Iron in PDB 7o9j: Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen

The structure of Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen, PDB code: 7o9j was solved by A.Rai, R.Fedorov, D.J.Manstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.25 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	141.03, 141.03, 95.56, 90, 90, 90
R / Rfree (%)	14.6 / 16.5

The structure of Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Iron atom in the Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen (pdb code 7o9j). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen, PDB code: 7o9j:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:21.4 occ:1.00 FE A:HEM401 0.0 21.4 1.0 ND A:HEM401 1.9 19.5 1.0 NA A:HEM401 2.0 20.8 1.0 NB A:HEM401 2.1 22.5 1.0 NC A:HEM401 2.1 20.1 1.0 NE2 A:HIS222 2.2 21.1 1.0 O2 A:OXY405 2.5 35.3 1.0 C1D A:HEM401 2.9 21.8 1.0 C4D A:HEM401 2.9 21.4 1.0 C1A A:HEM401 3.0 23.6 1.0 C4B A:HEM401 3.0 20.6 1.0 C4A A:HEM401 3.1 22.9 1.0 C1B A:HEM401 3.1 22.4 1.0 C4C A:HEM401 3.1 22.2 1.0 C1C A:HEM401 3.1 20.6 1.0 CD2 A:HIS222 3.1 21.5 1.0 CE1 A:HIS222 3.2 23.9 1.0 CHA A:HEM401 3.4 23.1 1.0 CHD A:HEM401 3.4 21.6 1.0 CHB A:HEM401 3.5 24.3 1.0 CHC A:HEM401 3.5 19.9 1.0 NH1 A:ARG239 4.1 21.6 1.0 C3D A:HEM401 4.2 21.4 1.0 C2D A:HEM401 4.2 21.5 1.0 C2A A:HEM401 4.2 22.1 1.0 C3A A:HEM401 4.2 22.4 1.0 ND1 A:HIS222 4.3 22.4 1.0 CG A:HIS222 4.3 21.4 1.0 C2B A:HEM401 4.3 22.5 1.0 C3C A:HEM401 4.3 22.0 1.0 C2C A:HEM401 4.3 21.2 1.0 C3B A:HEM401 4.3 20.4 1.0 O1 A:OXY405 4.7 31.1 1.0 CD A:ARG239 4.7 21.7 1.0 OD1 A:ASP149 4.7 41.9 1.0 CE1 A:PHE255 4.8 21.2 1.0 CZ A:ARG239 4.9 22.5 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:21.0 occ:1.00 FE B:HEM402 0.0 21.0 1.0 ND B:HEM402 1.9 19.3 1.0 NA B:HEM402 2.0 20.6 1.0 NC B:HEM402 2.1 19.3 1.0 NB B:HEM402 2.1 22.3 1.0 NE2 B:HIS222 2.2 21.7 1.0 O1 B:OXY405 2.5 34.1 1.0 C1D B:HEM402 2.9 20.0 1.0 C4D B:HEM402 3.0 21.5 1.0 C1A B:HEM402 3.0 20.7 1.0 C4C B:HEM402 3.0 21.7 1.0 C4B B:HEM402 3.0 21.5 1.0 C4A B:HEM402 3.1 21.7 1.0 C1B B:HEM402 3.1 22.9 1.0 C1C B:HEM402 3.1 20.0 1.0 CD2 B:HIS222 3.1 22.5 1.0 CE1 B:HIS222 3.2 24.6 1.0 CHD B:HEM402 3.4 22.2 1.0 CHA B:HEM402 3.4 23.3 1.0 CHC B:HEM402 3.5 21.9 1.0 CHB B:HEM402 3.5 24.5 1.0 NH1 B:ARG239 4.1 24.1 1.0 C2D B:HEM402 4.2 23.0 1.0 C3D B:HEM402 4.2 21.5 1.0 C2A B:HEM402 4.2 21.0 1.0 C3C B:HEM402 4.2 20.0 1.0 C3A B:HEM402 4.3 21.7 1.0 C2C B:HEM402 4.3 20.7 1.0 CG B:HIS222 4.3 21.8 1.0 ND1 B:HIS222 4.3 23.8 1.0 C2B B:HEM402 4.3 22.5 1.0 C3B B:HEM402 4.3 20.1 1.0 O2 B:OXY405 4.5 34.4 1.0 CD B:ARG239 4.7 21.0 1.0 CE1 B:PHE255 4.8 19.6 1.0 CZ B:ARG239 4.8 23.0 1.0 OD1 B:ASP149 4.9 43.7 1.0

A.Rai, J.P.Klare, P.Y.A.Reinke, F.Englmaier, J.Fohrer, R.Fedorov, M.H.Taft, I.Chizhov, U.Curth, O.Plettenburg, D.J.Manstein. Structural and Biochemical Characterization of A Dye-Decolorizing Peroxidase From Dictyostelium Discoideum . Int J Mol Sci V. 22 2021.
ISSN: ESSN 1422-0067
PubMed: 34200865
DOI: 10.3390/IJMS22126265