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Manganese in PDB 5lb6: Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) R371H Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl)Carbonyl]Glycine (IOX3/UN9)

Enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) R371H Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl)Carbonyl]Glycine (IOX3/UN9)

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) R371H Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl)Carbonyl]Glycine (IOX3/UN9):
1.14.11.29;

Protein crystallography data

The structure of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) R371H Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl)Carbonyl]Glycine (IOX3/UN9), PDB code: 5lb6 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) 36.39 / 1.70
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 111.159, 111.159, 40.380, 90.00, 90.00, 120.00
R / Rfree (%) 14.5 / 16.8

Other elements in 5lb6:

The structure of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) R371H Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl)Carbonyl]Glycine (IOX3/UN9) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) R371H Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl)Carbonyl]Glycine (IOX3/UN9) (pdb code 5lb6). 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) R371H Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl)Carbonyl]Glycine (IOX3/UN9), PDB code: 5lb6:

Manganese binding site 1 out of 1 in 5lb6

Go back to Manganese Binding Sites List in 5lb6
Manganese binding site 1 out of 1 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) R371H Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl)Carbonyl]Glycine (IOX3/UN9)


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) R371H Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl)Carbonyl]Glycine (IOX3/UN9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:13.1
occ:1.00
 O13 A:UN9502 2.2 14.2 1.0
OD1 A:ASP315 2.2 14.2 1.0
O A:HOH623 2.2 14.5 1.0
NE2 A:HIS313 2.2 12.4 1.0
NE2 A:HIS374 2.2 15.8 1.0
N8 A:UN9502 2.3 14.8 1.0
C12 A:UN9502 3.0 12.2 1.0
CE1 A:HIS313 3.1 14.4 1.0
CE1 A:HIS374 3.1 16.8 1.0
HE1 A:HIS313 3.1 17.3 1.0
C9 A:UN9502 3.2 13.4 1.0
CG A:ASP315 3.2 15.3 1.0
CD2 A:HIS374 3.2 15.2 1.0
CD2 A:HIS313 3.3 14.9 1.0
HE1 A:HIS374 3.3 20.1 1.0
C7 A:UN9502 3.3 13.7 1.0
HD2 A:HIS374 3.4 18.3 1.0
CL1 A:UN9502 3.5 17.1 1.0
OD2 A:ASP315 3.5 14.4 1.0
HD2 A:HIS313 3.5 17.9 1.0
HZ A:PHE366 3.9 17.4 1.0
ND1 A:HIS313 4.2 15.4 1.0
N14 A:UN9502 4.2 14.2 1.0
ND1 A:HIS374 4.3 17.1 1.0
O A:HOH635 4.3 15.0 1.0
CG A:HIS374 4.3 16.2 1.0
CG A:HIS313 4.4 15.3 1.0
HZ2 A:TRP389 4.4 16.5 1.0
HA A:ASP315 4.4 18.1 1.0
C10 A:UN9502 4.5 13.8 1.0
H152 A:UN9502 4.6 16.1 1.0
CB A:ASP315 4.6 15.6 1.0
C2 A:UN9502 4.6 17.0 1.0
HG21 A:THR325 4.8 15.5 1.0
CZ A:PHE366 4.8 14.5 1.0
C15 A:UN9502 4.9 13.5 1.0
HE1 A:PHE366 4.9 18.6 1.0
CA A:ASP315 4.9 15.0 1.0
HN14 A:UN9502 4.9 17.1 1.0
HD11 A:ILE327 4.9 18.2 1.0
H151 A:UN9502 5.0 16.1 1.0
HD1 A:HIS313 5.0 18.5 1.0
H A:ASP315 5.0 17.6 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 01:50:46 2024

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