Iron in PDB 7d8m: Crystal Structure of Dyp

The structure of Crystal Structure of Dyp, PDB code: 7d8m was solved by C.He, R.Jia, T.Wang, L.Q.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.40 / 2.00
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	118.959, 118.959, 65.347, 90, 90, 120
R / Rfree (%)	16.9 / 20.9

The binding sites of Iron atom in the Crystal Structure of Dyp (pdb code 7d8m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total only one binding site of Iron was determined in the Crystal Structure of Dyp, PDB code: 7d8m:

Iron binding site 1 out of 1 in the Crystal Structure of Dyp


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:24.0 occ:1.00 FE A:HEM601 0.0 24.0 1.0 NB A:HEM601 2.0 20.7 1.0 ND A:HEM601 2.0 22.8 1.0 NC A:HEM601 2.0 22.5 1.0 NA A:HEM601 2.1 22.9 1.0 NE2 A:HIS364 2.3 24.3 1.0 C4B A:HEM601 3.0 22.3 1.0 C1B A:HEM601 3.0 24.6 1.0 C1C A:HEM601 3.1 23.1 1.0 C4C A:HEM601 3.1 24.0 1.0 C1D A:HEM601 3.1 23.5 1.0 C4D A:HEM601 3.1 27.1 1.0 C4A A:HEM601 3.1 25.1 1.0 C1A A:HEM601 3.1 23.5 1.0 CD2 A:HIS364 3.2 23.5 1.0 CE1 A:HIS364 3.3 25.7 1.0 CHC A:HEM601 3.4 23.3 1.0 CHD A:HEM601 3.4 22.9 1.0 CHB A:HEM601 3.4 24.8 1.0 CHA A:HEM601 3.5 25.5 1.0 O2 A:OXY602 4.0 37.0 1.0 C3B A:HEM601 4.2 21.9 1.0 NH1 A:ARG387 4.3 27.8 1.0 C2B A:HEM601 4.3 25.2 1.0 C2C A:HEM601 4.3 24.0 1.0 C3C A:HEM601 4.3 24.3 1.0 C2D A:HEM601 4.3 23.6 1.0 C3D A:HEM601 4.3 24.9 1.0 C3A A:HEM601 4.3 25.4 1.0 C2A A:HEM601 4.3 27.0 1.0 CG A:HIS364 4.4 21.3 1.0 ND1 A:HIS364 4.4 21.6 1.0 CD A:ARG387 4.6 23.0 1.0 O1 A:OXY602 4.9 34.5 1.0 CZ A:ARG387 4.9 25.4 1.0

L.Li, T.Wang, T.Chen, W.Huang, Y.Zhang, R.Jia, C.He. Revealing Two Important Tryptophan Residues with Completely Different Roles in A Dye-Decolorizing Peroxidase From Irpex Lacteus F17. Biotechnol Biofuels V. 14 128 2021.
ISSN: ESSN 1754-6834
PubMed: 34059116
DOI: 10.1186/S13068-021-01978-Y