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Sodium in PDB 3dil: Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine

Protein crystallography data

The structure of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, PDB code: 3dil 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 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.216, 78.953, 139.988, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.9

Other elements in 3dil:

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

Magnesium (Mg) 1 atom
Potassium (K) 3 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine (pdb code 3dil). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 29 binding sites of Sodium where determined in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, PDB code: 3dil:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 29 in 3dil

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Sodium binding site 1 out of 29 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na812

b:7.5
occ:1.00
 O6 A:G71 2.4 16.2 1.0
O A:HOH1032 2.5 22.5 1.0
O A:HOH367 2.5 7.0 1.0
O A:HOH862 2.6 8.9 1.0
O A:HOH407 2.7 25.5 1.0
O A:HOH368 2.7 13.0 1.0
NA A:NA201 3.2 12.9 1.0
C6 A:G71 3.4 16.6 1.0
N1 A:G71 3.8 15.9 1.0
O A:HOH559 4.1 23.2 1.0
N4 A:C70 4.2 15.2 1.0
O A:HOH806 4.3 9.8 1.0
O A:HOH490 4.3 23.4 1.0
N7 A:G20 4.4 17.6 1.0
O A:HOH952 4.4 14.9 1.0
O A:HOH660 4.5 33.2 1.0
O A:HOH858 4.6 15.5 1.0
O A:HOH642 4.7 32.5 1.0
C5 A:G71 4.7 16.8 1.0
O A:HOH369 4.8 4.5 1.0
O6 A:G20 4.9 16.7 1.0
OP2 A:C19 4.9 21.6 1.0

Sodium binding site 2 out of 29 in 3dil

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Sodium binding site 2 out of 29 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:12.9
occ:1.00
 O A:HOH367 2.4 7.0 1.0
O6 A:G20 2.4 16.7 1.0
O A:HOH375 2.4 18.5 1.0
O6 A:G71 2.4 16.2 1.0
O A:HOH369 2.4 4.5 1.0
O A:HOH368 2.7 13.0 1.0
NA A:NA812 3.2 7.5 1.0
C6 A:G71 3.4 16.6 1.0
C6 A:G20 3.5 17.4 1.0
O A:HOH867 3.7 14.7 1.0
N7 A:G20 4.0 17.6 1.0
N7 A:G71 4.0 16.8 1.0
C5 A:G71 4.0 16.8 1.0
C5 A:G20 4.1 17.6 1.0
O A:HOH952 4.1 14.9 1.0
O A:HOH806 4.2 9.8 1.0
O A:HOH361 4.2 17.8 1.0
OP2 A:C19 4.3 21.6 1.0
O A:HOH804 4.5 6.8 1.0
N1 A:G71 4.6 15.9 1.0
N1 A:G20 4.6 17.2 1.0
OP2 A:C70 4.6 17.6 1.0
O A:HOH862 4.6 8.9 1.0
C5 A:C19 4.7 19.3 1.0
O A:HOH808 4.9 9.2 1.0

Sodium binding site 3 out of 29 in 3dil

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Sodium binding site 3 out of 29 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:13.4
occ:1.00
 O A:HOH864 2.2 14.5 1.0
O A:HOH793 2.4 11.6 1.0
O A:HOH944 2.5 12.4 1.0
O6 A:G69 2.7 16.1 1.0
N7 A:G68 2.8 17.5 1.0
O A:HOH907 2.9 14.6 1.0
O A:HOH529 3.4 26.3 1.0
C6 A:G69 3.4 16.1 1.0
C8 A:G68 3.7 17.7 1.0
N2 A:G25 3.7 13.2 1.0
N7 A:G69 3.8 16.8 1.0
N7 A:A67 3.8 17.3 1.0
C5 A:G69 3.9 16.7 1.0
C5 A:G68 3.9 17.9 1.0
O6 A:G68 4.0 17.2 1.0
C8 A:A67 4.2 17.9 1.0
OP2 A:G68 4.3 21.1 1.0
C2 A:G25 4.4 13.0 1.0
C6 A:G68 4.4 18.0 1.0
O4 A:U24 4.5 12.9 1.0
C5 A:A67 4.5 17.9 1.0
N3 A:G25 4.5 12.9 1.0
N1 A:G69 4.5 15.7 1.0
N6 A:A23 4.5 12.7 1.0
O A:HOH550 4.5 22.7 1.0
N3 A:U24 4.6 12.8 1.0
OP2 A:A67 4.6 21.6 1.0
O A:HOH374 4.7 31.3 1.0
C8 A:G69 4.9 16.3 1.0
N9 A:G68 5.0 18.2 1.0

Sodium binding site 4 out of 29 in 3dil

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Sodium binding site 4 out of 29 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:19.8
occ:1.00
 O A:HOH637 2.3 19.4 1.0
O A:HOH561 2.4 18.9 1.0
O A:HOH682 2.4 15.0 1.0
O A:HOH414 2.5 21.5 1.0
O A:HOH1202 2.5 14.9 1.0
O A:HOH1201 2.5 11.5 1.0
NA A:NA212 3.1 15.8 1.0
O A:HOH1009 4.0 21.1 1.0
O A:HOH661 4.0 37.1 1.0
OP2 A:C130 4.0 20.6 1.0
OP1 A:A129 4.1 23.0 1.0
O A:HOH985 4.3 12.3 1.0
O A:HOH883 4.3 15.0 1.0
O A:HOH953 4.4 21.3 1.0
O A:HOH415 4.9 22.4 1.0
O A:HOH426 4.9 21.5 1.0
O A:HOH1012 5.0 21.5 1.0

Sodium binding site 5 out of 29 in 3dil

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Sodium binding site 5 out of 29 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:15.3
occ:1.00
 O A:HOH1204 2.2 13.4 1.0
O A:HOH1205 2.3 22.8 1.0
O6 A:G12 2.5 16.6 1.0
O A:HOH1206 2.5 14.6 1.0
OP2 A:G11 2.5 18.2 1.0
O A:HOH1203 3.0 13.5 1.0
C6 A:G12 3.5 16.6 1.0
P A:G11 3.6 18.2 1.0
O A:HOH778 3.8 33.4 1.0
N2 A:G11 3.9 16.6 1.0
OP1 A:G11 3.9 18.9 1.0
O A:HOH712 4.0 30.2 1.0
N4 A:C79 4.2 15.5 1.0
C5 A:G12 4.3 17.1 1.0
O A:HOH919 4.3 15.8 1.0
O3' A:A10 4.4 19.5 1.0
OP1 A:A10 4.4 20.8 1.0
N1 A:G12 4.4 16.5 1.0
N7 A:G12 4.5 17.3 1.0
O A:HOH378 4.6 34.0 1.0
O5' A:A10 4.8 20.1 1.0
C3' A:A10 4.8 19.1 1.0
O A:HOH379 4.8 24.2 1.0
P A:A10 4.9 20.8 1.0
O5' A:G11 4.9 18.9 1.0
C4 A:C79 4.9 15.8 1.0
OP2 A:A10 4.9 21.2 1.0

Sodium binding site 6 out of 29 in 3dil

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Sodium binding site 6 out of 29 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:16.4
occ:1.00
 O A:HOH1210 2.3 13.0 1.0
O A:HOH1211 2.4 12.6 1.0
O A:HOH1209 2.4 9.3 1.0
O A:HOH1207 2.4 16.8 1.0
O A:HOH1208 2.5 11.4 1.0
O A:HOH1212 2.6 11.5 1.0
NA A:NA206 3.4 14.2 1.0
O A:HOH576 3.9 34.7 1.0
O A:HOH802 3.9 11.2 1.0
O A:HOH1216 4.0 10.1 1.0
O A:HOH1214 4.2 8.9 1.0
O A:HOH1217 4.3 5.7 1.0
O A:HOH747 4.4 12.6 1.0
O A:HOH938 4.4 21.6 1.0
O A:HOH749 4.5 7.6 1.0
OP1 A:C15 4.6 18.0 1.0
O A:HOH608 4.6 21.1 1.0
O A:HOH704 4.6 11.2 1.0
O2 A:C13 4.7 22.7 1.0
O A:HOH601 4.8 24.6 1.0
OP2 A:C15 4.9 17.9 1.0

Sodium binding site 7 out of 29 in 3dil

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Sodium binding site 7 out of 29 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:14.2
occ:1.00
 O A:HOH1212 2.4 11.5 1.0
O A:HOH1209 2.4 9.3 1.0
OP1 A:C131 2.5 20.2 1.0
O A:HOH1214 2.5 8.9 1.0
O A:HOH1216 2.7 10.1 1.0
O A:HOH1213 2.7 10.5 1.0
NA A:NA205 3.4 16.4 1.0
P A:C131 3.6 20.2 1.0
O A:HOH1218 3.8 13.7 1.0
O A:HOH1208 3.9 11.4 1.0
O A:HOH904 3.9 13.8 1.0
OP2 A:C131 3.9 20.2 1.0
O A:HOH1211 4.0 12.6 1.0
NA A:NA207 4.2 11.5 1.0
O3' A:C130 4.3 19.9 1.0
O A:HOH747 4.4 12.6 1.0
O A:HOH1217 4.4 5.7 1.0
O A:HOH601 4.4 24.6 1.0
O A:HOH882 4.4 11.9 1.0
O A:HOH829 4.6 16.9 1.0
O A:HOH823 4.7 11.5 1.0
O A:HOH1047 4.7 15.6 1.0
OP1 A:G117 4.8 20.4 1.0
O A:HOH938 4.8 21.6 1.0
O5' A:C131 4.9 20.0 1.0

Sodium binding site 8 out of 29 in 3dil

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Sodium binding site 8 out of 29 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:11.5
occ:1.00
 O A:HOH1219 2.3 20.6 1.0
O A:HOH1217 2.3 5.7 1.0
O A:HOH1218 2.3 13.7 1.0
O A:HOH1215 2.4 9.6 1.0
O A:HOH1216 2.4 10.1 1.0
O A:HOH1220 2.5 21.6 1.0
O A:HOH1029 3.8 25.3 1.0
O A:HOH1233 4.0 13.3 1.0
OP1 A:C15 4.0 18.0 1.0
O A:HOH1209 4.1 9.3 1.0
NA A:NA206 4.2 14.2 1.0
OP1 A:G16 4.3 19.2 1.0
O A:HOH1211 4.3 12.6 1.0
OP2 A:C132 4.4 19.6 1.0
O A:HOH1232 4.4 19.9 1.0
OP1 A:G117 4.5 20.4 1.0
O A:HOH851 4.5 25.4 1.0
OP1 A:C131 4.5 20.2 1.0
OP1 A:C132 4.6 20.8 1.0
OP2 A:G16 4.8 18.9 1.0
OP2 A:G117 4.8 19.9 1.0
P A:C132 5.0 20.4 1.0
P A:G117 5.0 20.1 1.0
P A:G16 5.0 18.5 1.0

Sodium binding site 9 out of 29 in 3dil

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Sodium binding site 9 out of 29 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na208

b:19.1
occ:1.00
 O A:HOH1221 2.3 15.4 1.0
O A:HOH1224 2.4 23.0 1.0
O A:HOH1226 2.4 13.7 1.0
O A:HOH1222 2.4 10.2 1.0
O A:HOH1225 2.5 10.6 1.0
O A:HOH1223 2.6 7.5 1.0
NA A:NA209 3.1 11.0 1.0
NA A:NA213 3.4 25.6 1.0
OP1 A:C79 4.0 19.9 1.0
O A:HOH885 4.1 21.8 1.0
O A:HOH913 4.1 13.2 1.0
OP1 A:G80 4.1 15.9 1.0
O A:HOH963 4.2 17.6 1.0
O A:HOH982 4.3 11.6 1.0
O A:HOH527 4.3 18.7 1.0
O A:HOH700 4.5 10.1 1.0
N7 A:G9 4.8 19.6 1.0
O A:HOH1228 4.8 12.2 1.0
O A:HOH1227 4.9 10.5 1.0
O A:HOH318 4.9 20.3 1.0
O A:HOH888 4.9 20.2 1.0
P A:C79 5.0 19.8 1.0

Sodium binding site 10 out of 29 in 3dil

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Sodium binding site 10 out of 29 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na209

b:11.0
occ:1.00
 O A:HOH1222 2.3 10.2 1.0
O A:HOH1228 2.4 12.2 1.0
O A:HOH1223 2.4 7.5 1.0
O6 A:G9 2.5 19.5 1.0
O A:HOH1225 2.5 10.6 1.0
O A:HOH1227 2.7 10.5 1.0
NA A:NA208 3.1 19.1 1.0
C6 A:G9 3.5 19.0 1.0
N7 A:G9 3.8 19.6 1.0
N4 A:C166 4.0 17.9 1.0
C5 A:G9 4.1 19.3 1.0
O A:HOH982 4.1 11.6 1.0
O6 A:G8 4.1 17.2 1.0
O A:HOH963 4.2 17.6 1.0
OP1 A:G80 4.2 15.9 1.0
O A:HOH700 4.5 10.1 1.0
O A:HOH1224 4.6 23.0 1.0
O6 A:G165 4.7 18.4 1.0
N1 A:G9 4.7 18.5 1.0
O A:HOH1226 4.8 13.7 1.0
N6 A:A10 4.9 19.2 1.0
O A:HOH654 4.9 31.0 1.0
O A:HOH1221 4.9 15.4 1.0
C6 A:G8 5.0 17.0 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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