Magnesium in PDB 7zmj: Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State

The structure of Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State, PDB code: 7zmj 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)	35.27 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.6, 121.3, 197.6, 90, 90, 90
R / Rfree (%)	20.2 / 23

The structure of Sfx Structure of Dye-Type Peroxidase Dtpb R243A 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 R243A Variant in the Ferric State (pdb code 7zmj). 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 R243A Variant in the Ferric State, PDB code: 7zmj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Sfx Structure of Dye-Type Peroxidase Dtpb R243A 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 R243A Variant in the Ferric State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:21.6 occ:1.00 O A:HOH565 2.0 21.1 1.0 OD2 A:ASP191 2.0 27.1 1.0 O A:HOH557 2.2 19.8 1.0 O A:HOH526 2.2 17.9 1.0 O A:HOH502 2.2 20.5 1.0 CG A:ASP191 3.1 22.8 1.0 OE1 A:GLU254 3.7 25.8 1.0 CB A:ASP191 3.8 21.0 1.0 NH1 C:ARG127 3.9 36.4 1.0 O A:HOH645 4.0 26.6 1.0 OD1 A:ASP189 4.1 18.3 1.0 O A:HOH652 4.1 25.7 1.0 OD1 A:ASP191 4.1 21.4 1.0 O A:HOH641 4.2 30.1 1.0 N A:ASP191 4.6 18.4 1.0 CA A:ASP191 4.8 19.0 1.0 CD A:GLU254 5.0 38.2 1.0

Magnesium binding site 2 out of 2 in the Sfx Structure of Dye-Type Peroxidase Dtpb R243A 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 R243A Variant in the Ferric State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:43.3 occ:1.00 O C:HOH644 2.1 32.1 1.0 O C:HOH641 2.2 49.1 1.0 O C:HOH524 2.3 27.2 1.0 O C:HOH642 2.4 40.0 1.0 O C:HOH610 3.9 49.9 1.0 O A:HOH622 4.1 34.0 1.0 OD2 C:ASP29 4.2 25.8 1.0 O C:VAL130 4.4 22.8 1.0 O C:HOH645 4.5 53.7 1.0 CA C:GLY128 4.6 34.4 1.0 N C:GLY128 4.7 29.6 1.0 OG1 C:THR131 4.7 25.1 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