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

Enzymatic activity of 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;

Protein crystallography data

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

Nickel Binding Sites:

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 4y3o

Go back to Nickel Binding Sites List in 4y3o
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 4y3o

Go back to Nickel Binding Sites List in 4y3o
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

Reference:

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
Page generated: Wed Dec 16 01:38:14 2020

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