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

Protein crystallography data

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

Other elements in 2oj3:

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

Cobalt Binding Sites:

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 2oj3

Go back to Cobalt Binding Sites List in 2oj3
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 2oj3

Go back to Cobalt Binding Sites List in 2oj3
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

Reference:

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
Page generated: Sun Dec 13 10:38:32 2020

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