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Thallium 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:

Cobalt (Co) 2 atoms

Thallium Binding Sites:

The binding sites of Thallium 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 Thallium atom.
In total 9 binding sites of Thallium 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 Thallium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Thallium binding site 1 out of 9 in 2oj3

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Thallium binding site 1 out of 9 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 Thallium with other atoms in the Tl 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:Tl202

b:97.7
occ:0.40
 N3 B:C157 2.8 84.0 1.0
O2 B:C157 3.1 82.1 1.0
C2 B:C157 3.3 81.7 1.0
C4 B:C157 3.9 84.0 1.0
N4 B:C157 4.2 84.2 1.0
N4 B:C156 4.5 81.6 1.0
N1 B:C157 4.7 79.6 1.0

Thallium binding site 2 out of 9 in 2oj3

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Thallium binding site 2 out of 9 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 Thallium with other atoms in the Tl 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:Tl204

b:0.1
occ:0.40
 N7 B:G169 2.6 85.7 1.0
O6 B:G169 3.4 86.6 1.0
C5 B:G169 3.5 86.0 1.0
C8 B:G169 3.6 87.5 1.0
C6 B:G169 3.8 85.6 1.0
N7 B:G168 3.9 76.6 1.0
C5 B:G168 4.2 75.6 1.0
O6 B:G168 4.2 70.8 1.0
C6 B:G168 4.4 73.5 1.0
C8 B:G168 4.6 79.1 1.0
N7 B:G170 4.6 89.1 1.0
C4 B:G169 4.7 86.4 1.0
N9 B:G169 4.8 88.8 1.0
O6 B:G170 4.9 89.3 1.0

Thallium binding site 3 out of 9 in 2oj3

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Thallium binding site 3 out of 9 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 Thallium with other atoms in the Tl binding site number 3 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:Tl207

b:0.8
occ:0.40
 O2' B:U100 2.8 0.5 1.0
OP1 B:G101 2.9 0.7 1.0
N7 B:G101 3.2 0.3 1.0
C8 B:G101 3.6 0.1 1.0
O6 B:G102 3.6 0.4 1.0
O2' B:U163 3.6 75.5 1.0
P B:G101 3.7 1.0 1.0
O3' B:U100 3.9 0.2 1.0
OP2 B:G101 4.0 0.2 1.0
C2' B:U100 4.1 0.7 1.0
O2 B:U163 4.1 77.4 1.0
C5 B:G101 4.4 0.6 1.0
C3' B:U100 4.6 0.5 1.0
C6 B:G102 4.7 0.3 1.0
C2' B:U163 4.7 74.4 1.0
N9 B:G101 4.8 0.1 1.0
N7 B:G102 4.9 0.2 1.0
C2 B:U163 4.9 78.4 1.0

Thallium binding site 4 out of 9 in 2oj3

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Thallium binding site 4 out of 9 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 Thallium with other atoms in the Tl binding site number 4 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:Tl208

b:0.2
occ:0.35
 O6 B:G139 4.1 99.6 1.0
N7 B:G138 4.2 1.0 1.0
O6 B:G138 4.2 0.7 1.0
N7 B:G139 4.3 0.2 1.0
C5 B:G138 4.7 0.6 1.0
C6 B:G138 4.7 0.1 1.0
C6 B:G139 4.9 99.8 1.0
O6 B:G140 5.0 85.1 1.0

Thallium binding site 5 out of 9 in 2oj3

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Thallium binding site 5 out of 9 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 Thallium with other atoms in the Tl binding site number 5 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:Tl209

b:77.2
occ:0.15
 N7 B:G134 3.1 0.2 1.0
O6 B:G134 3.1 0.7 1.0
C5 B:G134 3.6 0.4 1.0
C6 B:G134 3.6 0.5 1.0
O6 B:G135 3.8 0.2 1.0
C8 B:G134 4.1 0.3 1.0
N7 B:G135 4.2 0.0 1.0
N4 B:C133 4.3 0.2 1.0
C4 B:C133 4.4 0.1 1.0
N3 B:C133 4.5 0.2 1.0
C6 B:G135 4.5 0.9 1.0
C5 B:G135 4.7 0.2 1.0
C4 B:G134 4.8 0.5 1.0
N1 B:G134 4.9 0.5 1.0
O6 B:G105 4.9 0.7 1.0
C5 B:C133 5.0 0.9 1.0

Thallium binding site 6 out of 9 in 2oj3

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Thallium binding site 6 out of 9 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 Thallium with other atoms in the Tl binding site number 6 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:Tl210

b:89.2
occ:0.15
 TL B:TL212 2.8 0.6 0.2
N7 B:G110 3.0 0.7 1.0
O6 B:G110 3.0 0.9 1.0
C5 B:G110 3.4 0.5 1.0
C6 B:G110 3.4 0.4 1.0
N7 B:G111 3.9 0.7 1.0
C8 B:G110 4.0 0.9 1.0
O6 B:G111 4.3 0.5 1.0
C4 B:G110 4.5 0.8 1.0
N1 B:G110 4.6 0.8 1.0
C5 B:G111 4.7 0.4 1.0
N9 B:G110 4.8 0.7 1.0
C6 B:G111 4.9 0.9 1.0
C8 B:G111 4.9 0.6 1.0

Thallium binding site 7 out of 9 in 2oj3

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Thallium binding site 7 out of 9 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 Thallium with other atoms in the Tl binding site number 7 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:Tl211

b:0.9
occ:0.30
 N7 B:G128 3.0 0.8 1.0
O6 B:G128 3.1 0.7 1.0
C2' B:G125 3.1 0.4 1.0
O2' B:G125 3.3 0.2 1.0
C5 B:G128 3.6 0.7 1.0
C6 B:G128 3.7 0.6 1.0
C1' B:G125 3.9 0.5 1.0
N9 B:G125 4.0 0.2 1.0
C8 B:G125 4.0 0.0 1.0
O6 B:G129 4.1 74.7 1.0
C8 B:G128 4.1 0.5 1.0
C3' B:G125 4.4 0.1 1.0
N4 B:C118 4.5 75.0 1.0
N7 B:G125 4.7 0.8 1.0
C4 B:G125 4.7 0.6 1.0
O3' B:G125 4.8 0.7 1.0
O2' B:C126 4.8 1.0 1.0
C1' B:C126 4.9 0.2 1.0
C4 B:G128 4.9 0.0 1.0
C6 B:G129 4.9 74.3 1.0
O4' B:C126 5.0 0.2 1.0

Thallium binding site 8 out of 9 in 2oj3

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Thallium binding site 8 out of 9 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 Thallium with other atoms in the Tl binding site number 8 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:Tl212

b:0.6
occ:0.20
 TL B:TL210 2.8 89.2 0.1
N7 B:G111 3.3 0.7 1.0
O6 B:G111 3.5 0.5 1.0
O4 B:U112 3.9 0.1 1.0
C5 B:G111 4.0 0.4 1.0
C6 B:G111 4.1 0.9 1.0
C8 B:G111 4.3 0.6 1.0
C4 B:U112 4.9 0.9 1.0
O6 B:G110 5.0 0.9 1.0

Thallium binding site 9 out of 9 in 2oj3

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Thallium binding site 9 out of 9 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 Thallium with other atoms in the Tl binding site number 9 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:Tl213

b:0.4
occ:0.20
 O6 B:G105 2.9 0.7 1.0
N7 B:G105 3.2 0.8 1.0
C6 B:G105 3.4 0.1 1.0
C5 B:G105 3.4 0.5 1.0
O6 B:G106 3.9 0.1 1.0
N7 B:G106 3.9 0.7 1.0
C8 B:G105 4.2 0.3 1.0
N1 B:G105 4.5 0.5 1.0
C6 B:G106 4.6 0.5 1.0
C4 B:G105 4.6 0.7 1.0
C5 B:G106 4.6 0.6 1.0
N9 B:G105 5.0 0.3 1.0
N4 B:C107 5.0 0.3 1.0
C8 B:G106 5.0 0.1 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: Fri Oct 11 09:39:20 2024

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