Manganese in PDB 5l9v: Hif Prolyl Hydroxylase 2 (PHD2-R281C/P317C) Cross-Linked to Hif-1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-1)

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

The structure of Hif Prolyl Hydroxylase 2 (PHD2-R281C/P317C) Cross-Linked to Hif-1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-1), PDB code: 5l9v 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)	43.80 / 1.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.807, 73.088, 70.407, 90.00, 91.17, 90.00
R / Rfree (%)	16.9 / 19

The binding sites of Manganese atom in the Hif Prolyl Hydroxylase 2 (PHD2-R281C/P317C) Cross-Linked to Hif-1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-1) (pdb code 5l9v). 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) Cross-Linked to Hif-1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-1), PDB code: 5l9v:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Hif Prolyl Hydroxylase 2 (PHD2-R281C/P317C) Cross-Linked to Hif-1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-1)


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) Cross-Linked to Hif-1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:21.1 occ:1.00 O2' A:OGA502 2.2 26.0 1.0 NE2 A:HIS313 2.2 18.3 1.0 NE2 A:HIS374 2.2 22.3 1.0 OD1 A:ASP315 2.2 20.6 1.0 O A:HOH626 2.3 26.4 1.0 O2 A:OGA502 2.3 25.2 1.0 C2 A:OGA502 2.8 25.4 1.0 C1 A:OGA502 2.9 25.6 1.0 CE1 A:HIS313 3.0 19.0 1.0 HE1 A:HIS313 3.1 22.8 1.0 CG A:ASP315 3.1 20.0 1.0 CE1 A:HIS374 3.1 20.7 1.0 CD2 A:HIS374 3.2 17.5 1.0 CD2 A:HIS313 3.2 20.4 1.0 HG3 C:PRO402 3.3 28.9 1.0 HE1 A:HIS374 3.3 24.8 1.0 HD2 A:HIS374 3.3 21.0 1.0 OD2 A:ASP315 3.3 21.4 1.0 HD2 A:HIS313 3.5 24.5 1.0 HZ A:PHE366 3.9 23.8 1.0 HD3 C:PRO402 4.0 27.5 1.0 N1 A:OGA502 4.1 28.8 1.0 HZ2 A:TRP389 4.1 23.5 1.0 O1 A:OGA502 4.2 27.8 1.0 ND1 A:HIS313 4.2 22.0 1.0 CG C:PRO402 4.2 24.1 1.0 ND1 A:HIS374 4.3 17.1 1.0 CG A:HIS374 4.3 17.1 1.0 CG A:HIS313 4.3 22.2 1.0 O A:HOH636 4.3 29.1 1.0 HA A:ASP315 4.4 27.3 1.0 HE2 A:TYR310 4.5 23.1 1.0 H4C2 A:OGA502 4.5 30.0 1.0 CB A:ASP315 4.5 20.7 1.0 CD C:PRO402 4.6 22.9 1.0 CE2 A:TYR310 4.7 19.2 1.0 H4C1 A:OGA502 4.7 30.0 1.0 HG2 C:PRO402 4.7 28.9 1.0 C4 A:OGA502 4.7 25.0 1.0 HG21 A:THR325 4.7 31.7 1.0 H1 A:OGA502 4.8 34.6 1.0 HD2 C:PRO402 4.8 27.5 1.0 CZ A:PHE366 4.8 19.8 1.0 HB3 C:PRO402 4.8 24.4 1.0 HE1 A:TRP389 4.9 23.7 1.0 CA A:ASP315 4.9 22.7 1.0 H A:ASP315 4.9 23.0 1.0 HD1 A:HIS313 4.9 26.4 1.0 N A:ASP315 5.0 19.2 1.0 HE1 A:PHE366 5.0 23.9 1.0

Manganese binding site 2 out of 2 in the Hif Prolyl Hydroxylase 2 (PHD2-R281C/P317C) Cross-Linked to Hif-1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-1)


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) Cross-Linked to Hif-1ALPHA Nodd-L397C/D412C and N-Oxalylglycine (Nog) (Complex-1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:15.6 occ:1.00 NE2 B:HIS374 2.1 16.8 1.0 OD1 B:ASP315 2.2 23.2 1.0 NE2 B:HIS313 2.2 23.4 1.0 O1 B:OGA502 2.2 22.7 1.0 O2' B:OGA502 2.3 25.1 1.0 O B:HOH612 2.4 24.5 1.0 C2 B:OGA502 2.9 28.6 1.0 C1 B:OGA502 2.9 27.1 1.0 CE1 B:HIS374 3.0 26.8 1.0 CE1 B:HIS313 3.1 21.4 1.0 HE1 B:HIS374 3.1 32.2 1.0 CG B:ASP315 3.2 26.4 1.0 HE1 B:HIS313 3.2 25.7 1.0 CD2 B:HIS374 3.2 21.0 1.0 CD2 B:HIS313 3.3 20.3 1.0 HG3 D:PRO402 3.3 24.3 1.0 OD2 B:ASP315 3.5 22.7 1.0 HD2 B:HIS374 3.5 25.2 1.0 HD2 B:HIS313 3.5 24.4 1.0 HD3 D:PRO402 4.0 25.0 1.0 HZ B:PHE366 4.0 31.1 1.0 HZ2 B:TRP389 4.1 27.6 1.0 O B:HOH654 4.1 24.2 1.0 ND1 B:HIS374 4.1 25.4 1.0 O2 B:OGA502 4.2 28.0 1.0 CG D:PRO402 4.2 20.2 1.0 N1 B:OGA502 4.2 24.2 1.0 ND1 B:HIS313 4.2 22.1 1.0 CG B:HIS374 4.3 19.4 1.0 HA B:ASP315 4.3 28.6 1.0 CG B:HIS313 4.3 22.5 1.0 CB B:ASP315 4.5 25.8 1.0 CD D:PRO402 4.5 20.8 1.0 H4C2 B:OGA502 4.6 30.1 1.0 HE2 B:TYR310 4.6 25.4 1.0 HG2 D:PRO402 4.7 24.3 1.0 CE2 B:TYR310 4.7 21.1 1.0 HB3 D:PRO402 4.8 24.1 1.0 HG21 B:THR325 4.8 25.4 1.0 HD2 D:PRO402 4.8 25.0 1.0 H4C1 B:OGA502 4.8 30.1 1.0 C4 B:OGA502 4.8 25.1 1.0 CA B:ASP315 4.8 23.8 1.0 H1 B:OGA502 4.8 29.1 1.0 HD1 B:HIS374 4.9 30.5 1.0 CZ B:PHE366 4.9 25.9 1.0 HE1 B:PHE366 4.9 27.8 1.0 H B:ASP315 4.9 25.3 1.0 HE1 B:TRP389 5.0 30.9 1.0 N B:ASP315 5.0 21.1 1.0 HD1 B:HIS313 5.0 26.6 1.0 CZ2 B:TRP389 5.0 23.0 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