Iron in PDB 5ybr: Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha-V150L/A232S in Complex with Preaustinoid A3

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha-V150L/A232S in Complex with Preaustinoid A3, PDB code: 5ybr 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)	43.67 / 2.26
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	171.382, 171.382, 45.696, 90.00, 90.00, 120.00
R / Rfree (%)	21.2 / 25.9

The binding sites of Iron atom in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha-V150L/A232S in Complex with Preaustinoid A3 (pdb code 5ybr). 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 A3, PDB code: 5ybr:
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 A3


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 A3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:31.6 occ:1.00 O1 A:AKG302 2.1 42.5 1.0 NE2 A:HIS214 2.1 29.1 1.0 OD1 A:ASP132 2.1 35.3 1.0 NE2 A:HIS130 2.2 32.3 1.0 O5 A:AKG302 2.2 32.8 1.0 O A:HOH408 2.3 33.2 1.0 C1 A:AKG302 2.8 43.2 1.0 C2 A:AKG302 2.8 33.2 1.0 CE1 A:HIS214 2.9 30.1 1.0 CG A:ASP132 3.0 35.7 1.0 CE1 A:HIS130 3.1 31.3 1.0 OD2 A:ASP132 3.2 35.3 1.0 CD2 A:HIS130 3.2 31.8 1.0 CD2 A:HIS214 3.2 28.7 1.0 ND1 A:HIS214 4.1 26.4 1.0 O2 A:AKG302 4.1 41.9 1.0 C20 A:8T9303 4.1 54.1 1.0 C17 A:8T9303 4.1 56.0 1.0 ND1 A:HIS130 4.2 28.6 1.0 CG A:HIS214 4.2 28.9 1.0 CG A:HIS130 4.3 28.5 1.0 C3 A:AKG302 4.3 31.9 1.0 CB A:ASP132 4.4 32.2 1.0 C22 A:8T9303 4.5 49.8 1.0 CA A:ASP132 4.8 28.7 1.0 C4 A:AKG302 4.9 29.5 1.0 OE1 A:GLN127 4.9 37.1 1.0 CE A:MET208 4.9 31.5 1.0 N A:ASP132 5.0 29.0 1.0

Iron binding site 2 out of 2 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha-V150L/A232S in Complex with Preaustinoid A3


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 A3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:45.9 occ:1.00 O2 B:AKG302 2.0 53.1 1.0 NE2 B:HIS214 2.1 45.0 1.0 O B:HOH404 2.3 49.2 1.0 NE2 B:HIS130 2.3 50.6 1.0 OD1 B:ASP132 2.4 46.2 1.0 O5 B:AKG302 2.5 56.9 1.0 C1 B:AKG302 2.8 54.7 1.0 CE1 B:HIS130 2.9 51.4 1.0 CD2 B:HIS214 3.0 48.5 1.0 C2 B:AKG302 3.0 55.8 1.0 CE1 B:HIS214 3.1 47.7 1.0 CD2 B:HIS130 3.4 48.6 1.0 CG B:ASP132 3.5 44.9 1.0 OD2 B:ASP132 4.0 47.4 1.0 O1 B:AKG302 4.0 53.8 1.0 C17 B:8T9303 4.1 61.9 1.0 ND1 B:HIS130 4.1 51.6 1.0 CG B:HIS214 4.1 49.4 1.0 C20 B:8T9303 4.1 60.7 1.0 ND1 B:HIS214 4.2 46.4 1.0 C22 B:8T9303 4.4 56.0 1.0 CG B:HIS130 4.4 50.5 1.0 C3 B:AKG302 4.4 59.1 1.0 CB B:ASP132 4.7 43.2 1.0 OE1 B:GLN127 4.8 48.4 1.0 CA B:ASP132 4.8 42.4 1.0 CE B:MET208 4.9 51.3 1.0 C24 B:8T9303 5.0 52.3 1.0 N B:ASP132 5.0 43.2 1.0 C4 B:AKG302 5.0 57.9 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