Manganese in PDB 5l9r: Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with N-Oxalylglycine (Nog)

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

The structure of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with N-Oxalylglycine (Nog), PDB code: 5l9r 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)	39.95 / 1.81
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	71.233, 71.233, 48.245, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 18.8

The binding sites of Manganese atom in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with N-Oxalylglycine (Nog) (pdb code 5l9r). 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 N-Oxalylglycine (Nog), PDB code: 5l9r:

Manganese binding site 1 out of 1 in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with N-Oxalylglycine (Nog)


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 N-Oxalylglycine (Nog) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:22.4 occ:1.00 OD1 A:ASP315 2.1 24.9 1.0 O2' A:OGA502 2.1 26.2 1.0 NE2 A:HIS374 2.2 22.2 1.0 NE2 A:HIS313 2.2 22.9 1.0 O A:HOH650 2.3 23.3 1.0 O1 A:OGA502 2.3 25.1 1.0 C2 A:OGA502 2.9 26.3 1.0 C1 A:OGA502 2.9 25.2 1.0 CE1 A:HIS313 3.1 28.0 1.0 CE1 A:HIS374 3.1 24.0 1.0 CG A:ASP315 3.1 23.9 1.0 CD2 A:HIS374 3.1 25.4 1.0 CD2 A:HIS313 3.2 27.5 1.0 HE1 A:HIS313 3.2 33.6 1.0 HE1 A:HIS374 3.3 28.8 1.0 HD2 A:HIS374 3.3 30.5 1.0 HD2 A:HIS313 3.4 33.0 1.0 OD2 A:ASP315 3.5 25.2 1.0 HZ A:PHE366 4.0 24.4 1.0 N1 A:OGA502 4.1 27.8 1.0 O2 A:OGA502 4.2 26.8 1.0 ND1 A:HIS313 4.2 27.5 1.0 ND1 A:HIS374 4.2 23.4 1.0 CG A:HIS374 4.3 19.8 1.0 O A:HOH622 4.3 32.8 1.0 HZ2 A:TRP389 4.3 32.4 1.0 CG A:HIS313 4.3 25.1 1.0 HA A:ASP315 4.3 35.1 1.0 O A:HOH647 4.3 26.3 1.0 CB A:ASP315 4.5 26.9 1.0 H4C2 A:OGA502 4.5 31.2 1.0 H4C1 A:OGA502 4.6 31.2 1.0 C4 A:OGA502 4.7 26.0 1.0 HE2 A:TYR310 4.7 32.8 1.0 CA A:ASP315 4.8 29.3 1.0 CE2 A:TYR310 4.8 27.4 1.0 CZ A:PHE366 4.8 20.3 1.0 H1 A:OGA502 4.9 33.4 1.0 HG21 A:THR325 4.9 31.2 1.0 HE1 A:PHE366 4.9 25.1 1.0 H A:ASP315 5.0 32.7 1.0 HD1 A:HIS313 5.0 33.0 1.0 HB2 A:ASP315 5.0 32.3 1.0 N A:ASP315 5.0 27.2 1.0

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