Nickel in PDB 4bu2: 60S Ribosomal Protein L27A Histidine Hydroxylase (MINA53) in Complex with Ni(II) and 2-Oxoglutarate (2OG)

The structure of 60S Ribosomal Protein L27A Histidine Hydroxylase (MINA53) in Complex with Ni(II) and 2-Oxoglutarate (2OG), PDB code: 4bu2 was solved by R.Chowdhury, I.J.Clifton, M.A.Mcdonough, S.S.Ng, E.Pilka, U.Oppermann, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.69 / 2.78
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	184.632, 184.632, 184.632, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 23.3

The binding sites of Nickel atom in the 60S Ribosomal Protein L27A Histidine Hydroxylase (MINA53) in Complex with Ni(II) and 2-Oxoglutarate (2OG) (pdb code 4bu2). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the 60S Ribosomal Protein L27A Histidine Hydroxylase (MINA53) in Complex with Ni(II) and 2-Oxoglutarate (2OG), PDB code: 4bu2:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the 60S Ribosomal Protein L27A Histidine Hydroxylase (MINA53) in Complex with Ni(II) and 2-Oxoglutarate (2OG)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of 60S Ribosomal Protein L27A Histidine Hydroxylase (MINA53) in Complex with Ni(II) and 2-Oxoglutarate (2OG) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni601 b:34.8 occ:1.00 O2 A:AKG701 2.0 39.3 1.0 OD2 A:ASP181 2.1 47.2 1.0 O5 A:AKG701 2.1 45.9 1.0 O A:HOH2053 2.2 54.9 1.0 NE2 A:HIS179 2.3 36.4 1.0 NE2 A:HIS240 2.3 47.8 1.0 C1 A:AKG701 2.8 42.5 1.0 C2 A:AKG701 2.8 43.4 1.0 CE1 A:HIS240 3.0 46.2 1.0 CG A:ASP181 3.0 47.8 1.0 CE1 A:HIS179 3.1 38.0 1.0 OD1 A:ASP181 3.3 48.3 1.0 CD2 A:HIS179 3.4 39.4 1.0 CD2 A:HIS240 3.5 46.8 1.0 O1 A:AKG701 4.0 41.9 1.0 ND1 A:HIS240 4.2 45.7 1.0 ND1 A:HIS179 4.3 39.9 1.0 C3 A:AKG701 4.3 44.1 1.0 CG A:HIS179 4.4 39.6 1.0 CB A:ASP181 4.4 45.5 1.0 CG A:HIS240 4.5 45.1 1.0 C1 A:EDO902 4.6 52.2 1.0 C2 A:EDO902 4.7 51.7 1.0 OH A:TYR167 4.7 44.1 1.0

Nickel binding site 2 out of 2 in the 60S Ribosomal Protein L27A Histidine Hydroxylase (MINA53) in Complex with Ni(II) and 2-Oxoglutarate (2OG)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of 60S Ribosomal Protein L27A Histidine Hydroxylase (MINA53) in Complex with Ni(II) and 2-Oxoglutarate (2OG) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni602 b:45.7 occ:1.00 OD1 A:ASP243 2.1 55.4 1.0 ND1 A:HIS195 2.4 43.9 1.0 O A:HOH2122 2.4 43.3 1.0 CG A:ASP243 3.0 52.0 1.0 CG A:HIS195 3.2 43.9 1.0 OD2 A:ASP243 3.2 55.1 1.0 CE1 A:HIS195 3.3 44.0 1.0 CB A:HIS195 3.5 43.9 1.0 O A:HOH2088 4.1 59.6 1.0 NE2 A:HIS195 4.3 42.6 1.0 CD2 A:HIS195 4.3 41.4 1.0 CB A:ASP243 4.4 46.2 1.0 O A:ASP243 4.9 40.3 1.0

R.Chowdhury, R.Sekirnik, N.C.Brissett, T.Krojer, C.-H.Ho, S.S.Ng, I.J.Clifton, W.Ge, N.J.Kershaw, G.C.Fox, J.R.C.Muniz, M.Vollmar, C.Phillips, E.S.Pilka, K.L.Kavanagh, F.Von Deflt, U.Oppermann, M.A.Mcdonough, A.J.Doherty, C.J.Schofield. Ribosomal Oxygenases Are Structurally Conserved From Prokaryotes to Humans. Nature V. 510 422 2014.
ISSN: ISSN 0028-0836
PubMed: 24814345
DOI: 10.1038/NATURE13263