Atomistry » Manganese » PDB 5kg5-5lyw » 5lbc
Atomistry »
  Manganese »
    PDB 5kg5-5lyw »
      5lbc »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy