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

Protein crystallography data

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

Iron Binding Sites:

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 5ybs

Go back to Iron Binding Sites List in 5ybs
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 5ybs

Go back to Iron Binding Sites List in 5ybs
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

Reference:

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
Page generated: Sun Dec 13 16:18:33 2020

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