Thallium in PDB 1z5t: Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I.
Protein crystallography data
The structure of Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I., PDB code: 1z5t
was solved by
T.Moulaei,
T.Maehigashi,
G.T.Lountos,
S.Komeda,
D.Watkins,
M.P.Stone,
L.A.Marky,
J.S.Li,
B.Gold,
L.D.Williams,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
34.91 /
1.60
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
24.994,
41.057,
66.339,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.8 /
24.4
|
Thallium Binding Sites:
The binding sites of Thallium atom in the Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I.
(pdb code 1z5t). This binding sites where shown within
5.0 Angstroms radius around Thallium atom.
In total 8 binding sites of Thallium where determined in the
Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I., PDB code: 1z5t:
Jump to Thallium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Thallium binding site 1 out
of 8 in 1z5t
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Thallium Binding Sites List in 1z5t
Thallium binding site 1 out
of 8 in the Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I.
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 1 of Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl27
b:63.3
occ:0.22
|
O
|
A:HOH71
|
2.8
|
37.8
|
1.0
|
O
|
A:HOH38
|
2.9
|
26.6
|
1.0
|
C3'
|
A:DG12
|
3.6
|
27.3
|
1.0
|
C2'
|
A:DG12
|
4.0
|
24.0
|
1.0
|
O3'
|
A:DG12
|
4.0
|
29.3
|
1.0
|
O
|
A:HOH84
|
4.1
|
45.8
|
1.0
|
O5'
|
A:DG12
|
4.4
|
31.9
|
1.0
|
O
|
A:HOH113
|
4.7
|
55.6
|
1.0
|
OP2
|
A:DG12
|
4.9
|
46.2
|
1.0
|
C4'
|
A:DG12
|
4.9
|
25.6
|
1.0
|
|
Thallium binding site 2 out
of 8 in 1z5t
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Thallium Binding Sites List in 1z5t
Thallium binding site 2 out
of 8 in the Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I.
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 2 of Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl29
b:39.4
occ:0.16
|
N3
|
A:DG10
|
2.8
|
27.4
|
1.0
|
O4'
|
A:DC11
|
2.8
|
28.7
|
1.0
|
O
|
A:HOH48
|
2.9
|
33.4
|
1.0
|
N2
|
B:DG16
|
3.1
|
21.1
|
1.0
|
O4'
|
A:DG10
|
3.3
|
29.2
|
1.0
|
N2
|
A:DG10
|
3.5
|
20.4
|
1.0
|
C2
|
A:DG10
|
3.5
|
24.1
|
1.0
|
C1'
|
A:DG10
|
3.5
|
31.4
|
1.0
|
C4'
|
A:DC11
|
3.7
|
33.6
|
1.0
|
C4
|
A:DG10
|
3.8
|
25.7
|
1.0
|
N1
|
A:DC11
|
3.8
|
23.9
|
1.0
|
C4'
|
A:DG10
|
3.8
|
28.1
|
1.0
|
C1'
|
A:DC11
|
3.9
|
26.3
|
1.0
|
C5'
|
A:DC11
|
3.9
|
38.3
|
1.0
|
C2
|
A:DC11
|
4.0
|
28.6
|
1.0
|
O3'
|
A:DG10
|
4.0
|
33.4
|
1.0
|
N9
|
A:DG10
|
4.1
|
24.8
|
1.0
|
C6
|
A:DC11
|
4.1
|
30.2
|
1.0
|
O2
|
A:DC9
|
4.2
|
23.9
|
1.0
|
C2
|
B:DG16
|
4.3
|
21.0
|
1.0
|
O2
|
A:DC11
|
4.3
|
25.5
|
1.0
|
C3'
|
A:DG10
|
4.5
|
23.5
|
1.0
|
O
|
A:HOH35
|
4.5
|
24.1
|
1.0
|
N3
|
A:DC11
|
4.5
|
22.5
|
1.0
|
C5
|
A:DC11
|
4.6
|
26.4
|
1.0
|
O5'
|
A:DC11
|
4.6
|
33.9
|
1.0
|
C2'
|
A:DG10
|
4.8
|
30.4
|
1.0
|
C4
|
A:DC11
|
4.8
|
29.0
|
1.0
|
N1
|
A:DG10
|
4.8
|
24.0
|
1.0
|
N3
|
B:DG16
|
4.9
|
21.2
|
1.0
|
|
Thallium binding site 3 out
of 8 in 1z5t
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Thallium Binding Sites List in 1z5t
Thallium binding site 3 out
of 8 in the Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I.
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 3 of Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl30
b:41.3
occ:0.16
|
O
|
B:HOH40
|
2.8
|
29.0
|
1.0
|
O2
|
A:ZDU7
|
2.8
|
23.3
|
1.0
|
O2
|
B:ZDU19
|
2.8
|
24.4
|
1.0
|
O
|
A:HOH44
|
2.8
|
33.9
|
1.0
|
O4'
|
A:ZDU8
|
3.3
|
29.5
|
1.0
|
O4'
|
B:ZDU20
|
3.3
|
28.6
|
1.0
|
C4'
|
B:ZDU20
|
3.7
|
30.8
|
1.0
|
C4'
|
A:ZDU8
|
3.8
|
26.6
|
1.0
|
C2
|
B:ZDU19
|
4.0
|
22.1
|
1.0
|
C2
|
A:ZDU7
|
4.0
|
26.1
|
1.0
|
C5'
|
B:ZDU20
|
4.0
|
33.5
|
1.0
|
C1'
|
A:ZDU8
|
4.2
|
27.0
|
1.0
|
C5'
|
A:ZDU8
|
4.2
|
29.2
|
1.0
|
C1'
|
B:ZDU19
|
4.3
|
26.4
|
1.0
|
C1'
|
B:ZDU20
|
4.3
|
28.4
|
1.0
|
C1'
|
A:ZDU7
|
4.4
|
22.3
|
1.0
|
C2
|
B:DA18
|
4.4
|
20.1
|
1.0
|
C2
|
A:DA6
|
4.5
|
21.9
|
1.0
|
O
|
B:HOH37
|
4.6
|
24.4
|
1.0
|
N1
|
B:ZDU19
|
4.6
|
26.5
|
1.0
|
N1
|
A:ZDU8
|
4.7
|
22.2
|
1.0
|
N1
|
A:ZDU7
|
4.7
|
24.6
|
1.0
|
O2
|
A:ZDU8
|
4.8
|
23.2
|
1.0
|
N1
|
B:ZDU20
|
4.8
|
24.1
|
1.0
|
C2
|
A:ZDU8
|
4.9
|
24.1
|
1.0
|
O
|
B:HOH66
|
4.9
|
42.0
|
1.0
|
O
|
A:HOH39
|
4.9
|
27.6
|
1.0
|
N3
|
A:ZDU7
|
5.0
|
19.7
|
1.0
|
O5'
|
B:ZDU20
|
5.0
|
29.2
|
1.0
|
O
|
B:HOH54
|
5.0
|
40.4
|
1.0
|
N3
|
B:ZDU19
|
5.0
|
20.8
|
1.0
|
|
Thallium binding site 4 out
of 8 in 1z5t
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Thallium Binding Sites List in 1z5t
Thallium binding site 4 out
of 8 in the Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I.
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 4 of Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl32
b:80.6
occ:0.15
|
OP1
|
A:DA6
|
2.6
|
56.1
|
1.0
|
C5'
|
A:DA6
|
2.8
|
31.1
|
1.0
|
O5'
|
A:DA6
|
3.3
|
36.7
|
1.0
|
P
|
A:DA6
|
3.5
|
44.6
|
1.0
|
C4'
|
A:DA6
|
3.9
|
37.0
|
1.0
|
O3'
|
A:DA5
|
4.1
|
46.3
|
1.0
|
C3'
|
A:DA6
|
4.3
|
28.5
|
1.0
|
OP2
|
A:DA6
|
4.8
|
53.9
|
1.0
|
O3'
|
A:DA6
|
4.9
|
34.6
|
1.0
|
|
Thallium binding site 5 out
of 8 in 1z5t
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Thallium Binding Sites List in 1z5t
Thallium binding site 5 out
of 8 in the Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I.
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 5 of Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl33
b:79.9
occ:0.15
|
O
|
A:HOH58
|
3.2
|
33.9
|
1.0
|
C2'
|
A:ZDU8
|
3.6
|
27.7
|
1.0
|
C5
|
A:DC9
|
3.8
|
27.7
|
1.0
|
C6
|
A:ZDU8
|
3.8
|
25.7
|
1.0
|
C5B
|
A:ZDU8
|
4.0
|
33.1
|
1.0
|
N1
|
A:ZDU8
|
4.4
|
22.2
|
1.0
|
C5
|
A:ZDU8
|
4.4
|
22.4
|
1.0
|
C3'
|
A:ZDU8
|
4.5
|
29.4
|
1.0
|
C1'
|
A:ZDU8
|
4.5
|
27.0
|
1.0
|
C5A
|
A:ZDU8
|
4.6
|
27.6
|
1.0
|
C6
|
A:DC9
|
4.6
|
23.2
|
1.0
|
OP2
|
A:DC9
|
4.6
|
32.8
|
1.0
|
N4
|
A:DC9
|
4.8
|
19.5
|
1.0
|
C4
|
A:DC9
|
4.8
|
24.5
|
1.0
|
O
|
A:HOH49
|
4.8
|
37.1
|
1.0
|
O5'
|
A:ZDU8
|
4.9
|
32.0
|
1.0
|
|
Thallium binding site 6 out
of 8 in 1z5t
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Thallium Binding Sites List in 1z5t
Thallium binding site 6 out
of 8 in the Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I.
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 6 of Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Tl28
b:99.6
occ:0.20
|
C7
|
A:SPM25
|
3.4
|
74.6
|
1.0
|
O
|
A:HOH82
|
3.9
|
46.3
|
1.0
|
C8
|
A:SPM25
|
4.5
|
69.9
|
1.0
|
C6
|
A:SPM25
|
4.5
|
74.3
|
1.0
|
N5
|
A:SPM25
|
4.7
|
72.1
|
1.0
|
O
|
B:HOH123
|
5.0
|
60.7
|
1.0
|
|
Thallium binding site 7 out
of 8 in 1z5t
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Thallium Binding Sites List in 1z5t
Thallium binding site 7 out
of 8 in the Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I.
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 7 of Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Tl31
b:56.4
occ:0.16
|
O
|
A:HOH106
|
2.5
|
56.1
|
1.0
|
O
|
A:HOH39
|
2.6
|
27.6
|
1.0
|
C4'
|
B:DC21
|
3.4
|
36.0
|
1.0
|
O4'
|
B:DC21
|
3.6
|
30.1
|
1.0
|
C5'
|
A:ZDU7
|
3.7
|
29.0
|
1.0
|
O
|
A:HOH103
|
3.7
|
51.1
|
1.0
|
O4'
|
A:DA6
|
4.1
|
27.4
|
1.0
|
C1'
|
A:DA6
|
4.1
|
27.6
|
1.0
|
C1'
|
B:DC21
|
4.1
|
24.8
|
1.0
|
O3'
|
B:DC21
|
4.2
|
35.9
|
1.0
|
C4'
|
A:ZDU7
|
4.2
|
29.6
|
1.0
|
O3'
|
A:DA6
|
4.3
|
34.6
|
1.0
|
O
|
A:HOH87
|
4.3
|
43.9
|
1.0
|
C5'
|
B:DC21
|
4.4
|
38.5
|
1.0
|
O4'
|
A:ZDU7
|
4.4
|
23.5
|
1.0
|
C3'
|
B:DC21
|
4.4
|
35.8
|
1.0
|
C4'
|
A:DA6
|
4.5
|
37.0
|
1.0
|
N3
|
A:DA6
|
4.6
|
23.6
|
1.0
|
O
|
A:HOH80
|
4.6
|
47.1
|
1.0
|
O2
|
B:ZDU20
|
4.7
|
26.1
|
1.0
|
O5'
|
A:ZDU7
|
4.8
|
27.2
|
1.0
|
O2
|
B:DC21
|
4.8
|
26.2
|
1.0
|
C3'
|
A:DA6
|
4.9
|
28.5
|
1.0
|
O
|
A:HOH44
|
4.9
|
33.9
|
1.0
|
C2'
|
B:DC21
|
5.0
|
32.4
|
1.0
|
|
Thallium binding site 8 out
of 8 in 1z5t
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Thallium Binding Sites List in 1z5t
Thallium binding site 8 out
of 8 in the Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I.
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 8 of Crystal Structure of [D(Cgcgaa(Z3DU)(Z3DU)Cgcg)]2, Z3DU:5-(3- Aminopropyl)-2'-Deoxyuridine, in Presence of Thallium I. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Tl34
b:88.0
occ:0.15
|
O
|
B:HOH57
|
2.7
|
36.9
|
1.0
|
C4
|
B:SPM26
|
3.2
|
58.8
|
1.0
|
C6
|
B:SPM26
|
3.3
|
59.3
|
1.0
|
N5
|
B:SPM26
|
3.7
|
57.8
|
1.0
|
OP2
|
B:DG16
|
3.9
|
36.4
|
1.0
|
C8
|
B:DG16
|
4.2
|
20.9
|
1.0
|
O
|
B:HOH124
|
4.4
|
57.9
|
1.0
|
N7
|
B:DG16
|
4.4
|
23.0
|
1.0
|
C3
|
B:SPM26
|
4.5
|
56.6
|
1.0
|
O
|
A:HOH78
|
4.7
|
47.0
|
1.0
|
C2'
|
B:DG16
|
4.9
|
26.5
|
1.0
|
|
Reference:
T.Moulaei,
T.Maehigashi,
G.T.Lountos,
S.Komeda,
D.Watkins,
M.P.Stone,
L.A.Marky,
J.S.Li,
B.Gold,
L.D.Williams.
Structure of B-Dna with Cations Tethered in the Major Groove. Biochemistry V. 44 7458 2005.
ISSN: ISSN 0006-2960
PubMed: 15895989
DOI: 10.1021/BI050128Z
Page generated: Fri Oct 11 09:34:35 2024
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