Iron in PDB 9j0j: The Crystal Structure of Fe/2OG-Dependent Oxygenase Dfmd

The structure of The Crystal Structure of Fe/2OG-Dependent Oxygenase Dfmd, PDB code: 9j0j was solved by L.Wang, J.Chen, J.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.53 / 2.85
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	110.316, 110.316, 88.835, 90, 90, 120
R / Rfree (%)	18.8 / 22.5

The structure of The Crystal Structure of Fe/2OG-Dependent Oxygenase Dfmd also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Iron atom in the The Crystal Structure of Fe/2OG-Dependent Oxygenase Dfmd (pdb code 9j0j). 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 The Crystal Structure of Fe/2OG-Dependent Oxygenase Dfmd, PDB code: 9j0j:

Iron binding site 1 out of 1 in the The Crystal Structure of Fe/2OG-Dependent Oxygenase Dfmd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of Fe/2OG-Dependent Oxygenase Dfmd within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:62.0 occ:1.00 NE2 A:HIS358 2.2 46.9 1.0 NE2 A:HIS210 2.3 48.3 1.0 OD2 A:ASP212 2.6 53.7 1.0 O A:HOH537 2.8 40.5 1.0 CE1 A:HIS358 2.8 44.5 1.0 O A:HOH546 3.0 36.1 1.0 O A:HOH543 3.1 41.0 1.0 OD1 A:ASP212 3.1 42.2 1.0 CE1 A:HIS210 3.2 45.4 1.0 CG A:ASP212 3.2 47.6 1.0 CD2 A:HIS210 3.3 45.6 1.0 CD2 A:HIS358 3.4 42.8 1.0 ND1 A:HIS358 4.0 44.3 1.0 NE2 A:GLN223 4.3 41.6 1.0 ND1 A:HIS210 4.3 41.9 1.0 CG A:HIS358 4.4 43.1 1.0 CG A:HIS210 4.4 39.4 1.0 OE1 A:GLN223 4.6 35.9 1.0 CB A:ASP212 4.6 38.2 1.0 CD A:GLN223 4.9 37.2 1.0 O A:HOH548 5.0 36.6 1.0

X.Zhang, L.Wang, J.Liu, T.Y.Chen, S.Yan, W.C.Chang, S.Shaik, J.Zhou, B.Wang. An Alternative Mechanism For C-C Desaturation Underscores A Dual-Controlled Mechanism For the Fate of Radical Intermediate in Iron(II)- and 2-(Oxo)Glutarate-Dependent Oxygenase Dfmd. J.Am.Chem.Soc. 2025.
ISSN: ESSN 1520-5126
PubMed: 40480968
DOI: 10.1021/JACS.5C02361