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Thallium in PDB 2oih: Hepatitis Delta Virus Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+

Protein crystallography data

The structure of Hepatitis Delta Virus Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+, PDB code: 2oih 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) 66.49 / 2.40
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 107.962, 107.962, 189.119, 90.00, 90.00, 120.00
R / Rfree (%) 26.6 / 28.8

Thallium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Thallium atom in the Hepatitis Delta Virus Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+ (pdb code 2oih). This binding sites where shown within 5.0 Angstroms radius around Thallium atom.
In total 15 binding sites of Thallium where determined in the Hepatitis Delta Virus Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+, PDB code: 2oih:
Jump to Thallium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Thallium binding site 1 out of 15 in 2oih

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Thallium binding site 1 out of 15 in the Hepatitis Delta Virus Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+


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 Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl201

b:0.8
occ:0.65
O4 B:U163 2.5 67.0 1.0
O2 B:U120 2.5 48.4 1.0
OP1 B:C122 3.3 47.8 1.0
OP2 B:C122 3.5 47.7 1.0
C4 B:U163 3.6 65.1 1.0
C2 B:U120 3.6 50.1 1.0
O2' B:U120 3.6 50.7 1.0
P B:C122 3.8 50.8 1.0
OP1 B:U123 4.1 99.4 1.0
O6 B:G125 4.1 0.0 1.0
C5' B:C122 4.2 55.7 1.0
C5 B:U163 4.3 64.8 1.0
O5' B:U123 4.4 99.6 1.0
O B:HOH30 4.4 57.5 1.0
N3 B:U120 4.4 50.9 1.0
C5' B:U123 4.4 99.9 1.0
O5' B:C122 4.5 51.0 1.0
C1' B:U120 4.5 51.4 1.0
N1 B:U120 4.6 50.4 1.0
C2' B:U120 4.6 50.7 1.0
N3 B:U163 4.7 63.4 1.0
TL B:TL215 4.9 93.1 0.2
P B:U123 4.9 0.1 1.0

Thallium binding site 2 out of 15 in 2oih

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Thallium binding site 2 out of 15 in the Hepatitis Delta Virus Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+


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 Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl202

b:86.2
occ:0.40
N3 B:C157 2.8 56.9 1.0
O2 B:C157 2.8 55.9 1.0
C2 B:C157 3.2 55.6 1.0
C4 B:C157 3.9 57.1 1.0
N4 B:C156 4.0 66.1 1.0
N4 B:C157 4.3 56.5 1.0
N1 B:C157 4.5 55.5 1.0
C4 B:C156 4.8 65.8 1.0
N3 B:C156 5.0 66.4 1.0

Thallium binding site 3 out of 15 in 2oih

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Thallium binding site 3 out of 15 in the Hepatitis Delta Virus Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+


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 Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl203

b:86.4
occ:0.50
N7 B:G159 2.7 32.6 1.0
O6 B:G159 3.2 33.1 1.0
N7 B:G158 3.5 35.8 1.0
C5 B:G159 3.5 32.9 1.0
C5 B:G158 3.7 37.0 1.0
C6 B:G159 3.7 33.1 1.0
C8 B:G159 3.8 32.4 1.0
C6 B:G158 3.9 38.7 1.0
O6 B:G158 3.9 41.0 1.0
C8 B:G158 4.1 36.4 1.0
C4 B:G158 4.5 36.7 1.0
O4 B:U160 4.6 41.7 1.0
N9 B:G158 4.7 37.5 1.0
N1 B:G158 4.8 39.9 1.0
C4 B:G159 4.8 33.3 1.0
N9 B:G159 4.9 36.0 1.0

Thallium binding site 4 out of 15 in 2oih

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Thallium binding site 4 out of 15 in the Hepatitis Delta Virus Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+


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 Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl204

b:0.2
occ:0.40
O6 B:G169 2.4 78.3 1.0
N7 B:G169 2.8 78.4 1.0
C6 B:G169 3.1 77.9 1.0
C5 B:G169 3.3 78.3 1.0
N7 B:G168 3.8 70.1 1.0
O6 B:G168 4.0 67.2 1.0
C8 B:G169 4.0 79.5 1.0
C5 B:G168 4.2 69.4 1.0
C6 B:G168 4.2 68.7 1.0
N1 B:G169 4.5 77.6 1.0
O6 B:G170 4.6 73.3 1.0
C8 B:G168 4.6 71.9 1.0
C4 B:G169 4.6 78.5 1.0
N7 B:G170 4.9 74.7 1.0
N9 B:G169 5.0 79.9 1.0

Thallium binding site 5 out of 15 in 2oih

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Thallium binding site 5 out of 15 in the Hepatitis Delta Virus Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+


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 Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl205

b:89.0
occ:0.30
N7 B:G129 2.5 64.2 1.0
TL B:TL211 2.8 91.3 0.3
O6 B:G129 3.1 62.9 1.0
N7 B:G128 3.3 96.7 1.0
C5 B:G129 3.3 62.9 1.0
C6 B:G129 3.6 62.1 1.0
C8 B:G129 3.6 64.7 1.0
C8 B:G128 3.6 97.7 1.0
C5 B:G128 3.7 96.2 1.0
N9 B:G128 4.2 98.3 1.0
C4 B:G128 4.2 96.5 1.0
C6 B:G128 4.3 95.8 1.0
O6 B:G128 4.5 96.7 1.0
N4 B:C130 4.6 63.5 1.0
C4 B:G129 4.6 64.0 1.0
N9 B:G129 4.7 66.2 1.0
N1 B:G129 5.0 62.2 1.0

Thallium binding site 6 out of 15 in 2oih

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Thallium binding site 6 out of 15 in the Hepatitis Delta Virus Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+


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 Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl206

b:88.8
occ:0.40
O2 B:C156 2.9 64.8 1.0
O2' B:C156 3.1 61.5 1.0
C2' B:C156 3.7 61.9 1.0
C1' B:C156 3.9 62.8 1.0
C2 B:C156 4.0 65.4 1.0
O4' B:C157 4.0 52.5 1.0
N1 B:C156 4.5 64.3 1.0
C4' B:C157 4.8 51.0 1.0
C5' B:C157 4.8 52.2 1.0

Thallium binding site 7 out of 15 in 2oih

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Thallium binding site 7 out of 15 in the Hepatitis Delta Virus Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+


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 Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl207

b:0.9
occ:0.40
O2' B:U100 2.5 0.2 1.0
OP1 B:G101 2.6 83.6 1.0
N7 B:G101 2.9 75.5 1.0
C8 B:G101 3.3 76.0 1.0
O2' B:U163 3.6 59.8 1.0
P B:G101 3.7 83.8 1.0
C2' B:U100 3.8 0.4 1.0
O6 B:G102 3.8 81.1 1.0
O3' B:U100 3.8 0.3 1.0
OP2 B:G101 4.1 85.0 1.0
C5 B:G101 4.1 75.3 1.0
O2 B:U163 4.3 59.6 1.0
C3' B:U100 4.4 0.4 1.0
N9 B:G101 4.5 76.8 1.0
C2' B:U163 4.6 58.7 1.0
C6 B:G102 4.7 80.6 1.0
N7 B:G102 4.7 81.0 1.0
O6 B:G101 4.8 74.0 1.0
C6 B:G101 4.8 74.8 1.0
C4 B:G101 4.9 75.7 1.0
C1' B:U100 4.9 0.9 1.0
C2 B:U163 5.0 61.9 1.0

Thallium binding site 8 out of 15 in 2oih

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Thallium binding site 8 out of 15 in the Hepatitis Delta Virus Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+


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 Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl208

b:0.8
occ:0.35
O6 B:G139 2.5 80.8 1.0
N7 B:G139 2.7 81.2 1.0
C6 B:G139 3.1 80.4 1.0
O6 B:G138 3.1 92.2 1.0
C5 B:G139 3.2 80.5 1.0
N7 B:G138 3.3 93.3 1.0
C6 B:G138 3.4 92.1 1.0
C5 B:G138 3.5 92.7 1.0
C8 B:G139 3.9 81.8 1.0
C8 B:G138 4.3 93.5 1.0
O6 B:G140 4.3 65.3 1.0
N1 B:G138 4.4 92.1 1.0
N1 B:G139 4.4 78.9 1.0
C4 B:G138 4.5 92.9 1.0
C4 B:G139 4.5 80.4 1.0
N9 B:G139 4.9 81.8 1.0
N9 B:G138 4.9 93.5 1.0

Thallium binding site 9 out of 15 in 2oih

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Thallium binding site 9 out of 15 in the Hepatitis Delta Virus Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+


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 Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl209

b:81.7
occ:0.15
TL B:TL210 2.1 85.7 0.1
O6 B:G134 2.3 0.6 1.0
N7 B:G134 2.4 0.4 1.0
C5 B:G134 2.7 0.9 1.0
C6 B:G134 2.7 1.0 1.0
C8 B:G134 3.5 0.7 1.0
O6 B:G135 3.7 98.1 1.0
N7 B:G135 3.9 98.3 1.0
C4 B:G134 3.9 0.7 1.0
N1 B:G134 4.0 0.7 1.0
N4 B:C133 4.0 0.4 1.0
C4 B:C133 4.2 0.7 1.0
N9 B:G134 4.3 0.4 1.0
C6 B:G135 4.4 98.1 1.0
C5 B:G135 4.5 98.3 1.0
N3 B:C133 4.5 0.3 1.0
C5 B:C133 4.8 0.0 1.0
C2 B:G134 4.9 0.3 1.0
O6 B:G105 4.9 0.5 1.0
N3 B:G134 5.0 0.4 1.0
C8 B:G135 5.0 99.0 1.0

Thallium binding site 10 out of 15 in 2oih

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Thallium binding site 10 out of 15 in the Hepatitis Delta Virus Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 10 of Hepatitis Delta Virus Gemonic Ribozyme Precursor with C75U Mutation and Bound to Monovalent Cation Tl+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl210

b:85.7
occ:0.15
TL B:TL209 2.1 81.7 0.1
O6 B:G135 2.3 98.1 1.0
N7 B:G135 2.6 98.3 1.0
C6 B:G135 2.9 98.1 1.0
C5 B:G135 3.0 98.3 1.0
O6 B:G134 3.3 0.6 1.0
C6 B:G134 3.4 1.0 1.0
C5 B:G134 3.6 0.9 1.0
N7 B:G134 3.8 0.4 1.0
C8 B:G135 3.8 99.0 1.0
N1 B:G134 4.2 0.7 1.0
N1 B:G135 4.3 97.6 1.0
C4 B:G135 4.4 98.2 1.0
C4 B:G134 4.5 0.7 1.0
C8 B:G134 4.6 0.7 1.0
N9 B:G135 4.8 99.2 1.0
C2 B:G134 4.9 0.3 1.0
N9 B:G134 5.0 0.4 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

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