Magnesium in PDB 7qzg: Sfx Structure of Dye-Type Peroxidase Dtpb N245A Variant in the Ferric State

The structure of Sfx Structure of Dye-Type Peroxidase Dtpb N245A Variant in the Ferric State, PDB code: 7qzg 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)	32.10 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.95, 121.83, 199.5, 90, 90, 90
R / Rfree (%)	22.9 / 27.8

The structure of Sfx Structure of Dye-Type Peroxidase Dtpb N245A Variant 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 N245A Variant in the Ferric State (pdb code 7qzg). 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 N245A Variant in the Ferric State, PDB code: 7qzg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Sfx Structure of Dye-Type Peroxidase Dtpb N245A Variant 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 N245A Variant in the Ferric State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:25.6 occ:1.00 OD2 A:ASP191 1.9 26.4 1.0 O A:HOH543 2.0 26.9 1.0 O A:HOH502 2.2 20.2 1.0 O A:HOH517 2.3 15.3 1.0 CG A:ASP191 3.1 29.2 1.0 OE1 A:GLU254 3.8 40.6 1.0 NH1 C:ARG127 3.8 44.2 1.0 CB A:ASP191 3.9 27.2 1.0 O A:HOH604 3.9 27.3 1.0 OD1 A:ASP191 4.0 21.8 1.0 OD1 A:ASP189 4.1 20.7 1.0 O A:HOH597 4.3 29.4 1.0 N A:ASP191 4.6 29.9 1.0 CA A:ASP191 4.8 27.6 1.0

Magnesium binding site 2 out of 2 in the Sfx Structure of Dye-Type Peroxidase Dtpb N245A Variant in the Ferric 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 N245A Variant in the Ferric State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:42.5 occ:1.00 O D:HOH526 2.4 24.4 1.0 O D:HOH591 2.9 33.8 1.0 O D:HOH628 4.3 32.0 1.0 OD2 D:ASP291 4.4 26.9 1.0 OD1 D:ASP291 4.5 20.6 1.0 CG D:ASP291 4.6 18.5 1.0 CE1 D:HIS286 4.7 30.1 1.0 NE2 D:HIS286 4.9 36.9 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