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Manganese in PDB 5las: Hif Prolyl Hydroxylase 2 (PHD2-R281C/P317C/R396T) Cross-Linked to Hif- 1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-3)

Enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2-R281C/P317C/R396T) Cross-Linked to Hif- 1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-3)

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2-R281C/P317C/R396T) Cross-Linked to Hif- 1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-3):
1.14.11.29;

Protein crystallography data

The structure of Hif Prolyl Hydroxylase 2 (PHD2-R281C/P317C/R396T) Cross-Linked to Hif- 1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-3), PDB code: 5las 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) 43.57 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.579, 73.642, 70.146, 90.00, 91.25, 90.00
R / Rfree (%) 18.5 / 22.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Hif Prolyl Hydroxylase 2 (PHD2-R281C/P317C/R396T) Cross-Linked to Hif- 1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-3) (pdb code 5las). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Hif Prolyl Hydroxylase 2 (PHD2-R281C/P317C/R396T) Cross-Linked to Hif- 1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-3), PDB code: 5las:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 5las

Go back to Manganese Binding Sites List in 5las
Manganese binding site 1 out of 2 in the Hif Prolyl Hydroxylase 2 (PHD2-R281C/P317C/R396T) Cross-Linked to Hif- 1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-3)


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-R281C/P317C/R396T) Cross-Linked to Hif- 1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:28.7
occ:1.00
 OD1 A:ASP315 2.1 30.3 1.0
NE2 A:HIS313 2.1 24.6 1.0
NE2 A:HIS374 2.2 24.1 1.0
O2 A:OGA502 2.2 34.7 1.0
O2' A:OGA502 2.3 31.6 1.0
O A:HOH603 2.3 27.9 1.0
C2 A:OGA502 2.9 31.0 1.0
C1 A:OGA502 2.9 32.3 1.0
CE1 A:HIS313 2.9 26.4 1.0
HE1 A:HIS313 3.0 31.7 1.0
CE1 A:HIS374 3.0 22.0 1.0
CG A:ASP315 3.1 27.4 1.0
HE1 A:HIS374 3.1 26.4 1.0
CD2 A:HIS313 3.2 24.3 1.0
HG3 C:PRO402 3.2 35.5 1.0
CD2 A:HIS374 3.3 25.9 1.0
OD2 A:ASP315 3.4 22.4 1.0
HD2 A:HIS313 3.5 29.1 1.0
HD2 A:HIS374 3.5 31.0 1.0
HD3 C:PRO402 3.8 35.2 1.0
HZ2 A:TRP389 3.9 38.8 1.0
ND1 A:HIS313 4.1 28.3 1.0
HZ A:PHE366 4.1 35.1 1.0
CG C:PRO402 4.1 29.5 1.0
O1 A:OGA502 4.1 30.5 1.0
N1 A:OGA502 4.1 28.1 1.0
ND1 A:HIS374 4.2 24.2 1.0
HA A:ASP315 4.2 32.5 1.0
CG A:HIS313 4.2 26.6 1.0
CG A:HIS374 4.3 25.6 1.0
CD C:PRO402 4.3 29.4 1.0
O A:HOH645 4.4 29.7 1.0
CB A:ASP315 4.4 26.2 1.0
HD2 C:PRO402 4.6 35.2 1.0
HE2 A:TYR310 4.6 23.7 1.0
H4C1 A:OGA502 4.6 33.7 1.0
H A:ASP315 4.7 34.9 1.0
HG2 C:PRO402 4.7 35.5 1.0
CA A:ASP315 4.7 27.1 1.0
HG21 A:THR325 4.7 33.6 1.0
HB3 C:PRO402 4.7 36.7 1.0
CE2 A:TYR310 4.7 19.7 1.0
H4C2 A:OGA502 4.8 33.7 1.0
N A:ASP315 4.8 29.1 1.0
CZ2 A:TRP389 4.8 32.3 1.0
C4 A:OGA502 4.8 28.1 1.0
HD1 A:HIS313 4.8 34.0 1.0
H1 A:OGA502 4.8 33.7 1.0
HE1 A:TRP389 4.9 42.7 1.0
HD1 A:HIS374 4.9 29.1 1.0
HB2 A:ASP315 4.9 31.4 1.0
CZ A:PHE366 5.0 29.2 1.0
HB3 A:ASP315 5.0 31.4 1.0
HE1 A:PHE366 5.0 38.2 1.0

Manganese binding site 2 out of 2 in 5las

Go back to Manganese Binding Sites List in 5las
Manganese binding site 2 out of 2 in the Hif Prolyl Hydroxylase 2 (PHD2-R281C/P317C/R396T) Cross-Linked to Hif- 1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-3)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Hif Prolyl Hydroxylase 2 (PHD2-R281C/P317C/R396T) Cross-Linked to Hif- 1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:30.6
occ:1.00
 NE2 B:HIS374 2.1 27.8 1.0
OD1 B:ASP315 2.1 34.8 1.0
O1 B:OGA502 2.2 33.6 1.0
NE2 B:HIS313 2.2 29.3 1.0
O2' B:OGA502 2.5 32.5 1.0
O B:HOH636 2.5 31.6 1.0
C1 B:OGA502 2.9 32.8 1.0
CE1 B:HIS374 2.9 35.0 1.0
CE1 B:HIS313 3.0 30.9 1.0
C2 B:OGA502 3.0 32.2 1.0
HE1 B:HIS374 3.1 42.0 1.0
CG B:ASP315 3.1 34.5 1.0
HE1 B:HIS313 3.1 37.1 1.0
CD2 B:HIS374 3.1 26.6 1.0
HG3 D:PRO402 3.2 43.9 1.0
CD2 B:HIS313 3.3 29.2 1.0
OD2 B:ASP315 3.3 35.2 1.0
HD2 B:HIS374 3.4 31.9 1.0
HD2 B:HIS313 3.6 35.0 1.0
HD3 D:PRO402 3.8 41.3 1.0
CG D:PRO402 4.0 36.6 1.0
HZ B:PHE366 4.1 42.8 1.0
ND1 B:HIS374 4.1 32.4 1.0
HZ2 B:TRP389 4.1 40.7 1.0
O2 B:OGA502 4.1 31.4 1.0
ND1 B:HIS313 4.2 31.7 1.0
CG B:HIS374 4.2 27.4 1.0
N1 B:OGA502 4.3 32.6 1.0
HB3 D:PRO402 4.3 37.8 1.0
CD D:PRO402 4.3 34.4 1.0
CG B:HIS313 4.3 30.4 1.0
HA B:ASP315 4.4 43.0 1.0
HE2 B:TYR310 4.4 38.7 1.0
O B:HOH644 4.4 34.2 1.0
CB B:ASP315 4.5 36.7 1.0
CE2 B:TYR310 4.6 32.2 1.0
H4C2 B:OGA502 4.7 40.3 1.0
HD2 D:PRO402 4.7 41.3 1.0
HG2 D:PRO402 4.7 43.9 1.0
CB D:PRO402 4.8 31.5 1.0
HG21 B:THR325 4.8 43.4 1.0
CA B:ASP315 4.8 35.8 1.0
HD1 B:HIS374 4.8 38.8 1.0
H B:ASP315 4.9 37.3 1.0
HE1 B:TRP389 4.9 41.2 1.0
HD1 B:HIS313 4.9 38.0 1.0
CD2 B:TYR310 4.9 36.1 1.0
N B:ASP315 4.9 31.1 1.0
C4 B:OGA502 4.9 33.6 1.0
CZ B:PHE366 5.0 35.6 1.0
HB3 B:ASP315 5.0 44.0 1.0
CZ B:TYR310 5.0 28.4 1.0
H1 B:OGA502 5.0 39.1 1.0
HD2 B:TYR310 5.0 43.4 1.0
H4C1 B:OGA502 5.0 40.3 1.0
HD11 B:ILE327 5.0 47.6 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 01:50:27 2024

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