Manganese in PDB 6yvx: Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic Bb-287

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

The structure of Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic Bb-287, PDB code: 6yvx was solved by R.Chowdhury, B.Banerji, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.61 / 1.80
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	109.947, 109.947, 39.221, 90, 90, 120
R / Rfree (%)	16 / 18.9

The binding sites of Manganese atom in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic Bb-287 (pdb code 6yvx). 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 Bicyclic Bb-287, PDB code: 6yvx:

Manganese binding site 1 out of 1 in the Hif Prolyl Hydroxylase 2 (PHD2/ EGLN1) in Complex with Bicyclic Bb-287


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 Bicyclic Bb-287 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:24.8 occ:1.00 N1 A:2JP502 2.1 33.1 1.0 O2 A:2JP502 2.1 27.2 1.0 NE2 A:HIS374 2.2 24.9 1.0 OD1 A:ASP315 2.2 24.0 1.0 O A:HOH623 2.2 20.7 1.0 NE2 A:HIS313 2.2 22.9 1.0 H6 A:2JP502 2.9 37.4 1.0 C4 A:2JP502 3.0 31.2 1.0 CE1 A:HIS313 3.1 27.7 1.0 C12 A:2JP502 3.1 25.8 1.0 CE1 A:HIS374 3.1 25.3 1.0 HE1 A:HIS313 3.1 33.2 1.0 CD2 A:HIS374 3.2 26.1 1.0 CG A:ASP315 3.2 25.4 1.0 C10 A:2JP502 3.2 31.9 1.0 HE1 A:HIS374 3.3 30.4 1.0 CD2 A:HIS313 3.3 24.2 1.0 HD2 A:HIS374 3.3 31.3 1.0 OD2 A:ASP315 3.5 23.7 1.0 N2 A:2JP502 3.5 30.2 1.0 HD2 A:HIS313 3.6 29.0 1.0 HZ A:PHE366 4.1 28.2 1.0 ND1 A:HIS313 4.2 26.3 1.0 ND1 A:HIS374 4.2 24.4 1.0 HZ2 A:TRP389 4.3 35.9 1.0 O A:HOH646 4.3 28.8 1.0 CG A:HIS374 4.3 24.9 1.0 HA A:ASP315 4.3 32.1 1.0 C1 A:2JP502 4.3 42.0 1.0 CG A:HIS313 4.4 25.3 1.0 H7 A:2JP502 4.4 36.3 1.0 C13 A:2JP502 4.4 32.6 1.0 CB A:ASP315 4.5 22.8 1.0 C6 A:2JP502 4.5 39.9 1.0 H8 A:2JP502 4.7 39.1 1.0 H11 A:2JP502 4.7 44.3 1.0 H10 A:2JP502 4.8 44.3 1.0 CA A:ASP315 4.8 26.7 1.0 HG21 A:THR325 4.8 26.0 1.0 C11 A:2JP502 4.9 36.9 1.0 HD1 A:HIS313 5.0 31.5 1.0 CZ A:PHE366 5.0 23.5 1.0 HD1 A:HIS374 5.0 29.2 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