Nickel in PDB 4y3o: Crystal Structure of Ribosomal Oxygenase NO66 in Complex with Substrate RPL8 Peptide and Ni(II) and Cofactor N-Oxalyglycine

All present enzymatic activity of Crystal Structure of Ribosomal Oxygenase NO66 in Complex with Substrate RPL8 Peptide and Ni(II) and Cofactor N-Oxalyglycine:
1.14.11.27;

The structure of Crystal Structure of Ribosomal Oxygenase NO66 in Complex with Substrate RPL8 Peptide and Ni(II) and Cofactor N-Oxalyglycine, PDB code: 4y3o was solved by C.Wang, Q.Zhang, J.Zang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.57 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.500, 202.930, 85.680, 90.00, 118.94, 90.00
R / Rfree (%)	20.3 / 26.2

The binding sites of Nickel atom in the Crystal Structure of Ribosomal Oxygenase NO66 in Complex with Substrate RPL8 Peptide and Ni(II) and Cofactor N-Oxalyglycine (pdb code 4y3o). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Ribosomal Oxygenase NO66 in Complex with Substrate RPL8 Peptide and Ni(II) and Cofactor N-Oxalyglycine, PDB code: 4y3o:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Ribosomal Oxygenase NO66 in Complex with Substrate RPL8 Peptide and Ni(II) and Cofactor N-Oxalyglycine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Ribosomal Oxygenase NO66 in Complex with Substrate RPL8 Peptide and Ni(II) and Cofactor N-Oxalyglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni701 b:34.5 occ:1.00 OD2 A:ASP342 2.1 25.3 1.0 O2' A:OGA702 2.1 32.5 1.0 NE2 A:HIS405 2.3 21.9 1.0 CE1 A:HIS340 2.3 18.2 1.0 O2 A:OGA702 2.3 33.4 1.0 O A:HOH836 2.8 49.2 1.0 C2 A:OGA702 2.8 32.8 1.0 C1 A:OGA702 2.9 33.2 1.0 NE2 A:HIS340 2.9 18.4 1.0 CG A:ASP342 3.1 24.0 1.0 CD2 A:HIS405 3.2 21.6 1.0 CE1 A:HIS405 3.3 21.2 1.0 OD1 A:ASP342 3.4 24.5 1.0 ND1 A:HIS340 3.5 21.0 1.0 O1 A:OGA702 4.1 30.8 1.0 N1 A:OGA702 4.1 32.4 1.0 CD2 A:HIS340 4.2 18.3 1.0 CB C:HIS216 4.3 27.4 1.0 ND1 A:HIS405 4.4 21.6 1.0 CG A:HIS405 4.4 20.4 1.0 CB A:ASP342 4.4 20.5 1.0 N C:HIS216 4.5 28.8 1.0 CG A:HIS340 4.5 18.1 1.0 CB C:ASN215 4.6 29.1 1.0 OH A:TYR328 4.8 20.0 1.0 C4 A:OGA702 4.9 34.2 1.0 CA C:HIS216 5.0 27.3 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Ribosomal Oxygenase NO66 in Complex with Substrate RPL8 Peptide and Ni(II) and Cofactor N-Oxalyglycine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Ribosomal Oxygenase NO66 in Complex with Substrate RPL8 Peptide and Ni(II) and Cofactor N-Oxalyglycine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni701 b:32.9 occ:1.00 OD2 B:ASP342 2.1 27.7 1.0 O2' B:OGA702 2.2 35.7 1.0 CE1 B:HIS340 2.2 19.6 1.0 O B:HOH1082 2.3 50.8 1.0 O2 B:OGA702 2.3 30.5 1.0 NE2 B:HIS405 2.3 19.7 1.0 NE2 B:HIS340 2.9 20.6 1.0 C2 B:OGA702 2.9 36.4 1.0 C1 B:OGA702 3.0 35.5 1.0 CG B:ASP342 3.1 25.5 1.0 CD2 B:HIS405 3.2 17.7 1.0 CE1 B:HIS405 3.3 19.1 1.0 O B:HOH839 3.3 41.5 1.0 ND1 B:HIS340 3.4 22.3 1.0 OD1 B:ASP342 3.4 23.8 1.0 CD2 B:HIS340 4.2 19.5 1.0 N1 B:OGA702 4.2 38.4 1.0 O1 B:OGA702 4.3 29.7 1.0 CB D:HIS216 4.4 24.7 1.0 CG B:HIS340 4.4 18.0 1.0 CG B:HIS405 4.4 17.2 1.0 ND1 B:HIS405 4.4 19.1 1.0 CB B:ASP342 4.5 21.9 1.0 N D:HIS216 4.5 27.6 1.0 CB D:ASN215 4.6 27.6 1.0 C4 B:OGA702 4.7 41.4 1.0 OH B:TYR328 4.8 21.5 1.0

C.Wang, Q.Zhang, T.Hang, Y.Tao, X.Ma, M.Wu, X.Zhang, J.Zang. Structure of the Jmjc Domain-Containing Protein NO66 Complexed with Ribosomal Protein RPL8. Acta Crystallogr.,Sect.D V. 71 1955 2015.
ISSN: ESSN 1399-0047
PubMed: 26327385
DOI: 10.1107/S1399004715012948