Nickel in PDB 4y4r: Crystal Structure of Ribosomal Oxygenase NO66 Dimer Mutant

All present enzymatic activity of Crystal Structure of Ribosomal Oxygenase NO66 Dimer Mutant:
1.14.11.27;

The structure of Crystal Structure of Ribosomal Oxygenase NO66 Dimer Mutant, PDB code: 4y4r was solved by C.Wang, T.Hang, J.Zang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.060, 144.210, 144.210, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 27.1

The binding sites of Nickel atom in the Crystal Structure of Ribosomal Oxygenase NO66 Dimer Mutant (pdb code 4y4r). 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 Dimer Mutant, PDB code: 4y4r:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Ribosomal Oxygenase NO66 Dimer Mutant


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 Dimer Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni701 b:87.2 occ:1.00 CE1 A:HIS340 2.0 84.2 1.0 NE2 A:HIS340 2.2 92.7 1.0 NE2 A:HIS405 2.3 90.4 1.0 OXT A:ACT702 2.6 49.9 1.0 O A:HOH801 2.6 49.9 1.0 OD2 A:ASP342 2.9 97.7 1.0 O A:ACT702 3.1 54.6 1.0 CE1 A:HIS405 3.2 91.8 1.0 C A:ACT702 3.2 54.6 1.0 ND1 A:HIS340 3.2 86.3 1.0 CD2 A:HIS405 3.3 89.2 1.0 CD2 A:HIS340 3.5 0.9 1.0 CG A:HIS340 4.0 99.7 1.0 CG A:ASP342 4.1 89.6 1.0 ND1 A:HIS405 4.3 87.7 1.0 CG A:HIS405 4.4 85.2 1.0 CH3 A:ACT702 4.7 52.2 1.0 OD1 A:ASP342 4.9 82.8 1.0 CB A:ASP342 5.0 88.0 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Ribosomal Oxygenase NO66 Dimer Mutant


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 Dimer Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni701 b:0.4 occ:1.00 O B:HOH802 2.0 75.7 1.0 CE1 B:HIS340 2.2 1.0 1.0 NE2 B:HIS405 2.2 0.1 1.0 NE2 B:HIS340 2.4 0.9 1.0 OD2 B:ASP342 2.6 0.5 1.0 O B:HOH801 2.8 67.1 1.0 O B:HOH803 3.0 64.0 1.0 CE1 B:HIS405 3.2 0.8 1.0 CD2 B:HIS405 3.2 0.7 1.0 ND1 B:HIS340 3.3 0.1 1.0 CD2 B:HIS340 3.7 0.0 1.0 CG B:ASP342 3.7 0.9 1.0 CG B:HIS340 4.1 1.0 1.0 ND1 B:HIS405 4.3 0.0 1.0 OD1 B:ASP342 4.3 0.9 1.0 CG B:HIS405 4.4 0.4 1.0 CB B:ASP342 4.8 1.0 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