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Manganese in PDB 5ox6: Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Vadadustat

Enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Vadadustat

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Vadadustat:
1.14.11.29;

Protein crystallography data

The structure of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Vadadustat, PDB code: 5ox6 was solved by R.Chowdhury, D.Zhang, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.36 / 1.99
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 111.088, 111.088, 39.971, 90.00, 90.00, 120.00
R / Rfree (%) 17.4 / 20.5

Other elements in 5ox6:

The structure of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Vadadustat 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) in Complex with Vadadustat (pdb code 5ox6). 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) in Complex with Vadadustat, PDB code: 5ox6:

Manganese binding site 1 out of 1 in 5ox6

Go back to Manganese Binding Sites List in 5ox6
Manganese binding site 1 out of 1 in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Vadadustat


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) in Complex with Vadadustat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:19.8
occ:1.00
 N11 A:A1Z502 2.0 23.2 1.0
O10 A:A1Z502 2.0 23.3 1.0
OD1 A:ASP315 2.1 30.3 1.0
NE2 A:HIS374 2.1 24.7 1.0
O A:HOH616 2.1 21.8 1.0
NE2 A:HIS313 2.1 27.8 1.0
C04 A:A1Z502 2.8 24.2 1.0
C03 A:A1Z502 2.9 26.3 1.0
C12 A:A1Z502 3.0 26.1 1.0
H121 A:A1Z502 3.0 31.3 1.0
CE1 A:HIS374 3.0 23.4 1.0
CD2 A:HIS374 3.0 23.9 1.0
CG A:ASP315 3.1 25.9 1.0
CE1 A:HIS313 3.1 23.8 1.0
CD2 A:HIS313 3.1 24.6 1.0
HE1 A:HIS374 3.2 28.1 1.0
HE1 A:HIS313 3.2 28.5 1.0
HD2 A:HIS374 3.2 28.7 1.0
HD2 A:HIS313 3.3 29.3 1.0
OD2 A:ASP315 3.4 26.5 1.0
HZ A:PHE366 4.0 33.7 1.0
ND1 A:HIS374 4.1 24.9 1.0
O A:HOH647 4.1 27.1 1.0
CG A:HIS374 4.1 25.0 1.0
N05 A:A1Z502 4.2 23.0 1.0
ND1 A:HIS313 4.2 24.8 1.0
C02 A:A1Z502 4.2 26.9 1.0
CG A:HIS313 4.2 28.6 1.0
C13 A:A1Z502 4.3 27.9 1.0
HZ2 A:TRP389 4.3 32.1 1.0
HA A:ASP315 4.4 29.7 1.0
CB A:ASP315 4.4 24.8 1.0
H062 A:A1Z502 4.5 27.9 1.0
C06 A:A1Z502 4.7 23.2 1.0
H061 A:A1Z502 4.8 27.9 1.0
C21 A:A1Z502 4.8 27.1 1.0
HG21 A:THR325 4.8 26.4 1.0
H051 A:A1Z502 4.8 27.6 1.0
CA A:ASP315 4.8 24.7 1.0
CZ A:PHE366 4.8 28.0 1.0
H A:ASP315 4.8 30.2 1.0
HD1 A:HIS374 4.9 29.9 1.0
HE1 A:PHE366 4.9 37.3 1.0
HD11 A:ILE327 4.9 29.5 1.0
HB2 A:ASP315 4.9 29.8 1.0
N A:ASP315 4.9 25.1 1.0
HD1 A:HIS313 5.0 29.8 1.0
HB3 A:ASP315 5.0 29.8 1.0

Reference:

T.L.Yeh, T.M.Leissing, M.I.Abboud, C.C.Thinnes, O.Atasoylu, J.P.Holt-Martyn, D.Zhang, A.Tumber, K.Lippl, C.T.Lohans, I.K.H.Leung, H.Morcrette, I.J.Clifton, T.D.W.Claridge, A.Kawamura, E.Flashman, X.Lu, P.J.Ratcliffe, R.Chowdhury, C.W.Pugh, C.J.Schofield. Molecular and Cellular Mechanisms of Hif Prolyl Hydroxylase Inhibitors in Clinical Trials. Chem Sci V. 8 7651 2017.
ISSN: ISSN 2041-6520
PubMed: 29435217
DOI: 10.1039/C7SC02103H
Page generated: Sun Oct 6 02:25:39 2024

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