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Iron in PDB 8ruv: Hif Prolyl Hydroxylase 2 (PHD2) T387I Variant Bound to Fe(III), 2- Oxoglutarate (2OG) and Hypoxia-Inducible Factor 2ALPHA (HIF2ALPHA)

Enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2) T387I Variant Bound to Fe(III), 2- Oxoglutarate (2OG) and Hypoxia-Inducible Factor 2ALPHA (HIF2ALPHA)

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2) T387I Variant Bound to Fe(III), 2- Oxoglutarate (2OG) and Hypoxia-Inducible Factor 2ALPHA (HIF2ALPHA):
1.14.11.29;

Protein crystallography data

The structure of Hif Prolyl Hydroxylase 2 (PHD2) T387I Variant Bound to Fe(III), 2- Oxoglutarate (2OG) and Hypoxia-Inducible Factor 2ALPHA (HIF2ALPHA), PDB code: 8ruv was solved by G.Fiorini, C.J.Schofield, F.Arif, M.M.Kibria, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.25 / 1.66
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 38.116, 42.956, 130.508, 90, 90, 90
R / Rfree (%) 23.8 / 25.7

Iron Binding Sites:

The binding sites of Iron atom in the Hif Prolyl Hydroxylase 2 (PHD2) T387I Variant Bound to Fe(III), 2- Oxoglutarate (2OG) and Hypoxia-Inducible Factor 2ALPHA (HIF2ALPHA) (pdb code 8ruv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total only one binding site of Iron was determined in the Hif Prolyl Hydroxylase 2 (PHD2) T387I Variant Bound to Fe(III), 2- Oxoglutarate (2OG) and Hypoxia-Inducible Factor 2ALPHA (HIF2ALPHA), PDB code: 8ruv:

Iron binding site 1 out of 1 in 8ruv

Go back to Iron Binding Sites List in 8ruv
Iron binding site 1 out of 1 in the Hif Prolyl Hydroxylase 2 (PHD2) T387I Variant Bound to Fe(III), 2- Oxoglutarate (2OG) and Hypoxia-Inducible Factor 2ALPHA (HIF2ALPHA)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hif Prolyl Hydroxylase 2 (PHD2) T387I Variant Bound to Fe(III), 2- Oxoglutarate (2OG) and Hypoxia-Inducible Factor 2ALPHA (HIF2ALPHA) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:19.0
occ:1.00
 O2 A:AKG502 1.9 20.8 1.0
O5 A:AKG502 2.1 21.8 1.0
OD1 A:ASP315 2.1 21.5 1.0
NE2 A:HIS374 2.1 20.0 1.0
NE2 A:HIS313 2.1 19.0 1.0
O A:HOH605 2.3 23.3 1.0
C2 A:AKG502 2.6 23.5 1.0
C1 A:AKG502 2.6 23.5 1.0
CE1 A:HIS313 2.9 22.1 1.0
HE1 A:HIS313 3.0 26.7 1.0
CG A:ASP315 3.0 21.0 1.0
CE1 A:HIS374 3.1 19.0 1.0
CD2 A:HIS374 3.1 21.5 1.0
HE1 A:HIS374 3.2 23.0 1.0
CD2 A:HIS313 3.3 21.2 1.0
HD2 A:HIS374 3.3 26.0 1.0
OD2 A:ASP315 3.3 19.3 1.0
HG3 B:PRO531 3.5 26.7 1.0
HD2 A:HIS313 3.6 25.6 1.0
O1 A:AKG502 3.8 27.1 1.0
HZ A:PHE366 4.1 19.6 1.0
HD3 B:PRO531 4.1 24.4 1.0
C3 A:AKG502 4.1 23.4 1.0
ND1 A:HIS313 4.1 20.5 1.0
ND1 A:HIS374 4.2 20.7 1.0
CG A:HIS374 4.2 20.7 1.0
HA A:ASP315 4.3 25.7 1.0
CG A:HIS313 4.3 19.3 1.0
HZ2 A:TRP389 4.3 26.2 1.0
CG B:PRO531 4.4 22.1 1.0
CB A:ASP315 4.4 19.1 1.0
H41 A:AKG502 4.5 27.7 1.0
H32 A:AKG502 4.5 28.3 1.0
H42 A:AKG502 4.5 27.7 1.0
HE2 A:TYR310 4.6 25.2 1.0
CD B:PRO531 4.6 20.2 1.0
H31 A:AKG502 4.6 28.3 1.0
C4 A:AKG502 4.6 23.0 1.0
CE2 A:TYR310 4.7 20.9 1.0
CA A:ASP315 4.7 21.2 1.0
H A:ASP315 4.8 24.7 1.0
HD1 A:HIS313 4.8 24.8 1.0
HD2 B:PRO531 4.9 24.4 1.0
N A:ASP315 4.9 20.4 1.0
HG2 B:PRO531 4.9 26.7 1.0
HB3 A:ASP315 4.9 23.1 1.0
HG21 A:THR325 4.9 20.5 1.0
CZ A:PHE366 4.9 16.2 1.0
HE1 A:TRP389 4.9 24.6 1.0
CD2 A:TYR310 5.0 22.4 1.0
HD1 A:HIS374 5.0 25.0 1.0
HB2 A:ASP315 5.0 23.1 1.0
HB3 B:PRO531 5.0 27.2 1.0
HE1 A:PHE366 5.0 22.2 1.0

Reference:

G.Fiorini, C.J.Schofield. Investigating Gatekeeper Residues in Prolyl Hydroxylase 2 To Be Published.
Page generated: Tue Feb 25 09:44:19 2025

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