Atomistry » Thallium » PDB 1f1h-4wfh » 2oj3
Atomistry »
  Thallium »
    PDB 1f1h-4wfh »
      2oj3 »

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

Go back to Thallium Binding Sites List in 2oj3
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

Go back to Thallium Binding Sites List in 2oj3
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

Go back to Thallium Binding Sites List in 2oj3
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

Go back to Thallium Binding Sites List in 2oj3
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

Go back to Thallium Binding Sites List in 2oj3
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

Go back to Thallium Binding Sites List in 2oj3
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

Go back to Thallium Binding Sites List in 2oj3
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

Go back to Thallium Binding Sites List in 2oj3
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

Go back to Thallium Binding Sites List in 2oj3
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: Wed Dec 16 02:28:39 2020

Last articles

Zn in 7O75
Zn in 7O73
Zn in 7O4I
Zn in 7O72
Zn in 7O4J
Zn in 7NVR
Zn in 7NVY
Zn in 7NVZ
Zn in 7NW0
Zn in 7O4K
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy