Iron in PDB 5ybq: Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha-V150L/A232S in Complex with Preaustinoid A2

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha-V150L/A232S in Complex with Preaustinoid A2, PDB code: 5ybq 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)	43.55 / 2.25
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	171.361, 171.361, 45.559, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 25.5

The binding sites of Iron atom in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha-V150L/A232S in Complex with Preaustinoid A2 (pdb code 5ybq). 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-V150L/A232S in Complex with Preaustinoid A2, PDB code: 5ybq:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha-V150L/A232S in Complex with Preaustinoid A2


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-V150L/A232S in Complex with Preaustinoid A2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:29.9 occ:1.00 O1 A:AKG302 2.0 30.5 1.0 O A:HOH415 2.1 30.8 1.0 O5 A:AKG302 2.1 30.0 1.0 NE2 A:HIS214 2.1 25.7 1.0 NE2 A:HIS130 2.2 27.8 1.0 OD1 A:ASP132 2.2 31.8 1.0 C1 A:AKG302 2.6 32.7 1.0 C2 A:AKG302 2.6 27.6 1.0 CE1 A:HIS130 3.0 27.6 1.0 CE1 A:HIS214 3.0 29.1 1.0 CG A:ASP132 3.1 30.8 1.0 CD2 A:HIS214 3.2 28.4 1.0 CD2 A:HIS130 3.3 29.8 1.0 OD2 A:ASP132 3.3 28.9 1.0 O2 A:AKG302 3.9 34.3 1.0 C3 A:AKG302 4.1 31.4 1.0 ND1 A:HIS214 4.2 22.6 1.0 ND1 A:HIS130 4.2 27.2 1.0 CG A:HIS214 4.3 24.1 1.0 CG A:HIS130 4.3 27.0 1.0 CB A:ASP132 4.5 28.1 1.0 C4 A:AKG302 4.6 29.3 1.0 C18 A:8T0303 4.7 40.9 1.0 OE1 A:GLN127 4.7 27.5 1.0 C24 A:8T0303 4.7 33.6 1.0 C19 A:8T0303 4.7 35.5 1.0 C20 A:8T0303 4.8 37.1 1.0 CA A:ASP132 4.8 25.3 1.0 CE A:MET208 5.0 24.7 1.0

Iron binding site 2 out of 2 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha-V150L/A232S in Complex with Preaustinoid A2


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-V150L/A232S in Complex with Preaustinoid A2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:40.4 occ:1.00 O B:HOH401 1.9 42.2 1.0 O2 B:AKG302 1.9 42.2 1.0 O5 B:AKG302 2.1 47.0 1.0 NE2 B:HIS214 2.1 39.3 1.0 NE2 B:HIS130 2.2 40.5 1.0 OD1 B:ASP132 2.3 39.4 1.0 C1 B:AKG302 2.7 43.2 1.0 C2 B:AKG302 2.7 45.7 1.0 CE1 B:HIS130 3.0 44.4 1.0 CD2 B:HIS214 3.1 43.0 1.0 CE1 B:HIS214 3.1 40.8 1.0 CD2 B:HIS130 3.3 40.8 1.0 CG B:ASP132 3.3 38.4 1.0 OD2 B:ASP132 3.7 40.1 1.0 O1 B:AKG302 3.9 44.6 1.0 C18 B:8T0303 4.1 48.8 1.0 C3 B:AKG302 4.2 51.6 1.0 ND1 B:HIS130 4.2 43.7 1.0 ND1 B:HIS214 4.2 43.1 1.0 CG B:HIS214 4.2 47.3 1.0 CG B:HIS130 4.3 41.1 1.0 CB B:ASP132 4.6 37.2 1.0 OE1 B:GLN127 4.7 42.9 1.0 C4 B:AKG302 4.7 53.9 1.0 CA B:ASP132 4.8 38.0 1.0 C24 B:8T0303 4.8 40.0 1.0 C20 B:8T0303 4.8 43.3 1.0 C19 B:8T0303 4.9 44.2 1.0 N B:ASP132 5.0 36.3 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