Magnesium in PDB 7qze: Sfx Structure of Dye-Type Peroxidase Dtpb D152A Variant in the Ferryl State

The structure of Sfx Structure of Dye-Type Peroxidase Dtpb D152A Variant in the Ferryl State, PDB code: 7qze was solved by M.Lucic, J.A.R.Worrall, M.A.Hough, A.Shilova, D.A.Axford, R.L.Owen, T.Tosha, H.Sugimoto, S.Owada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.52, 120.9, 197.41, 90, 90, 90
R / Rfree (%)	16.6 / 20.1

The structure of Sfx Structure of Dye-Type Peroxidase Dtpb D152A Variant 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 D152A Variant in the Ferryl State (pdb code 7qze). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Sfx Structure of Dye-Type Peroxidase Dtpb D152A Variant in the Ferryl State, PDB code: 7qze:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Sfx Structure of Dye-Type Peroxidase Dtpb D152A Variant 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 D152A Variant in the Ferryl State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:22.4 occ:1.00 OD2 A:ASP191 2.0 22.4 1.0 O A:HOH526 2.1 21.4 1.0 O A:HOH557 2.1 22.4 1.0 O A:HOH502 2.2 23.6 1.0 CG A:ASP191 3.1 23.5 1.0 CB A:ASP191 3.6 23.8 1.0 OE1 A:GLU254 3.8 28.6 1.0 O A:HOH639 4.0 28.1 1.0 OD1 A:ASP189 4.0 21.3 1.0 NH1 C:ARG127 4.0 36.2 1.0 O A:HOH648 4.1 31.6 1.0 OD1 A:ASP191 4.1 23.8 1.0 O A:HOH521 4.2 33.2 1.0 N A:ASP191 4.5 21.1 1.0 CA A:ASP191 4.7 23.0 1.0

Magnesium binding site 2 out of 3 in the Sfx Structure of Dye-Type Peroxidase Dtpb D152A Variant 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 D152A Variant in the Ferryl State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:38.6 occ:1.00 O D:HOH585 2.1 31.3 1.0 O D:HOH581 2.1 24.5 1.0 OD2 D:ASP291 4.2 26.7 1.0 OD1 D:ASP291 4.3 26.6 1.0 O D:HOH643 4.3 28.0 1.0 CG D:ASP291 4.5 22.8 1.0 CE1 D:HIS286 4.6 22.2 1.0 NE2 D:HIS286 4.8 23.3 1.0

Magnesium binding site 3 out of 3 in the Sfx Structure of Dye-Type Peroxidase Dtpb D152A Variant in the Ferryl State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Sfx Structure of Dye-Type Peroxidase Dtpb D152A Variant in the Ferryl State within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:53.1 occ:1.00 O F:HOH522 1.9 42.9 1.0 OE1 F:GLU155 2.2 32.4 1.0 O F:HOH642 2.3 46.1 1.0 O F:HOH621 2.4 48.7 1.0 O F:HOH548 2.5 38.9 1.0 CD F:GLU155 3.1 32.7 1.0 CG F:GLU155 3.4 30.1 1.0 O F:HOH535 3.5 38.2 1.0 O1D F:HEM401 3.7 27.1 1.0 CB F:GLU155 3.8 27.7 1.0 O2D F:HEM401 3.9 28.9 1.0 O F:HOH502 4.1 43.8 1.0 OE2 F:GLU155 4.2 37.3 1.0 CGD F:HEM401 4.2 29.0 1.0 NH2 E:ARG48 4.5 34.8 1.0 O F:HOH626 4.6 44.6 1.0 OE1 F:GLU214 4.7 48.7 1.0 CA F:GLU155 4.9 25.5 1.0

M.Lucic, M.T.Wilson, T.Tosha, H.Sugimoto, A.Shilova, D.Axford, R.L.Owen, M.A.Hough, J.A.R.Worrall. Serial Femtosecond Crystallography Reveals the Role of Water in the One- or Two-Electron Redox Chemistry of Compound I in the Catalytic Cycle of the B-Type Dye-Decolorizing Peroxidase Dtpb. Acs Catalysis V. 12 13349 2022.
ISSN: ESSN 2155-5435
PubMed: 36366763
DOI: 10.1021/ACSCATAL.2C03754