Nickel in PDB 6t8m: Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum

The structure of Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum, PDB code: 6t8m was solved by R.Chowdhury, M.A.Mcdonough, T.Liu, I.J.Clifton, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.92 / 2.02
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	45.216, 81.781, 379.210, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 25.7

The structure of Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Nickel atom in the Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum (pdb code 6t8m). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum, PDB code: 6t8m:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in the Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:22.3 occ:1.00 O2' A:OGA503 1.9 34.8 1.0 NE2 A:HIS266 2.1 60.4 1.0 NE2 A:HIS191 2.1 51.6 1.0 O A:HOH614 2.2 42.3 1.0 OD1 A:ASP193 2.2 40.9 1.0 O2 A:OGA503 2.2 33.0 1.0 C2 A:OGA503 2.5 36.8 1.0 C1 A:OGA503 2.7 32.6 1.0 CE1 A:HIS266 2.9 43.2 1.0 CE1 A:HIS191 3.0 53.6 1.0 CG A:ASP193 3.1 39.6 1.0 CD2 A:HIS266 3.2 43.4 1.0 CD2 A:HIS191 3.2 48.3 1.0 OD2 A:ASP193 3.3 36.4 1.0 N1 A:OGA503 3.9 36.8 1.0 O1 A:OGA503 4.0 32.9 1.0 ND1 A:HIS266 4.0 41.5 1.0 ND1 A:HIS191 4.1 49.9 1.0 O A:HOH641 4.2 27.9 1.0 CG A:HIS266 4.2 44.1 1.0 CG A:HIS191 4.3 56.0 1.0 O A:HOH609 4.3 18.8 1.0 C4 A:OGA503 4.5 37.5 1.0 CB A:ASP193 4.5 36.9 1.0 CZ2 A:TRP282 4.6 30.8 1.0 CE2 A:TYR188 4.8 40.0 1.0 CA A:ASP193 4.9 34.9 1.0 N A:ASP193 5.0 35.6 1.0

Nickel binding site 2 out of 5 in the Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni504 b:52.2 occ:1.00 O B:SER58 1.9 47.3 1.0 O A:SER58 2.0 51.7 1.0 N B:SER58 2.0 52.0 1.0 N A:SER58 2.0 61.1 1.0 O B:HOH439 2.3 55.5 1.0 C B:SER58 2.5 43.4 1.0 C A:SER58 2.6 53.1 1.0 CA A:SER58 2.6 67.8 1.0 CA B:SER58 2.7 56.6 1.0 CB A:SER58 3.2 91.7 1.0 CB B:SER58 3.7 75.5 1.0 O A:HOH661 3.8 41.3 1.0 N B:MET59 3.8 64.0 1.0 N A:MET59 3.9 61.9 1.0 OG A:SER58 4.2 0.9 1.0 CA B:MET59 4.6 62.2 1.0 CA A:MET59 4.7 60.1 1.0 OG B:SER58 4.7 86.4 1.0 O B:LYS60 4.8 52.7 1.0 N B:LYS60 5.0 64.9 1.0

Nickel binding site 3 out of 5 in the Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:38.5 occ:1.00 O2' B:OGA303 1.9 43.5 1.0 OD1 B:ASP193 2.0 44.3 1.0 NE2 B:HIS266 2.2 41.5 1.0 O2 B:OGA303 2.2 44.0 1.0 NE2 B:HIS191 2.3 53.1 1.0 O B:HOH406 2.4 39.3 1.0 C2 B:OGA303 2.6 43.7 1.0 C1 B:OGA303 2.7 42.4 1.0 CG B:ASP193 2.9 42.1 1.0 CE1 B:HIS191 3.0 53.8 1.0 OD2 B:ASP193 3.1 42.7 1.0 CD2 B:HIS266 3.1 41.8 1.0 CE1 B:HIS266 3.2 39.9 1.0 CD2 B:HIS191 3.3 53.6 1.0 N1 B:OGA303 3.9 42.6 1.0 O1 B:OGA303 4.0 43.6 1.0 ND1 B:HIS191 4.2 54.6 1.0 CB B:ASP193 4.3 39.7 1.0 ND1 B:HIS266 4.3 42.1 1.0 CG B:HIS266 4.3 40.5 1.0 O B:HOH417 4.3 37.0 1.0 CG B:HIS191 4.3 54.3 1.0 O B:HOH422 4.5 29.3 1.0 C4 B:OGA303 4.5 40.6 1.0 CA B:ASP193 4.7 36.5 1.0 N B:ASP193 4.7 34.4 1.0 CE2 B:TYR188 4.9 44.2 1.0 CZ2 B:TRP282 4.9 35.5 1.0 CZ B:PHE259 4.9 42.0 1.0

Nickel binding site 4 out of 5 in the Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni301 b:52.4 occ:1.00 OD2 C:ASP193 1.8 69.4 1.0 O2' C:OGA303 1.8 65.3 1.0 NE2 C:HIS266 2.0 86.6 1.0 O1 C:OGA303 2.1 74.6 1.0 NE2 C:HIS191 2.4 51.7 1.0 C2 C:OGA303 2.5 69.9 1.0 O C:HOH417 2.6 54.1 1.0 C1 C:OGA303 2.7 71.3 1.0 CG C:ASP193 2.8 70.6 1.0 CD2 C:HIS266 2.8 51.1 1.0 OD1 C:ASP193 3.1 73.4 1.0 CE1 C:HIS266 3.2 49.5 1.0 CE1 C:HIS191 3.2 52.8 1.0 CD2 C:HIS191 3.3 52.0 1.0 N1 C:OGA303 3.9 65.9 1.0 O2 C:OGA303 3.9 74.2 1.0 CG C:HIS266 4.1 51.3 1.0 CB C:ASP193 4.1 65.0 1.0 O C:HOH414 4.1 38.7 1.0 ND1 C:HIS266 4.2 50.2 1.0 ND1 C:HIS191 4.3 54.0 1.0 CG C:HIS191 4.4 53.5 1.0 O C:HOH407 4.4 39.6 1.0 C4 C:OGA303 4.5 65.3 1.0 N C:ASP193 4.6 47.3 1.0 CA C:ASP193 4.7 52.8 1.0 CZ2 C:TRP282 4.9 48.1 1.0 CE2 C:TYR188 5.0 54.8 1.0 CZ C:PHE259 5.0 52.2 1.0

Nickel binding site 5 out of 5 in the Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Prolyl Hydroxylase (Phd) Involved in Hypoxia Sensing By Dictyostelium Discoideum within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni305 b:83.2 occ:0.50 N C:SER58 1.9 1.0 1.0 O C:SER58 1.9 0.0 1.0 C C:SER58 2.6 0.5 1.0 CA C:SER58 2.6 0.6 1.0 CB C:SER58 3.3 0.0 1.0 N C:MET59 3.9 0.9 1.0 OG C:SER58 4.5 0.3 1.0 CA C:MET59 4.7 0.8 1.0

T.Liu, M.I.Abboud, R.Chowdhury, A.Tumber, A.P.Hardy, K.Lippl, C.T.Lohans, E.Pires, J.Wickens, M.A.Mcdonough, C.M.West, C.J.Schofield. Biochemical and Biophysical Analyses of Hypoxia Sensing Prolyl Hydroxylases From Dictyostelium Discoideum and Toxoplasma Gondii. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32934009
DOI: 10.1074/JBC.RA120.013998