Magnesium in PDB 6yrd: Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State

The structure of Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State, PDB code: 6yrd 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 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.3, 120, 198.45, 90, 90, 90
R / Rfree (%)	16.7 / 19.9

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

Magnesium binding site 1 out of 2 in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl 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 Ferryl State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:24.9 occ:1.00 OD2 A:ASP191 2.0 27.3 1.0 O A:HOH573 2.1 26.4 1.0 O A:HOH501 2.1 27.6 1.0 O A:HOH524 2.2 24.0 1.0 CG A:ASP191 3.1 29.5 1.0 CB A:ASP191 3.7 24.7 1.0 OE1 A:GLU254 3.8 30.1 1.0 OD1 A:ASP189 4.0 26.1 1.0 O A:HOH640 4.1 32.4 1.0 OD1 A:ASP191 4.1 30.4 1.0 O A:HOH651 4.1 36.9 1.0 NH1 C:ARG127 4.3 36.2 1.0 O A:HOH559 4.3 36.5 1.0 N A:ASP191 4.5 22.8 1.0 CA A:ASP191 4.7 23.6 1.0 CG A:ASP189 5.0 26.9 1.0

Magnesium binding site 2 out of 2 in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:39.3 occ:1.00 O C:HOH512 2.1 34.6 1.0 O C:HOH634 2.1 46.8 1.0 O C:HOH630 2.1 37.6 1.0 OD2 C:ASP29 4.1 37.5 1.0 O C:VAL130 4.3 27.2 1.0 O C:HOH608 4.3 51.2 1.0 O A:HOH520 4.5 47.2 1.0 OG1 C:THR131 4.5 28.5 1.0 N C:GLY128 4.6 40.3 1.0 CA C:GLY128 4.7 37.9 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