Manganese in PDB 5ybl: Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Ause

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Ause, PDB code: 5ybl 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)	48.41 / 2.11
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	220.342, 223.923, 53.694, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 26.6

The binding sites of Manganese atom in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Ause (pdb code 5ybl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Ause, PDB code: 5ybl:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Ause


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Ause within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:41.8 occ:1.00 O5 A:AKG302 2.3 34.9 1.0 OD1 A:ASP132 2.4 27.0 1.0 NE2 A:HIS214 2.4 28.5 1.0 NE2 A:HIS130 2.5 35.6 1.0 O2 A:AKG302 2.7 41.0 1.0 O A:HOH446 2.7 30.5 1.0 C2 A:AKG302 3.0 33.7 1.0 CE1 A:HIS214 3.1 30.0 1.0 C1 A:AKG302 3.2 36.2 1.0 CD2 A:HIS130 3.3 34.1 1.0 CG A:ASP132 3.5 29.4 1.0 CE1 A:HIS130 3.5 33.2 1.0 CD2 A:HIS214 3.5 29.2 1.0 OD2 A:ASP132 3.9 30.7 1.0 ND1 A:HIS214 4.3 25.8 1.0 CG A:HIS130 4.4 33.1 1.0 O1 A:AKG302 4.4 35.9 1.0 ND1 A:HIS130 4.5 35.0 1.0 C3 A:AKG302 4.5 27.4 1.0 CG A:HIS214 4.5 30.3 1.0 CB A:ASP132 4.7 27.8 1.0 O A:HOH408 4.7 30.0 1.0 CA A:ASP132 4.8 24.8 1.0 C4 A:AKG302 4.8 28.9 1.0 N A:ASP132 5.0 24.6 1.0

Manganese binding site 2 out of 4 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Ause


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Ause within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:36.7 occ:1.00 OD1 B:ASP132 2.2 29.4 1.0 NE2 B:HIS214 2.2 25.9 1.0 NE2 B:HIS130 2.3 27.3 1.0 CE1 B:HIS214 2.9 26.2 1.0 CG B:ASP132 3.1 27.2 1.0 CE1 B:HIS130 3.2 26.1 1.0 CD2 B:HIS130 3.3 24.6 1.0 OD2 B:ASP132 3.4 32.9 1.0 CD2 B:HIS214 3.4 26.6 1.0 ND1 B:HIS214 4.1 26.6 1.0 ND1 B:HIS130 4.3 29.0 1.0 CG B:HIS214 4.4 25.8 1.0 CG B:HIS130 4.4 28.2 1.0 CB B:ASP132 4.5 27.8 1.0 CA B:ASP132 4.8 25.0 1.0

Manganese binding site 3 out of 4 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Ause


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Ause within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:30.1 occ:0.71 O C:HOH403 1.7 32.4 1.0 NE2 C:HIS130 2.1 27.3 1.0 O2 C:AKG302 2.3 43.7 1.0 OD1 C:ASP132 2.3 28.5 1.0 O5 C:AKG302 2.3 35.3 1.0 NE2 C:HIS214 2.6 30.6 1.0 C1 C:AKG302 2.8 38.5 1.0 C2 C:AKG302 2.9 34.7 1.0 CE1 C:HIS130 2.9 24.4 1.0 CD2 C:HIS130 3.3 23.3 1.0 CE1 C:HIS214 3.3 28.2 1.0 CG C:ASP132 3.3 27.5 1.0 OD2 C:ASP132 3.6 35.7 1.0 CD2 C:HIS214 3.7 26.2 1.0 O1 C:AKG302 3.9 41.1 1.0 ND1 C:HIS130 4.1 23.3 1.0 CG C:HIS130 4.3 24.8 1.0 C3 C:AKG302 4.4 32.7 1.0 ND1 C:HIS214 4.5 24.6 1.0 O C:HOH448 4.5 33.4 1.0 CB C:ASP132 4.6 25.0 1.0 CG C:HIS214 4.7 24.8 1.0 C4 C:AKG302 4.8 33.5 1.0 NE2 C:GLN127 4.8 35.7 1.0 CA C:ASP132 4.9 20.9 1.0 O C:HOH451 5.0 38.3 1.0

Manganese binding site 4 out of 4 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Ause


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Ause within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn301 b:40.1 occ:0.76 O D:HOH401 1.6 26.1 1.0 NE2 D:HIS130 1.9 25.7 1.0 OD1 D:ASP132 2.5 26.9 1.0 CE1 D:HIS130 2.7 23.8 1.0 NE2 D:HIS214 2.8 29.6 1.0 CD2 D:HIS130 3.1 22.6 1.0 CE1 D:HIS214 3.6 32.1 1.0 CG D:ASP132 3.7 28.8 1.0 CD2 D:HIS214 3.8 28.8 1.0 ND1 D:HIS130 3.9 25.9 1.0 CG D:HIS130 4.1 23.8 1.0 OD2 D:ASP132 4.4 30.1 1.0 CA D:ASP132 4.7 23.8 1.0 ND1 D:HIS214 4.8 29.0 1.0 CB D:ASP132 4.8 25.3 1.0 OE1 D:GLN127 4.8 37.6 1.0 NE2 D:GLN127 4.9 39.7 1.0 CG D:HIS214 4.9 28.6 1.0 N D:ASP132 5.0 24.0 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