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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 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 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 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 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 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 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 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 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: Wed Dec 16 02:28:38 2020

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