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Sodium in PDB 3dj2: Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak

Protein crystallography data

The structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak, PDB code: 3dj2 was solved by A.A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.086, 78.751, 140.992, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25.1

Other elements in 3dj2:

The structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak also contains other interesting chemical elements:

Thallium (Tl) 11 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak (pdb code 3dj2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak, PDB code: 3dj2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3dj2

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Sodium binding site 1 out of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:36.0
occ:1.00
 O A:HOH315 2.4 22.6 1.0
O A:HOH414 2.4 19.0 1.0
N7 A:G146 3.1 27.8 1.0
O A:HOH415 3.6 21.4 1.0
O6 A:G146 3.6 27.9 1.0
N7 A:G147 3.7 26.7 1.0
N4 A:C145 3.8 26.1 1.0
C5 A:G146 3.9 28.0 1.0
O6 A:G147 3.9 27.1 1.0
C4 A:C145 4.0 26.1 1.0
C5 A:C145 4.0 26.1 1.0
C8 A:G146 4.1 27.8 1.0
C6 A:G146 4.1 27.9 1.0
C5 A:G147 4.5 27.2 1.0
C6 A:G147 4.5 27.1 1.0
N3 A:C145 4.7 26.3 1.0
C8 A:G147 4.8 26.9 1.0
C6 A:C145 4.8 26.2 1.0

Sodium binding site 2 out of 8 in 3dj2

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Sodium binding site 2 out of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:12.2
occ:1.00
 O A:HOH321 2.2 9.8 1.0
O6 A:G71 2.4 23.0 1.0
O A:HOH344 2.5 10.8 1.0
O6 A:G20 2.6 21.3 1.0
O A:HOH310 3.3 14.9 1.0
C6 A:G71 3.4 22.6 1.0
C6 A:G20 3.6 21.4 1.0
N7 A:G71 3.9 22.1 1.0
C5 A:G71 4.0 22.6 1.0
N7 A:G20 4.1 20.4 1.0
C5 A:G20 4.2 20.9 1.0
OP2 A:C70 4.4 22.5 1.0
OP2 A:C19 4.4 25.4 1.0
O A:HOH311 4.5 11.9 1.0
N1 A:G71 4.6 22.2 1.0
N1 A:G20 4.8 21.3 1.0

Sodium binding site 3 out of 8 in 3dj2

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Sodium binding site 3 out of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:37.0
occ:1.00
 O A:HOH306 3.5 40.4 1.0
OP2 A:C130 4.0 27.7 1.0
OP1 A:A129 4.2 31.3 1.0

Sodium binding site 4 out of 8 in 3dj2

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Sodium binding site 4 out of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:21.4
occ:1.00
 O A:HOH351 2.5 18.8 1.0
OP2 A:G11 2.5 24.0 1.0
O A:HOH352 2.6 21.2 1.0
O6 A:G12 2.7 25.3 1.0
P A:G11 3.5 23.8 1.0
C6 A:G12 3.7 25.3 1.0
OP1 A:G11 3.8 24.4 1.0
N2 A:G11 4.1 23.1 1.0
O3' A:A10 4.2 25.0 1.0
N4 A:C79 4.3 24.1 1.0
O A:HOH329 4.3 8.3 1.0
OP1 A:A10 4.4 27.6 1.0
C5 A:G12 4.4 25.6 1.0
N7 A:G12 4.4 25.5 1.0
C3' A:A10 4.7 26.0 1.0
N1 A:G12 4.7 24.7 1.0
O5' A:A10 4.8 25.8 1.0
O5' A:G11 4.9 23.9 1.0
P A:A10 4.9 26.9 1.0

Sodium binding site 5 out of 8 in 3dj2

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Sodium binding site 5 out of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:27.1
occ:1.00
 O A:HOH330 2.6 6.2 1.0
OP1 A:C15 4.1 24.2 1.0
OP2 A:C132 4.2 24.1 1.0
OP1 A:G16 4.3 24.8 1.0
OP1 A:C131 4.5 25.6 1.0
OP1 A:G117 4.5 25.2 1.0
O A:HOH380 4.5 15.5 1.0
OP1 A:C132 4.6 24.6 1.0
OP2 A:G16 4.7 24.5 1.0
OP2 A:G117 4.8 24.7 1.0
P A:C132 4.9 25.3 1.0
P A:G16 5.0 23.9 1.0
P A:G117 5.0 25.4 1.0

Sodium binding site 6 out of 8 in 3dj2

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Sodium binding site 6 out of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:30.5
occ:1.00
 O A:HOH334 2.6 10.9 1.0
O6 A:G9 2.6 26.6 1.0
O A:HOH417 2.9 20.1 1.0
C6 A:G9 3.6 26.2 1.0
N7 A:G9 3.7 25.6 1.0
C5 A:G9 4.0 25.7 1.0
O A:HOH404 4.1 29.8 1.0
O6 A:G8 4.1 23.8 1.0
OP1 A:G80 4.2 22.4 1.0
O A:HOH313 4.3 9.8 1.0
N4 A:C166 4.3 22.7 1.0
O A:HOH305 4.6 14.9 1.0
C6 A:G8 4.9 23.7 1.0
N1 A:G9 4.9 26.1 1.0
C8 A:G9 4.9 26.1 1.0
N6 A:A10 4.9 26.7 1.0
O6 A:G165 5.0 25.4 1.0

Sodium binding site 7 out of 8 in 3dj2

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Sodium binding site 7 out of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:30.8
occ:1.00
 O A:HOH305 2.5 14.9 1.0
O A:HOH417 3.0 20.1 1.0
OP2 A:G8 3.5 24.9 1.0
O A:HOH403 3.5 15.8 1.0
OP1 A:C79 4.4 26.0 1.0
P A:G8 4.6 25.4 1.0
O A:HOH404 4.6 29.8 1.0
OP2 A:C79 4.8 26.7 1.0
OP1 A:G8 4.9 25.4 1.0
O5' A:G8 5.0 24.7 1.0

Sodium binding site 8 out of 8 in 3dj2

Go back to Sodium Binding Sites List in 3dj2
Sodium binding site 8 out of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na208

b:35.5
occ:1.00
 O A:HOH309 2.4 8.7 1.0
OP2 A:A133 4.1 25.0 1.0
OP2 A:G116 4.3 23.2 1.0
OP1 A:A133 4.4 26.6 1.0
OP1 A:G116 4.5 25.3 1.0
OP1 A:C132 4.5 24.6 1.0
O2' A:G83 4.6 23.1 1.0
P A:A133 4.8 25.2 1.0
P A:G116 4.9 23.4 1.0

Reference:

A.Serganov, L.Huang, D.J.Patel. Structural Insights Into Amino Acid Binding and Gene Control By A Lysine Riboswitch. Nature V. 455 1263 2008.
ISSN: ISSN 0028-0836
PubMed: 18784651
DOI: 10.1038/NATURE07326
Page generated: Mon Oct 7 08:33:54 2024

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