Iron in PDB 5ybn: Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha in Complex with (Alpha)Ketoglutarate

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Prha in Complex with (Alpha)Ketoglutarate, PDB code: 5ybn 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)	43.09 / 2.10
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	172.350, 172.350, 45.291, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 22.5

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

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


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 in Complex with (Alpha)Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:28.2 occ:1.00 O2 A:AKG302 2.0 31.1 1.0 NE2 A:HIS214 2.1 26.2 1.0 OD1 A:ASP132 2.1 25.2 1.0 O5 A:AKG302 2.3 30.4 1.0 O A:HOH434 2.3 32.9 1.0 NE2 A:HIS130 2.3 26.5 1.0 C1 A:AKG302 2.7 34.6 1.0 C2 A:AKG302 2.8 28.9 1.0 CE1 A:HIS214 2.9 25.3 1.0 CG A:ASP132 3.0 26.6 1.0 CE1 A:HIS130 3.1 26.6 1.0 CD2 A:HIS214 3.2 25.0 1.0 OD2 A:ASP132 3.3 25.5 1.0 CD2 A:HIS130 3.4 24.8 1.0 O1 A:AKG302 4.0 32.6 1.0 ND1 A:HIS214 4.1 24.8 1.0 CG A:HIS214 4.2 23.5 1.0 ND1 A:HIS130 4.3 26.1 1.0 C3 A:AKG302 4.3 32.0 1.0 CG A:HIS130 4.4 25.8 1.0 CB A:ASP132 4.5 24.9 1.0 O A:HOH519 4.6 37.1 1.0 OE1 A:GLN127 4.7 29.2 1.0 CE A:MET208 4.7 23.2 1.0 C4 A:AKG302 4.8 30.1 1.0 CA A:ASP132 4.9 22.4 1.0

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


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 in Complex with (Alpha)Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:36.3 occ:1.00 O5 B:AKG302 2.0 44.8 1.0 NE2 B:HIS130 2.2 37.0 1.0 O B:HOH419 2.2 44.0 1.0 NE2 B:HIS214 2.3 39.8 1.0 OD1 B:ASP132 2.3 34.1 1.0 O1 B:AKG302 2.4 42.1 1.0 C2 B:AKG302 2.8 42.8 1.0 C1 B:AKG302 3.0 42.0 1.0 CE1 B:HIS130 3.0 36.9 1.0 CE1 B:HIS214 3.1 38.7 1.0 CD2 B:HIS130 3.2 36.2 1.0 CG B:ASP132 3.2 35.4 1.0 CD2 B:HIS214 3.3 38.7 1.0 OD2 B:ASP132 3.5 35.8 1.0 ND1 B:HIS130 4.1 38.4 1.0 O2 B:AKG302 4.2 42.1 1.0 C3 B:AKG302 4.3 44.3 1.0 ND1 B:HIS214 4.3 35.7 1.0 CG B:HIS130 4.3 37.0 1.0 CG B:HIS214 4.4 38.5 1.0 CB B:ASP132 4.6 30.4 1.0 C4 B:AKG302 4.7 43.6 1.0 O B:HOH489 4.7 43.6 1.0 CA B:ASP132 4.9 29.4 1.0 OE1 B:GLN127 4.9 37.4 1.0 O B:HOH519 5.0 44.3 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