Iron in PDB 6yw0: Lysine-N,N-Dimethylated Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bb-287

All present enzymatic activity of Lysine-N,N-Dimethylated Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bb-287:
1.14.11.29;

The structure of Lysine-N,N-Dimethylated Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bb-287, PDB code: 6yw0 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)	32.02 / 2.20
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	110.927, 110.927, 39.66, 90, 90, 120
R / Rfree (%)	19.2 / 22.1

The binding sites of Iron atom in the Lysine-N,N-Dimethylated Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bb-287 (pdb code 6yw0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total only one binding site of Iron was determined in the Lysine-N,N-Dimethylated Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bb-287, PDB code: 6yw0:

Iron binding site 1 out of 1 in the Lysine-N,N-Dimethylated Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bb-287


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Lysine-N,N-Dimethylated Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bb-287 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:32.9 occ:1.00 O2 A:2JP502 2.0 29.9 1.0 N1 A:2JP502 2.1 33.6 1.0 NE2 A:HIS374 2.1 40.8 1.0 OD1 A:ASP315 2.1 39.0 1.0 NE2 A:HIS313 2.1 46.8 1.0 O A:HOH623 2.4 28.3 1.0 H6 A:2JP502 2.5 46.1 1.0 C4 A:2JP502 2.7 38.4 1.0 CE1 A:HIS313 2.9 38.2 1.0 HE1 A:HIS313 3.0 46.0 1.0 CE1 A:HIS374 3.0 29.3 1.0 C12 A:2JP502 3.0 34.7 1.0 CD2 A:HIS374 3.1 30.4 1.0 CG A:ASP315 3.1 33.8 1.0 C10 A:2JP502 3.1 38.0 1.0 HE1 A:HIS374 3.2 34.8 1.0 CD2 A:HIS313 3.3 41.2 1.0 HD2 A:HIS374 3.3 36.5 1.0 OD2 A:ASP315 3.5 32.4 1.0 N2 A:2JP502 3.5 34.2 1.0 HD2 A:HIS313 3.6 49.5 1.0 C1 A:2JP502 4.1 42.9 1.0 ND1 A:HIS313 4.1 39.9 1.0 ND1 A:HIS374 4.2 32.8 1.0 O A:HOH633 4.2 39.6 1.0 CG A:HIS374 4.2 33.8 1.0 HZ2 A:TRP389 4.3 38.7 1.0 HZ A:PHE366 4.3 40.2 1.0 HA A:ASP315 4.3 37.0 1.0 CG A:HIS313 4.3 40.8 1.0 C13 A:2JP502 4.4 33.5 1.0 C6 A:2JP502 4.4 40.1 1.0 H7 A:2JP502 4.4 41.1 1.0 H8 A:2JP502 4.5 40.2 1.0 CB A:ASP315 4.5 30.5 1.0 H10 A:2JP502 4.7 39.9 1.0 C2 A:2JP502 4.8 44.2 1.0 CA A:ASP315 4.8 31.1 1.0 H11 A:2JP502 4.8 39.9 1.0 HG21 A:THR325 4.8 43.4 1.0 HD1 A:HIS313 4.9 48.0 1.0 C11 A:2JP502 4.9 33.2 1.0 HD1 A:HIS374 4.9 39.4 1.0 H A:ASP315 4.9 40.5 1.0 N A:ASP315 5.0 33.7 1.0 HB2 A:ASP315 5.0 36.6 1.0

R.Chowdhury, M.I.Abboud, T.E.Mcallister, B.Banerji, B.Bhushan, J.L.Sorensen, A.Kawamura, C.J.Schofield. Use of Cyclic Peptides to Induce Crystallization: Case Study with Prolyl Hydroxylase Domain 2. Sci Rep V. 10 21964 2020.
ISSN: ESSN 2045-2322
PubMed: 33319810
DOI: 10.1038/S41598-020-76307-8