iron

(Fe)

6 atoms

The binding sites of Magnesium atom in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure (pdb code 6yr4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure, PDB code: 6yr4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:21.8 occ:1.00 O A:HOH585 2.0 18.1 1.0 OD2 A:ASP191 2.0 21.1 1.0 O A:HOH589 2.1 17.5 1.0 O A:HOH502 2.2 22.6 1.0 CG A:ASP191 3.1 21.8 1.0 CB A:ASP191 3.6 20.3 1.0 NH1 C:ARG127 3.8 25.0 0.5 OD1 A:ASP189 3.9 20.8 1.0 OE1 A:GLU254 4.0 29.3 1.0 O A:HOH679 4.0 20.9 1.0 O A:HOH701 4.1 33.1 1.0 OD1 A:ASP191 4.2 22.2 1.0 O A:HOH628 4.2 26.3 1.0 N A:ASP191 4.4 19.9 1.0 NH1 C:ARG127 4.7 27.4 0.5 CA A:ASP191 4.7 19.6 1.0 CG A:ASP189 5.0 20.4 1.0

Magnesium binding site 2 out of 2 in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:24.7 occ:1.00 O C:HOH587 2.1 34.9 1.0 O C:HOH685 2.1 28.9 1.0 O C:HOH504 2.1 18.7 1.0 O C:HOH547 2.2 27.6 1.0 OD2 C:ASP29 4.1 26.4 1.0 O C:VAL130 4.1 18.4 1.0 O C:ARG127 4.1 30.3 0.5 O C:ARG127 4.2 30.6 0.5 O C:HOH565 4.2 30.9 1.0 O C:HOH707 4.3 30.2 1.0 OG1 C:THR131 4.3 23.7 1.0 O A:HOH546 4.3 25.8 1.0 O C:HOH663 4.3 28.0 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