Nickel in PDB 4jzr: Structure of Prolyl Hydroxylase Domain-Containing Protein (Phd) with Inhibitors

All present enzymatic activity of Structure of Prolyl Hydroxylase Domain-Containing Protein (Phd) with Inhibitors:
1.14.11.29;

The structure of Structure of Prolyl Hydroxylase Domain-Containing Protein (Phd) with Inhibitors, PDB code: 4jzr was solved by Y.Ma, L.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	111.455, 111.455, 39.974, 90.00, 90.00, 120.00
R / Rfree (%)	23.1 / 25.9

The binding sites of Nickel atom in the Structure of Prolyl Hydroxylase Domain-Containing Protein (Phd) with Inhibitors (pdb code 4jzr). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Structure of Prolyl Hydroxylase Domain-Containing Protein (Phd) with Inhibitors, PDB code: 4jzr:

Nickel binding site 1 out of 1 in the Structure of Prolyl Hydroxylase Domain-Containing Protein (Phd) with Inhibitors


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Prolyl Hydroxylase Domain-Containing Protein (Phd) with Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:20.9 occ:1.00 N2 A:4JR402 1.9 37.6 1.0 NE2 A:HIS374 2.0 17.9 1.0 OD2 A:ASP315 2.1 19.1 1.0 NE2 A:HIS313 2.1 21.2 1.0 O A:HOH537 2.3 18.7 1.0 N3 A:4JR402 2.3 41.9 1.0 C4 A:4JR402 2.7 41.0 1.0 C5 A:4JR402 2.8 41.9 1.0 CD2 A:HIS374 3.0 18.3 1.0 CE1 A:HIS374 3.0 18.8 1.0 CE1 A:HIS313 3.0 20.3 1.0 CG A:ASP315 3.1 21.5 1.0 C6 A:4JR402 3.1 43.0 1.0 C3 A:4JR402 3.1 40.8 1.0 CD2 A:HIS313 3.2 20.8 1.0 C25 A:4JR402 3.3 42.9 1.0 OD1 A:ASP315 3.3 19.4 1.0 N1 A:4JR402 3.9 41.9 1.0 C2 A:4JR402 4.0 41.8 1.0 ND1 A:HIS374 4.1 18.3 1.0 CG A:HIS374 4.1 19.4 1.0 ND1 A:HIS313 4.2 20.7 1.0 CG A:HIS313 4.3 21.9 1.0 O A:HOH536 4.3 19.5 1.0 CB A:ASP315 4.4 21.9 1.0 C7 A:4JR402 4.6 43.5 1.0 C24 A:4JR402 4.7 43.9 1.0 CA A:ASP315 4.7 21.9 1.0 N A:ASP315 4.9 22.0 1.0 CZ A:PHE366 4.9 23.2 1.0

G.Deng, B.Zhao, Y.Ma, Q.Xu, H.Wang, L.Yang, Q.Zhang, T.B.Guo, W.Zhang, Y.Jiao, X.Cai, J.Zhang, H.Liu, X.Guan, H.Lu, J.Xiang, J.D.Elliott, X.Lin, F.Ren. Novel Complex Crystal Structure of Prolyl Hydroxylase Domain-Containing Protein 2 (PHD2): 2,8-Diazaspiro[4.5]Decan-1-Ones As Potent, Orally Bioavailable PHD2 Inhibitors Bioorg.Med.Chem. V. 21 6349 2013.
ISSN: ISSN 0968-0896
PubMed: 24055079
DOI: 10.1016/J.BMC.2013.08.046