Iron in PDB 5ybo: Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha in Complex with Preaustinoid A1

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha in Complex with Preaustinoid A1, PDB code: 5ybo was solved by Y.Nakashima, M.Senda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.66 / 2.20
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	171.816, 171.816, 45.665, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 26.2

The binding sites of Iron atom in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha in Complex with Preaustinoid A1 (pdb code 5ybo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha in Complex with Preaustinoid A1, PDB code: 5ybo:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha in Complex with Preaustinoid A1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha in Complex with Preaustinoid A1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:35.0 occ:1.00 O2 A:AKG302 1.8 38.9 1.0 NE2 A:HIS214 2.1 31.9 1.0 OD1 A:ASP132 2.1 31.5 1.0 O5 A:AKG302 2.2 37.4 1.0 O A:HOH408 2.3 35.9 1.0 NE2 A:HIS130 2.4 32.7 1.0 C1 A:AKG302 2.5 43.1 1.0 C2 A:AKG302 2.7 35.2 1.0 CE1 A:HIS214 3.0 33.6 1.0 CD2 A:HIS214 3.1 35.4 1.0 CG A:ASP132 3.1 33.4 1.0 CE1 A:HIS130 3.2 33.9 1.0 OD2 A:ASP132 3.3 33.4 1.0 CD2 A:HIS130 3.3 31.8 1.0 O1 A:AKG302 3.8 44.1 1.0 ND1 A:HIS214 4.1 30.2 1.0 O A:HOH462 4.1 37.7 1.0 CG A:HIS214 4.2 31.3 1.0 C3 A:AKG302 4.2 33.9 1.0 ND1 A:HIS130 4.3 32.2 1.0 CG A:HIS130 4.4 34.7 1.0 CB A:ASP132 4.5 32.4 1.0 C4 A:AKG302 4.8 33.1 1.0 CA A:ASP132 4.8 26.1 1.0 CE A:MET208 4.8 30.4 1.0 OE1 A:GLN127 4.9 36.5 1.0 N A:ASP132 4.9 28.5 1.0

Iron binding site 2 out of 2 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha in Complex with Preaustinoid A1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha in Complex with Preaustinoid A1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:46.7 occ:1.00 O B:HOH421 1.9 47.2 1.0 NE2 B:HIS130 2.2 50.5 1.0 NE2 B:HIS214 2.2 44.8 1.0 O2 B:AKG302 2.3 55.2 1.0 O5 B:AKG302 2.4 55.9 1.0 OD1 B:ASP132 2.4 48.4 1.0 C2 B:AKG302 2.8 55.8 1.0 C1 B:AKG302 2.9 56.4 1.0 CD2 B:HIS214 3.1 49.6 1.0 CE1 B:HIS130 3.2 52.2 1.0 CD2 B:HIS130 3.2 48.2 1.0 CE1 B:HIS214 3.3 50.8 1.0 CG B:ASP132 3.5 49.3 1.0 OD2 B:ASP132 3.9 48.5 1.0 O1 B:AKG302 4.0 54.9 1.0 C3 B:AKG302 4.1 59.2 1.0 C18 B:8SX303 4.3 64.5 1.0 ND1 B:HIS130 4.3 50.4 1.0 CG B:HIS214 4.3 52.4 1.0 CG B:HIS130 4.3 47.7 1.0 C20 B:8SX303 4.3 56.3 1.0 ND1 B:HIS214 4.4 49.0 1.0 C24 B:8SX303 4.5 51.0 1.0 C4 B:AKG302 4.8 61.0 1.0 CB B:ASP132 4.8 45.1 1.0 OE1 B:GLN127 4.8 50.0 1.0 NE2 B:GLN127 4.9 58.4 1.0 CA B:ASP132 4.9 44.2 1.0

Y.Nakashima, T.Mori, H.Nakamura, T.Awakawa, S.Hoshino, M.Senda, T.Senda, I.Abe. Structure Function and Engineering of Multifunctional Non-Heme Iron Dependent Oxygenases in Fungal Meroterpenoid Biosynthesis. Nat Commun V. 9 104 2018.
ISSN: ESSN 2041-1723
PubMed: 29317628
DOI: 10.1038/S41467-017-02371-W