Iron in PDB 5ybt: Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha- V150L/A232S/M241V in Complex with Berkeleyone A

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha- V150L/A232S/M241V in Complex with Berkeleyone A, PDB code: 5ybt 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)	49.53 / 2.35
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	171.569, 171.569, 45.605, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 26.4

The binding sites of Iron atom in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha- V150L/A232S/M241V in Complex with Berkeleyone A (pdb code 5ybt). 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/M241V in Complex with Berkeleyone A, PDB code: 5ybt:
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/M241V 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/M241V in Complex with Berkeleyone A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:38.2 occ:1.00 O2 A:AKG302 2.0 39.9 1.0 NE2 A:HIS214 2.1 33.8 1.0 O A:HOH401 2.1 35.7 1.0 OD1 A:ASP132 2.1 36.9 1.0 NE2 A:HIS130 2.1 37.3 1.0 O5 A:AKG302 2.2 39.1 1.0 C1 A:AKG302 2.7 37.5 1.0 C2 A:AKG302 2.8 37.4 1.0 CG A:ASP132 3.0 36.2 1.0 CE1 A:HIS214 3.0 34.8 1.0 CD2 A:HIS214 3.0 33.4 1.0 CE1 A:HIS130 3.1 34.3 1.0 OD2 A:ASP132 3.1 34.4 1.0 CD2 A:HIS130 3.2 36.2 1.0 O1 A:AKG302 3.9 37.8 1.0 C24 A:8TC303 4.0 44.3 1.0 ND1 A:HIS214 4.1 32.0 1.0 CG A:HIS214 4.1 32.4 1.0 ND1 A:HIS130 4.2 36.4 1.0 CG A:HIS130 4.3 35.7 1.0 C3 A:AKG302 4.3 37.7 1.0 CB A:ASP132 4.4 34.8 1.0 OE1 A:GLN127 4.7 40.5 1.0 CA A:ASP132 4.8 30.8 1.0 C02 A:8TC303 4.8 36.9 1.0 C4 A:AKG302 4.8 38.2 1.0 N A:ASP132 4.9 31.9 1.0

Iron binding site 2 out of 2 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha- V150L/A232S/M241V 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/M241V in Complex with Berkeleyone A within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:45.4 occ:1.00 O B:HOH409 2.1 47.6 1.0 NE2 B:HIS214 2.1 48.7 1.0 O1 B:AKG302 2.2 51.8 1.0 NE2 B:HIS130 2.2 48.8 1.0 OD1 B:ASP132 2.2 48.0 1.0 O5 B:AKG302 2.2 49.9 1.0 C1 B:AKG302 2.9 51.2 1.0 C2 B:AKG302 2.9 52.9 1.0 CE1 B:HIS130 2.9 50.1 1.0 CG B:ASP132 3.0 47.6 1.0 CD2 B:HIS214 3.1 50.1 1.0 CE1 B:HIS214 3.1 51.8 1.0 OD2 B:ASP132 3.1 47.6 1.0 CD2 B:HIS130 3.4 47.8 1.0 C24 B:8TC303 4.1 50.4 1.0 O2 B:AKG302 4.1 49.9 1.0 ND1 B:HIS130 4.1 51.1 1.0 ND1 B:HIS214 4.2 49.9 1.0 CG B:HIS214 4.2 50.9 1.0 C3 B:AKG302 4.3 54.5 1.0 CG B:HIS130 4.4 47.6 1.0 CB B:ASP132 4.4 43.2 1.0 C02 B:8TC303 4.7 46.5 1.0 OE1 B:GLN127 4.7 48.4 1.0 C15 B:8TC303 4.8 45.8 1.0 CA B:ASP132 4.8 43.9 1.0 C4 B:AKG302 4.8 55.6 1.0 CE B:MET208 4.9 53.8 1.0 NE2 B:GLN127 4.9 50.8 1.0 ND2 B:ASN152 5.0 50.7 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