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Sodium in PDB 3diq: Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Homoarginine

Protein crystallography data

The structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Homoarginine, PDB code: 3diq 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 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.746, 78.794, 140.069, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.1

Other elements in 3diq:

The structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Homoarginine also contains other interesting chemical elements:

Potassium (K) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Homoarginine (pdb code 3diq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Homoarginine, PDB code: 3diq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 3diq

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Sodium binding site 1 out of 9 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Homoarginine


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 Homoarginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:21.1
occ:1.00
 O A:HOH300 2.7 27.4 1.0
O A:HOH306 2.9 2.0 1.0
OP1 A:C79 4.1 9.9 1.0
O A:HOH307 4.1 10.6 1.0
OP1 A:G80 4.2 8.7 1.0
O A:HOH301 4.2 2.0 1.0
N7 A:G9 4.3 9.5 1.0
O6 A:G9 4.6 10.8 1.0
OP2 A:C79 4.8 11.9 1.0
P A:C79 4.9 11.2 1.0

Sodium binding site 2 out of 9 in 3diq

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Sodium binding site 2 out of 9 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Homoarginine


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 Homoarginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:35.7
occ:1.00
 O6 A:G12 2.5 13.2 1.0
OP2 A:G11 2.8 5.7 1.0
C6 A:G12 3.7 11.9 1.0
P A:G11 3.8 6.9 1.0
N2 A:G11 3.9 4.4 1.0
N4 A:C79 4.0 6.3 1.0
OP1 A:G11 4.1 5.7 1.0
OP1 A:A10 4.2 9.9 1.0
O A:HOH338 4.3 2.0 1.0
O5' A:A10 4.4 7.9 1.0
O3' A:A10 4.5 6.6 1.0
OP2 A:A10 4.5 10.7 1.0
N1 A:G12 4.5 12.0 1.0
P A:A10 4.6 10.3 1.0
C5 A:G12 4.6 12.0 1.0
C3' A:A10 4.7 6.8 1.0
C4 A:C79 4.7 6.7 1.0
N7 A:G12 4.8 11.6 1.0
C5' A:A10 5.0 7.1 1.0

Sodium binding site 3 out of 9 in 3diq

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Sodium binding site 3 out of 9 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Homoarginine


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 Homoarginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:16.4
occ:1.00
 O A:HOH339 2.9 7.0 1.0
O2 A:C13 3.4 19.0 1.0
C2 A:C13 4.4 18.8 1.0
O2' A:C13 4.4 16.7 1.0
O A:HOH305 4.6 12.3 1.0
OP2 A:C15 4.9 11.1 1.0

Sodium binding site 4 out of 9 in 3diq

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Sodium binding site 4 out of 9 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Homoarginine


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 Homoarginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:18.4
occ:1.00
 O A:HOH302 2.6 2.0 1.0
OP1 A:C15 3.9 11.1 1.0
OP1 A:G117 4.2 13.7 1.0
OP2 A:C132 4.3 11.2 1.0
OP1 A:G16 4.4 9.1 1.0
OP1 A:C131 4.4 14.5 1.0
O A:HOH305 4.4 12.3 1.0
OP1 A:C132 4.7 11.2 1.0
OP2 A:G117 4.7 13.4 1.0
P A:G117 4.8 14.3 1.0
OP2 A:G16 4.8 7.7 1.0
O3' A:G116 5.0 13.4 1.0
P A:C132 5.0 12.1 1.0

Sodium binding site 5 out of 9 in 3diq

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Sodium binding site 5 out of 9 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Homoarginine


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 Homoarginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:23.9
occ:1.00
 O A:HOH312 2.8 9.1 1.0
OP2 A:A133 3.2 10.6 1.0
O A:HOH311 3.3 13.1 1.0
OP1 A:A133 3.6 12.0 1.0
P A:A133 3.9 11.4 1.0
O2' A:G83 4.3 8.9 1.0
OP2 A:G116 4.9 11.2 1.0
O3' A:C132 4.9 11.5 1.0
OP1 A:C132 5.0 11.2 1.0

Sodium binding site 6 out of 9 in 3diq

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Sodium binding site 6 out of 9 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Homoarginine


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 Homoarginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:12.8
occ:1.00
 O6 A:G20 2.4 9.8 1.0
O6 A:G71 2.7 8.5 1.0
N7 A:G71 3.5 8.6 1.0
C6 A:G71 3.5 7.8 1.0
C6 A:G20 3.5 9.8 1.0
C5 A:G71 3.8 7.9 1.0
OP2 A:C70 4.2 7.0 1.0
C5 A:G20 4.3 10.0 1.0
N7 A:G20 4.3 9.8 1.0
O A:HOH329 4.4 7.1 1.0
N1 A:G20 4.6 9.6 1.0
C8 A:G71 4.7 8.3 1.0
OP2 A:C19 4.8 11.9 1.0
N1 A:G71 4.8 7.5 1.0
C5 A:C70 5.0 10.1 1.0

Sodium binding site 7 out of 9 in 3diq

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Sodium binding site 7 out of 9 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Homoarginine


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 Homoarginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:20.9
occ:1.00
 O A:HOH308 2.6 4.3 1.0
N7 A:G68 2.9 8.7 1.0
O6 A:G69 3.0 10.7 1.0
C8 A:G68 3.6 9.0 1.0
C6 A:G69 3.8 10.0 1.0
N2 A:G25 3.8 12.4 1.0
N7 A:G69 3.9 9.0 1.0
OP2 A:G68 3.9 13.3 1.0
N7 A:A67 3.9 14.7 1.0
C8 A:A67 4.1 15.0 1.0
C5 A:G69 4.1 9.3 1.0
C5 A:G68 4.2 8.5 1.0
OP2 A:A67 4.3 18.7 1.0
O6 A:G68 4.5 9.2 1.0
C5 A:A67 4.7 14.3 1.0
C2 A:G25 4.7 12.5 1.0
C6 A:G68 4.7 8.8 1.0
O5' A:A67 4.8 18.0 1.0
N6 A:A23 4.8 6.4 1.0
N9 A:A67 4.9 15.0 1.0
N1 A:G69 4.9 9.6 1.0
N9 A:G68 4.9 9.3 1.0
O4 A:U24 5.0 14.0 1.0
C3' A:A67 5.0 15.9 1.0

Sodium binding site 8 out of 9 in 3diq

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Sodium binding site 8 out of 9 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Homoarginine


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 Homoarginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na208

b:27.0
occ:1.00
 OP2 A:C130 4.0 18.4 1.0
OP2 A:C131 4.8 14.7 1.0
OP2 A:G118 4.8 17.2 1.0
P A:C130 5.0 18.8 1.0
OP1 A:C130 5.0 18.6 1.0

Sodium binding site 9 out of 9 in 3diq

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Sodium binding site 9 out of 9 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Homoarginine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Homoarginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na209

b:19.7
occ:1.00
 N7 A:G147 3.0 27.6 1.0
C8 A:G147 3.6 27.9 1.0
N7 A:G146 4.0 27.0 1.0
C5 A:G147 4.2 27.6 1.0
C8 A:G146 4.4 27.0 1.0
OP2 A:G147 4.5 31.2 1.0
C5 A:G146 4.6 26.7 1.0
O6 A:G147 4.7 27.8 1.0
OP2 A:G146 4.8 26.5 1.0
C6 A:G147 4.9 27.8 1.0
N9 A:G147 4.9 28.2 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 08:26:56 2024

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