Cobalt in PDB 2oj3: Hepatitis Delta Virus Ribozyme Precursor Structure, with C75U Mutation, Bound to Tl+ and Cobalt Hexammine (Co(NH3) 63+)

The structure of Hepatitis Delta Virus Ribozyme Precursor Structure, with C75U Mutation, Bound to Tl+ and Cobalt Hexammine (Co(NH3) 63+), PDB code: 2oj3 was solved by A.Ke, F.Ding, J.D.Batchelor, J.A.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.07 / 2.90
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	108.607, 108.607, 188.211, 90.00, 90.00, 120.00
R / Rfree (%)	22.8 / 26.3

The structure of Hepatitis Delta Virus Ribozyme Precursor Structure, with C75U Mutation, Bound to Tl+ and Cobalt Hexammine (Co(NH3) 63+) also contains other interesting chemical elements:

Thallium

(Tl)

9 atoms

The binding sites of Cobalt atom in the Hepatitis Delta Virus Ribozyme Precursor Structure, with C75U Mutation, Bound to Tl+ and Cobalt Hexammine (Co(NH3) 63+) (pdb code 2oj3). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Hepatitis Delta Virus Ribozyme Precursor Structure, with C75U Mutation, Bound to Tl+ and Cobalt Hexammine (Co(NH3) 63+), PDB code: 2oj3:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Hepatitis Delta Virus Ribozyme Precursor Structure, with C75U Mutation, Bound to Tl+ and Cobalt Hexammine (Co(NH3) 63+)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Hepatitis Delta Virus Ribozyme Precursor Structure, with C75U Mutation, Bound to Tl+ and Cobalt Hexammine (Co(NH3) 63+) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:77.4 occ:0.80 CO B:NCO301 0.0 77.4 0.8 N5 B:NCO301 1.9 77.0 0.8 N4 B:NCO301 2.0 78.0 0.8 N2 B:NCO301 2.0 77.8 0.8 N1 B:NCO301 2.0 77.7 0.8 N6 B:NCO301 2.0 78.3 0.8 N3 B:NCO301 2.0 78.2 0.8 OP1 B:U123 3.8 0.2 1.0 O4 B:U163 3.9 81.4 1.0 N1 B:G125 4.2 0.5 1.0 C5' B:U123 4.3 0.8 1.0 O2 B:U120 4.3 68.0 1.0 N2 B:G125 4.4 0.6 1.0 C2 B:G125 4.9 0.8 1.0 O5' B:U123 4.9 0.9 1.0 P B:U123 4.9 0.3 1.0 O6 B:G125 5.0 1.0 1.0

Cobalt binding site 2 out of 2 in the Hepatitis Delta Virus Ribozyme Precursor Structure, with C75U Mutation, Bound to Tl+ and Cobalt Hexammine (Co(NH3) 63+)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Hepatitis Delta Virus Ribozyme Precursor Structure, with C75U Mutation, Bound to Tl+ and Cobalt Hexammine (Co(NH3) 63+) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co302 b:46.9 occ:0.60 CO B:NCO302 0.0 46.9 0.6 N5 B:NCO302 1.9 47.2 0.6 N2 B:NCO302 2.0 48.0 0.6 N4 B:NCO302 2.0 47.8 0.6 N6 B:NCO302 2.0 49.3 0.6 N1 B:NCO302 2.0 48.9 0.6 N3 B:NCO302 2.0 46.9 0.6 N7 B:G158 4.4 53.5 1.0 NH2 A:ARG52 4.4 42.5 1.0 O6 B:G158 4.5 53.6 1.0 O B:HOH10 4.5 67.2 1.0 O6 B:G159 4.6 58.5 1.0 O A:HOH119 4.6 86.0 1.0

A.Ke, F.Ding, J.D.Batchelor, J.A.Doudna. Structural Roles of Monovalent Cations in the Hdv Ribozyme. Structure V. 15 281 2007.
ISSN: ISSN 0969-2126
PubMed: 17355864
DOI: 10.1016/J.STR.2007.01.017