Iron in PDB 5ybs: Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha-V150L/A232S in Complex with Berkeleyone A

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha-V150L/A232S in Complex with Berkeleyone A, PDB code: 5ybs 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)	49.49 / 2.30
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	171.452, 171.452, 45.794, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 26.9

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


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 Berkeleyone A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:32.2 occ:1.00 O2 A:AKG302 2.0 32.5 1.0 NE2 A:HIS214 2.1 30.1 1.0 NE2 A:HIS130 2.2 32.0 1.0 OD1 A:ASP132 2.2 36.2 1.0 O5 A:AKG302 2.3 35.8 1.0 O A:HOH407 2.4 37.8 1.0 C1 A:AKG302 2.7 38.5 1.0 C2 A:AKG302 2.8 37.5 1.0 CE1 A:HIS214 2.9 31.8 1.0 CE1 A:HIS130 3.0 31.7 1.0 CG A:ASP132 3.1 34.9 1.0 CD2 A:HIS214 3.2 31.3 1.0 CD2 A:HIS130 3.2 30.1 1.0 OD2 A:ASP132 3.3 29.7 1.0 O1 A:AKG302 4.0 38.0 1.0 ND1 A:HIS214 4.0 28.2 1.0 ND1 A:HIS130 4.2 30.0 1.0 CG A:HIS214 4.2 30.4 1.0 C3 A:AKG302 4.3 34.3 1.0 CG A:HIS130 4.3 29.7 1.0 CB A:ASP132 4.5 34.1 1.0 OE1 A:GLN127 4.8 34.0 1.0 CA A:ASP132 4.8 29.9 1.0 C4 A:AKG302 4.8 34.3 1.0 N A:ASP132 5.0 28.6 1.0 CE A:MET208 5.0 29.2 1.0

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


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 Berkeleyone A within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:48.0 occ:1.00 O5 B:AKG302 2.1 55.1 1.0 O B:HOH410 2.2 51.6 1.0 NE2 B:HIS214 2.2 47.3 1.0 NE2 B:HIS130 2.3 48.2 1.0 OD1 B:ASP132 2.5 50.3 1.0 O1 B:AKG302 2.6 56.6 1.0 C2 B:AKG302 2.9 57.6 1.0 CE1 B:HIS130 3.1 52.4 1.0 C1 B:AKG302 3.1 55.8 1.0 CD2 B:HIS214 3.2 48.5 1.0 CE1 B:HIS214 3.2 50.5 1.0 CD2 B:HIS130 3.3 47.8 1.0 CG B:ASP132 3.4 49.5 1.0 OD2 B:ASP132 3.7 48.7 1.0 C3 B:AKG302 4.2 62.0 1.0 ND1 B:HIS130 4.2 51.9 1.0 C24 B:8TC303 4.3 59.5 1.0 ND1 B:HIS214 4.3 51.4 1.0 CG B:HIS214 4.4 53.6 1.0 O2 B:AKG302 4.4 56.8 1.0 CG B:HIS130 4.4 49.0 1.0 CB B:ASP132 4.7 48.0 1.0 C02 B:8TC303 4.7 56.2 1.0 C4 B:AKG302 4.8 60.6 1.0 CA B:ASP132 4.9 44.0 1.0 C15 B:8TC303 4.9 52.4 1.0 NE2 B:GLN127 4.9 58.1 1.0 OE1 B:GLN127 5.0 56.4 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