Iron in PDB 5ybp: Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha-V150L/A232S in Complex with Preaustinoid A1

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha-V150L/A232S in Complex with Preaustinoid A1, PDB code: 5ybp 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)	49.60 / 2.31
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	171.803, 171.803, 45.913, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 26.4

The binding sites of Iron atom in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha-V150L/A232S in Complex with Preaustinoid A1 (pdb code 5ybp). 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 A1, PDB code: 5ybp:
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 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-V150L/A232S in Complex with Preaustinoid A1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:30.1 occ:1.00 O1 A:AKG302 2.0 32.3 1.0 NE2 A:HIS214 2.0 25.2 1.0 O5 A:AKG302 2.1 33.5 1.0 OD1 A:ASP132 2.2 31.9 1.0 NE2 A:HIS130 2.3 28.6 1.0 O A:HOH403 2.3 30.6 1.0 C1 A:AKG302 2.7 34.9 1.0 C2 A:AKG302 2.8 32.9 1.0 CE1 A:HIS214 2.8 27.3 1.0 CG A:ASP132 3.0 29.1 1.0 CD2 A:HIS214 3.2 27.0 1.0 CE1 A:HIS130 3.2 28.7 1.0 CD2 A:HIS130 3.2 28.1 1.0 OD2 A:ASP132 3.2 27.4 1.0 O2 A:AKG302 4.0 29.5 1.0 ND1 A:HIS214 4.0 27.7 1.0 CG A:HIS214 4.2 28.2 1.0 C3 A:AKG302 4.2 27.1 1.0 ND1 A:HIS130 4.3 29.9 1.0 CG A:HIS130 4.3 26.8 1.0 CB A:ASP132 4.4 28.9 1.0 C4 A:AKG302 4.7 29.1 1.0 OE1 A:GLN127 4.8 30.2 1.0 CA A:ASP132 4.8 26.4 1.0 CE A:MET208 5.0 26.5 1.0

Iron binding site 2 out of 2 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha-V150L/A232S 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-V150L/A232S in Complex with Preaustinoid A1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:45.8 occ:1.00 O5 B:AKG302 2.2 55.5 1.0 NE2 B:HIS130 2.2 47.7 1.0 NE2 B:HIS214 2.2 46.9 1.0 O B:HOH412 2.2 47.7 1.0 O2 B:AKG302 2.4 50.6 1.0 OD1 B:ASP132 2.4 46.4 1.0 C2 B:AKG302 2.9 56.3 1.0 CE1 B:HIS130 3.0 50.6 1.0 C1 B:AKG302 3.0 51.7 1.0 CE1 B:HIS214 3.2 48.7 1.0 CD2 B:HIS214 3.2 46.4 1.0 CD2 B:HIS130 3.3 45.6 1.0 CG B:ASP132 3.4 47.0 1.0 OD2 B:ASP132 3.8 47.8 1.0 C18 B:8SX303 4.1 59.8 1.0 ND1 B:HIS130 4.1 49.6 1.0 C20 B:8SX303 4.2 54.8 1.0 C3 B:AKG302 4.2 58.2 1.0 O1 B:AKG302 4.2 51.8 1.0 ND1 B:HIS214 4.3 46.2 1.0 CG B:HIS130 4.3 47.6 1.0 CG B:HIS214 4.4 47.7 1.0 C24 B:8SX303 4.4 51.1 1.0 OE1 B:GLN127 4.7 48.5 1.0 CB B:ASP132 4.7 44.3 1.0 C4 B:AKG302 4.8 55.4 1.0 CA B:ASP132 4.9 43.4 1.0 C21 B:8SX303 4.9 58.3 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