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Thallium in PDB 1jgr: Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions.

Protein crystallography data

The structure of Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions., PDB code: 1jgr was solved by S.B.Howerton, C.C.Sines, D.Vanderveer, L.D.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 25.944, 40.744, 66.202, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 22.2

Other elements in 1jgr:

The structure of Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Thallium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Thallium atom in the Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions. (pdb code 1jgr). This binding sites where shown within 5.0 Angstroms radius around Thallium atom.
In total 13 binding sites of Thallium where determined in the Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions., PDB code: 1jgr:
Jump to Thallium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Thallium binding site 1 out of 13 in 1jgr

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Thallium binding site 1 out of 13 in the Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions.


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 1 of Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl2103

b:23.9
occ:0.20
O A:HOH3123 1.6 35.1 0.8
O A:HOH3122 1.7 24.7 0.8
N7 A:DG1004 2.3 25.7 1.0
O6 A:DG1004 2.9 24.9 1.0
C5 A:DG1004 3.1 24.1 1.0
O A:HOH3047 3.2 39.5 1.0
C6 A:DG1004 3.3 23.1 1.0
C8 A:DG1004 3.4 25.7 1.0
O B:HOH3027 3.7 28.8 1.0
C5 A:DC1003 3.7 19.6 1.0
C6 A:DC1003 3.9 18.2 1.0
N6 A:DA1005 4.0 17.7 1.0
C4 A:DC1003 4.2 18.4 1.0
C4 A:DG1004 4.4 24.4 1.0
O A:HOH3019 4.5 31.4 1.0
N9 A:DG1004 4.5 25.1 1.0
O A:HOH3072 4.5 40.7 1.0
N1 A:DC1003 4.5 17.6 1.0
O4 B:DT2008 4.7 18.8 1.0
N1 A:DG1004 4.7 22.1 1.0
N4 A:DC1003 4.7 19.7 1.0
N3 A:DC1003 4.8 16.9 1.0
C2 A:DC1003 5.0 15.3 1.0
O A:HOH3059 5.0 38.2 1.0

Thallium binding site 2 out of 13 in 1jgr

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Thallium binding site 2 out of 13 in the Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions.


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 2 of Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl2104

b:28.3
occ:0.20
N3 A:DA1005 2.7 17.4 1.0
O B:HOH3003 2.8 13.8 0.8
O4' A:DA1006 3.1 16.4 1.0
O B:HOH3040 3.1 32.2 1.0
C2 A:DA1005 3.1 17.2 1.0
O2 B:DC2009 3.4 22.2 1.0
C4' A:DA1006 3.7 16.8 1.0
N2 A:DG1004 3.9 21.7 1.0
C4 A:DA1005 4.0 17.8 1.0
TL B:TL2109 4.0 22.2 0.1
C1' A:DA1006 4.1 14.8 1.0
C5' A:DA1006 4.2 19.3 1.0
C1' A:DA1005 4.4 19.7 1.0
N1 A:DA1005 4.5 16.9 1.0
C2 B:DC2009 4.5 22.0 1.0
N9 A:DA1006 4.6 14.6 1.0
N9 A:DA1005 4.6 19.0 1.0
O B:HOH3005 4.6 18.6 1.0
C1' B:DC2009 4.7 21.3 1.0
C4 A:DA1006 4.8 13.7 1.0
N3 A:DA1006 4.8 15.0 1.0
C2 A:DG1004 4.9 22.4 1.0
O2 B:DT2008 4.9 18.4 1.0

Thallium binding site 3 out of 13 in 1jgr

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Thallium binding site 3 out of 13 in the Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions.


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 3 of Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl2105

b:26.4
occ:0.17
O A:HOH3120 2.6 41.5 1.0
N3 A:DG1004 2.7 22.4 1.0
O4' A:DA1005 3.0 21.3 1.0
C2 A:DG1004 3.5 22.4 1.0
N2 A:DG1004 3.5 21.7 1.0
C1' A:DG1004 3.5 27.5 1.0
O4' A:DG1004 3.5 27.4 1.0
C4 A:DG1004 3.6 24.4 1.0
C4' A:DA1005 3.8 21.0 1.0
N9 A:DG1004 4.0 25.1 1.0
C5' A:DA1005 4.1 22.4 1.0
C1' A:DA1005 4.1 19.7 1.0
N9 A:DA1005 4.3 19.0 1.0
O B:HOH3104 4.4 31.2 1.0
C4' A:DG1004 4.4 25.9 1.0
N2 B:DG2010 4.5 17.3 1.0
O B:HOH3103 4.5 23.4 0.8
O3' A:DG1004 4.5 32.9 1.0
C8 A:DA1005 4.6 19.5 1.0
C4 A:DA1005 4.7 17.8 1.0
N1 A:DG1004 4.8 22.1 1.0
O5' A:DA1005 4.8 25.8 1.0
C2' A:DG1004 4.9 28.4 1.0
C3' A:DG1004 4.9 28.4 1.0
C5 A:DG1004 5.0 24.1 1.0
O2 A:DC1003 5.0 17.1 1.0

Thallium binding site 4 out of 13 in 1jgr

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Thallium binding site 4 out of 13 in the Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions.


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 4 of Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl2108

b:62.7
occ:0.10
O A:HOH3136 1.2 17.0 0.8
TL B:TL2107 1.5 26.0 0.1
MG A:MG2013 2.0 18.1 0.8
O A:HOH3139 2.1 19.9 0.8
O6 A:DG1002 2.5 16.0 1.0
O B:HOH3135 2.7 18.3 0.8
N7 A:DG1002 2.9 17.4 1.0
O A:HOH3137 3.2 17.1 0.8
C6 A:DG1002 3.2 14.5 1.0
C5 A:DG1002 3.4 15.8 1.0
O6 B:DG2010 3.4 18.9 1.0
C5 A:DC1001 3.4 16.6 1.0
O B:HOH3140 3.6 17.3 0.8
C4 A:DC1001 3.8 15.7 1.0
O A:HOH3011 3.8 26.3 1.0
C6 A:DC1001 3.9 17.3 1.0
O A:HOH3138 4.0 20.2 0.8
N4 A:DC1001 4.0 17.4 1.0
C6 B:DG2010 4.1 17.8 1.0
C8 A:DG1002 4.2 18.8 1.0
N4 A:DC1003 4.3 19.7 1.0
N3 A:DC1001 4.5 15.8 1.0
N1 A:DG1002 4.6 14.7 1.0
N1 A:DC1001 4.6 16.4 1.0
N4 B:DC2011 4.7 17.8 1.0
C4 A:DG1002 4.7 16.3 1.0
C5 B:DG2010 4.8 18.6 1.0
O B:HOH3008 4.8 24.9 1.0
O A:HOH3007 4.8 21.8 1.0
N7 B:DG2010 4.9 19.7 1.0
C2 A:DC1001 4.9 16.2 1.0
O A:HOH3034 4.9 24.4 1.0
N1 B:DG2010 5.0 17.2 1.0

Thallium binding site 5 out of 13 in 1jgr

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Thallium binding site 5 out of 13 in the Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions.


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 5 of Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl2110

b:24.9
occ:0.15
O A:HOH3116 1.6 28.3 0.8
O A:HOH3115 2.0 26.3 0.8
N7 A:DG1010 2.6 16.9 1.0
O6 A:DG1010 2.7 15.5 1.0
TL A:TL2113 2.7 25.5 0.1
C5 A:DG1010 3.2 14.6 1.0
O A:HOH3130 3.2 45.2 1.0
C6 A:DG1010 3.2 15.0 1.0
TL B:TL2102 3.5 23.9 0.3
C5 A:DC1009 3.7 14.6 1.0
C8 A:DG1010 3.8 17.3 1.0
C6 A:DC1009 4.2 14.3 1.0
C4 A:DC1009 4.2 12.9 1.0
O A:HOH3080 4.2 40.0 1.0
O A:HOH3010 4.3 21.5 1.0
C4 A:DG1010 4.5 15.4 1.0
N4 A:DC1009 4.6 13.1 1.0
N1 A:DG1010 4.6 13.6 1.0
O6 B:DG2002 4.8 16.2 1.0
N9 A:DG1010 4.8 16.5 1.0
N1 A:DC1009 5.0 14.2 1.0
N3 A:DC1009 5.0 13.6 1.0

Thallium binding site 6 out of 13 in 1jgr

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Thallium binding site 6 out of 13 in the Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions.


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 6 of Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl2111

b:24.7
occ:0.18
O4' A:DC1001 2.8 18.2 1.0
O A:HOH3079 2.9 29.8 1.0
N1 A:DC1001 3.4 16.4 1.0
C6 A:DC1001 3.5 17.3 1.0
C2 A:DC1001 3.7 16.2 1.0
C1' A:DC1001 3.7 17.6 1.0
C5 A:DC1001 3.9 16.6 1.0
C4' A:DC1001 3.9 19.2 1.0
C5' A:DC1001 4.0 19.7 1.0
N3 A:DC1001 4.1 15.8 1.0
C4 A:DC1001 4.2 15.7 1.0
O2 A:DC1001 4.3 16.9 1.0
C2' A:DC1001 4.9 19.6 1.0

Thallium binding site 7 out of 13 in 1jgr

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Thallium binding site 7 out of 13 in the Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions.


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 7 of Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl2113

b:25.5
occ:0.15
TL B:TL2102 1.4 23.9 0.3
TL A:TL2110 2.7 24.9 0.1
O6 B:DG2002 2.8 16.2 1.0
O6 A:DG1010 3.1 15.5 1.0
O A:HOH3115 3.4 26.3 0.8
C6 A:DG1010 3.5 15.0 1.0
O A:HOH3130 3.7 45.2 1.0
N7 A:DG1010 3.8 16.9 1.0
C5 A:DG1010 3.8 14.6 1.0
O A:HOH3116 3.8 28.3 0.8
C6 B:DG2002 3.9 14.2 1.0
N4 A:DC1011 4.2 19.1 1.0
N7 B:DG2002 4.2 15.9 1.0
C5 B:DC2001 4.2 21.9 1.0
N4 B:DC2001 4.2 22.8 1.0
C4 B:DC2001 4.4 20.6 1.0
C5 B:DG2002 4.4 14.6 1.0
N1 A:DG1010 4.5 13.6 1.0
C8 A:DG1010 4.8 17.3 1.0
C4 A:DG1010 4.9 15.4 1.0
O A:HOH3022 4.9 32.4 1.0

Thallium binding site 8 out of 13 in 1jgr

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Thallium binding site 8 out of 13 in the Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions.


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 8 of Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl2101

b:16.8
occ:0.34
O B:HOH3081 1.6 17.7 0.7
O B:HOH3082 1.6 21.6 0.7
N7 B:DG2004 2.8 14.2 1.0
O6 B:DG2004 3.0 12.4 1.0
O B:HOH3046 3.1 29.5 1.0
O A:HOH3026 3.2 26.5 1.0
C5 B:DG2004 3.5 12.7 1.0
O B:HOH3073 3.5 35.3 0.5
C6 B:DG2004 3.5 12.7 1.0
O B:HOH3064 3.6 36.6 1.0
C5 B:DC2003 3.6 15.3 1.0
O B:HOH3133 3.9 36.0 0.5
C8 B:DG2004 3.9 15.6 1.0
C6 B:DC2003 4.0 15.4 1.0
C4 B:DC2003 4.1 13.2 1.0
N6 B:DA2005 4.1 12.8 1.0
O B:HOH3050 4.2 31.4 1.0
N4 B:DC2003 4.5 16.2 1.0
O4 A:DT1008 4.5 12.9 1.0
N1 B:DC2003 4.6 14.7 1.0
N3 B:DC2003 4.7 13.0 1.0
C4 B:DG2004 4.8 13.7 1.0
O B:HOH3056 4.8 34.5 1.0
N1 B:DG2004 4.9 12.8 1.0
C2 B:DC2003 4.9 13.8 1.0

Thallium binding site 9 out of 13 in 1jgr

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Thallium binding site 9 out of 13 in the Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions.


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 9 of Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl2102

b:23.9
occ:0.29
TL A:TL2113 1.4 25.5 0.1
O6 B:DG2002 2.6 16.2 1.0
N7 B:DG2002 2.9 15.9 1.0
O6 A:DG1010 3.1 15.5 1.0
C6 B:DG2002 3.3 14.2 1.0
O A:HOH3115 3.4 26.3 0.8
C5 B:DG2002 3.4 14.6 1.0
TL A:TL2110 3.5 24.9 0.1
C6 A:DG1010 3.8 15.0 1.0
C5 B:DC2001 3.9 21.9 1.0
N4 B:DC2003 4.2 16.2 1.0
C8 B:DG2002 4.2 16.0 1.0
C4 B:DC2001 4.2 20.6 1.0
C6 B:DC2001 4.3 22.7 1.0
N4 B:DC2001 4.5 22.8 1.0
N1 A:DG1010 4.5 13.6 1.0
C5 A:DG1010 4.5 14.6 1.0
N1 B:DG2002 4.7 14.7 1.0
C4 B:DG2002 4.8 14.4 1.0
N7 A:DG1010 4.8 16.9 1.0
O A:HOH3116 4.8 28.3 0.8
O A:HOH3130 4.9 45.2 1.0
N3 B:DC2001 4.9 19.7 1.0
C4 B:DC2003 4.9 13.2 1.0
N4 A:DC1011 4.9 19.1 1.0
N1 B:DC2001 5.0 21.0 1.0

Thallium binding site 10 out of 13 in 1jgr

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Thallium binding site 10 out of 13 in the Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions.


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 10 of Crystal Structure Analysis of the B-Dna Dodecamer Cgcgaattcgcg with Thallium Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl2106

b:35.7
occ:0.10
O A:HOH3001 0.5 13.9 0.9
O2 B:DT2007 2.5 16.7 1.0
O2 A:DT1007 2.7 15.3 1.0
O B:HOH3024 2.9 24.5 1.0
O A:HOH3015 3.0 25.0 1.0
O4' B:DT2008 3.2 21.5 1.0
O4' A:DT1008 3.6 17.0 1.0
C4' B:DT2008 3.7 24.5 1.0
C2 B:DT2007 3.7 16.8 1.0
C2 A:DT1007 3.8 14.6 1.0
C1' B:DT2008 4.1 19.8 1.0
C4' A:DT1008 4.2 18.1 1.0
C2 A:DA1006 4.2 13.9 1.0
C5' B:DT2008 4.2 26.7 1.0
C1' B:DT2007 4.3 17.9 1.0
C1' A:DT1007 4.3 15.2 1.0
C2 B:DA2006 4.3 14.7 1.0
N1 B:DT2007 4.5 17.1 1.0
C1' A:DT1008 4.5 15.9 1.0
C5' A:DT1008 4.5 19.9 1.0
O B:HOH3005 4.5 18.6 1.0
N1 A:DT1007 4.5 14.2 1.0
N1 B:DT2008 4.7 19.0 1.0
N3 B:DT2007 4.7 15.3 1.0
N3 A:DT1007 4.8 13.6 1.0
O A:HOH3002 4.8 16.4 1.0
O2 B:DT2008 4.9 18.4 1.0
N3 A:DA1006 4.9 15.0 1.0
C2 B:DT2008 4.9 18.1 1.0
N1 A:DA1006 4.9 13.7 1.0
N1 A:DT1008 4.9 13.9 1.0
O A:HOH3083 5.0 44.0 1.0
O4' A:DT1007 5.0 15.9 1.0

Reference:

S.B.Howerton, C.C.Sines, D.Vanderveer, L.D.Williams. Locating Monovalent Cations in the Grooves of B-Dna. Biochemistry V. 40 10023 2001.
ISSN: ISSN 0006-2960
PubMed: 11513580
DOI: 10.1021/BI010391+
Page generated: Wed Dec 16 02:28:32 2020

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