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Manganese in PDB 5lbc: Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) I280V/R281L/I292V Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl) Carbonyl]Glycine (IOX3/FG2216)

Enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) I280V/R281L/I292V Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl) Carbonyl]Glycine (IOX3/FG2216)

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) I280V/R281L/I292V Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl) Carbonyl]Glycine (IOX3/FG2216):
1.14.11.29;

Protein crystallography data

The structure of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) I280V/R281L/I292V Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl) Carbonyl]Glycine (IOX3/FG2216), PDB code: 5lbc was solved by R.Chowdhury, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.07 / 1.82
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 111.006, 111.006, 40.283, 90.00, 90.00, 120.00
R / Rfree (%) 15.8 / 18.1

Other elements in 5lbc:

The structure of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) I280V/R281L/I292V Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl) Carbonyl]Glycine (IOX3/FG2216) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) I280V/R281L/I292V Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl) Carbonyl]Glycine (IOX3/FG2216) (pdb code 5lbc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) I280V/R281L/I292V Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl) Carbonyl]Glycine (IOX3/FG2216), PDB code: 5lbc:

Manganese binding site 1 out of 1 in 5lbc

Go back to Manganese Binding Sites List in 5lbc
Manganese binding site 1 out of 1 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) I280V/R281L/I292V Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl) Carbonyl]Glycine (IOX3/FG2216)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) I280V/R281L/I292V Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl) Carbonyl]Glycine (IOX3/FG2216) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:16.8
occ:1.00
 OD1 A:ASP315 2.2 17.1 1.0
O13 A:UN9503 2.2 17.9 1.0
NE2 A:HIS374 2.2 16.6 1.0
NE2 A:HIS313 2.2 15.3 1.0
O A:HOH618 2.3 18.4 1.0
N8 A:UN9503 2.3 24.9 1.0
C12 A:UN9503 3.0 17.6 1.0
CE1 A:HIS313 3.0 16.2 1.0
CE1 A:HIS374 3.1 15.5 1.0
HE1 A:HIS313 3.1 19.5 1.0
C9 A:UN9503 3.1 16.6 1.0
CG A:ASP315 3.1 16.1 1.0
HE1 A:HIS374 3.2 18.6 1.0
CD2 A:HIS374 3.2 14.4 1.0
C7 A:UN9503 3.3 35.5 1.0
CD2 A:HIS313 3.3 19.1 1.0
HD2 A:HIS374 3.4 17.3 1.0
OD2 A:ASP315 3.4 17.1 1.0
CL1 A:UN9503 3.5 30.1 1.0
HD2 A:HIS313 3.6 22.9 1.0
HZ A:PHE366 4.0 21.3 1.0
O A:HOH630 4.2 21.8 1.0
ND1 A:HIS313 4.2 19.3 1.0
ND1 A:HIS374 4.2 16.5 1.0
N14 A:UN9503 4.3 17.3 1.0
HZ2 A:TRP389 4.3 22.3 1.0
CG A:HIS374 4.3 16.3 1.0
CG A:HIS313 4.4 16.9 1.0
HA A:ASP315 4.4 24.5 1.0
C10 A:UN9503 4.5 17.9 1.0
H151 A:UN9503 4.5 21.4 1.0
CB A:ASP315 4.5 17.9 1.0
C2 A:UN9503 4.6 24.9 1.0
HG21 A:THR325 4.8 19.7 1.0
C15 A:UN9503 4.8 17.8 1.0
H152 A:UN9503 4.8 21.4 1.0
CZ A:PHE366 4.9 17.7 1.0
CA A:ASP315 4.9 20.4 1.0
HD11 A:ILE327 4.9 21.9 1.0
HE1 A:PHE366 4.9 22.2 1.0
HD1 A:HIS313 5.0 23.2 1.0
H A:ASP315 5.0 20.8 1.0
HN14 A:UN9503 5.0 20.8 1.0
HD1 A:HIS374 5.0 19.8 1.0

Reference:

R.Chowdhury, I.K.Leung, Y.M.Tian, M.I.Abboud, W.Ge, C.Domene, F.X.Cantrelle, I.Landrieu, A.P.Hardy, C.W.Pugh, P.J.Ratcliffe, T.D.Claridge, C.J.Schofield. Structural Basis For Oxygen Degradation Domain Selectivity of the Hif Prolyl Hydroxylases. Nat Commun V. 7 12673 2016.
ISSN: ESSN 2041-1723
PubMed: 27561929
DOI: 10.1038/NCOMMS12673
Page generated: Sun Oct 6 01:51:20 2024

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