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Sodium in PDB 6yl5: Crystal Structure of the Sam-Sah Riboswitch with Sah

Protein crystallography data

The structure of Crystal Structure of the Sam-Sah Riboswitch with Sah, PDB code: 6yl5 was solved by L.Huang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.61 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 86.750, 147.610, 74.660, 90.00, 92.07, 90.00
R / Rfree (%) 17.2 / 20

Other elements in 6yl5:

The structure of Crystal Structure of the Sam-Sah Riboswitch with Sah also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Bromine (Br) 6 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of the Sam-Sah Riboswitch with Sah (pdb code 6yl5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Crystal Structure of the Sam-Sah Riboswitch with Sah, PDB code: 6yl5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in 6yl5

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Sodium binding site 1 out of 14 in the Crystal Structure of the Sam-Sah Riboswitch with Sah


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 Sam-Sah Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na103

b:62.6
occ:1.00
 O A:HOH378 2.3 63.7 1.0
O A:HOH310 2.5 54.9 1.0
O A:HOH320 3.2 34.9 1.0
HN42 A:CBV10 3.3 51.1 1.0
HN41 A:CBV10 3.4 51.1 1.0
H61 A:A11 3.5 41.7 1.0
H62 A:A11 3.5 41.7 1.0
O A:HOH361 3.7 39.3 1.0
O A:HOH385 3.7 56.7 1.0
N4 A:CBV10 3.7 42.5 1.0
O4 A:U28 3.7 34.7 1.0
O A:HOH374 3.7 45.8 1.0
N6 A:A11 3.8 34.7 1.0
O6 A:G29 4.1 38.4 1.0
O A:HOH382 4.1 43.2 1.0
O A:HOH317 4.3 63.3 1.0
NA A:NA104 4.9 45.2 1.0
C4 A:U28 4.9 37.9 1.0
C4 A:CBV10 5.0 40.5 1.0

Sodium binding site 2 out of 14 in 6yl5

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Sodium binding site 2 out of 14 in the Crystal Structure of the Sam-Sah Riboswitch with Sah


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 Sam-Sah Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na104

b:45.2
occ:1.00
 OP2 A:G27 2.6 36.2 1.0
O A:HOH374 2.9 45.8 1.0
O A:HOH385 3.0 56.7 1.0
H8 A:G27 3.1 45.5 1.0
N7 A:G27 3.1 32.2 1.0
OP2 A:C26 3.1 36.3 1.0
O A:HOH320 3.3 34.9 1.0
C8 A:G27 3.4 37.9 1.0
O A:HOH367 3.5 58.4 1.0
P A:C26 3.7 34.5 1.0
O5' A:C26 3.8 32.9 1.0
OP1 A:C26 3.9 33.1 1.0
P A:G27 3.9 36.7 1.0
H3' A:C26 4.1 47.6 1.0
O5' A:G27 4.1 35.4 1.0
H5 A:U28 4.3 49.0 1.0
H5'' A:C26 4.3 44.4 1.0
C5 A:G27 4.4 32.7 1.0
C5' A:C26 4.6 37.0 1.0
N9 A:G27 4.7 34.9 1.0
O4 A:U28 4.8 34.7 1.0
C3' A:C26 4.8 39.6 1.0
NA A:NA103 4.9 62.6 1.0
H3' A:G27 4.9 42.2 1.0
O3' A:C26 4.9 35.7 1.0
C5 A:U28 5.0 40.8 1.0

Sodium binding site 3 out of 14 in 6yl5

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Sodium binding site 3 out of 14 in the Crystal Structure of the Sam-Sah Riboswitch with Sah


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 Sam-Sah Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na105

b:60.0
occ:1.00
 O A:HOH323 2.7 49.1 1.0
O2 A:U28 3.0 32.7 1.0
O2 A:C12 3.1 32.6 1.0
H1' A:C12 3.4 43.3 1.0
H2 A:A11 3.4 36.3 1.0
H1' A:G29 3.5 50.9 1.0
H1' A:U28 3.9 51.8 1.0
H21 A:G27 3.9 41.9 1.0
HO2' A:C12 4.1 41.1 1.0
O2' A:C12 4.1 34.2 1.0
C2 A:C12 4.2 31.7 1.0
C2 A:U28 4.2 32.6 1.0
C2 A:A11 4.2 30.2 1.0
HO2' A:G29 4.2 44.1 1.0
C1' A:C12 4.2 36.1 1.0
O2' A:U28 4.3 40.3 1.0
C1' A:G29 4.3 42.4 1.0
N2 A:G27 4.4 34.8 1.0
H22 A:G27 4.4 41.9 1.0
O A:HOH360 4.4 52.9 1.0
O4' A:G29 4.5 38.0 1.0
N3 A:A11 4.6 34.0 1.0
C2' A:C12 4.6 30.4 1.0
C1' A:U28 4.6 43.1 1.0
H2' A:U28 4.7 46.4 1.0
H2' A:C12 4.7 36.5 1.0
N1 A:C12 4.7 31.5 1.0
HO2' A:U28 4.7 48.4 1.0
C2' A:U28 4.8 38.6 1.0
N1 A:U28 4.9 35.6 1.0
N9 A:G29 5.0 36.0 1.0

Sodium binding site 4 out of 14 in 6yl5

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Sodium binding site 4 out of 14 in the Crystal Structure of the Sam-Sah Riboswitch with Sah


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 Sam-Sah Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na106

b:63.0
occ:1.00
 H1 A:G25 2.0 33.2 1.0
O A:HOH301 2.4 49.2 1.0
OXT A:SAH101 2.4 43.3 1.0
O A:HOH309 2.6 43.3 1.0
N1 A:G25 2.9 27.6 1.0
H21 A:G25 2.9 39.3 1.0
N7 A:A13 3.2 37.3 1.0
C A:SAH101 3.3 48.4 1.0
N2 A:G25 3.5 32.7 1.0
C8 A:A13 3.5 32.7 1.0
O6 A:G25 3.6 33.0 1.0
C5 A:A13 3.6 32.1 1.0
C6 A:G25 3.7 30.5 1.0
C2 A:G25 3.7 30.1 1.0
O A:SAH101 3.7 42.0 1.0
O A:HOH333 3.7 46.0 1.0
H8 A:A13 3.8 39.2 1.0
H41 A:C15 3.8 40.0 1.0
O A:HOH356 3.8 53.0 1.0
H62 A:A13 4.0 40.2 1.0
O A:HOH353 4.2 38.8 1.0
C6 A:A13 4.2 31.2 1.0
N9 A:A13 4.2 33.5 1.0
C4 A:A13 4.2 29.6 1.0
HA A:SAH101 4.3 38.7 1.0
H3' A:A13 4.3 47.2 1.0
H22 A:G25 4.3 39.3 1.0
N6 A:A13 4.3 33.5 1.0
OP2 A:A14 4.4 45.0 1.0
H2' A:A13 4.4 45.8 1.0
CA A:SAH101 4.4 32.2 1.0
H42 A:C15 4.4 40.0 1.0
N4 A:C15 4.4 33.3 1.0
HB1 A:SAH101 4.5 45.2 1.0
OP2 A:A13 4.9 35.6 1.0
N3 A:G25 4.9 29.7 1.0
H61 A:A13 5.0 40.2 1.0
C5 A:G25 5.0 30.6 1.0

Sodium binding site 5 out of 14 in 6yl5

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Sodium binding site 5 out of 14 in the Crystal Structure of the Sam-Sah Riboswitch with Sah


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 Sam-Sah Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na107

b:65.0
occ:1.00
 H22 A:G8 2.9 87.4 1.0
O A:HOH369 3.3 60.5 1.0
HO2' A:C32 3.3 75.6 1.0
H1' A:C32 3.4 79.8 1.0
N2 A:G8 3.6 72.8 1.0
H21 A:G8 3.9 87.4 1.0
HO2' A:U9 4.1 80.1 1.0
O2' A:C32 4.2 63.0 1.0
C1' A:C32 4.2 66.5 1.0
H1' A:U9 4.2 58.1 1.0
O4' A:C32 4.3 65.1 1.0
H4' A:C32 4.5 71.7 1.0
C2 A:G8 4.8 54.9 1.0
O2' A:U9 4.9 66.7 1.0
C2' A:C32 4.9 71.0 1.0
O2 A:C31 4.9 50.5 1.0
C4' A:C32 5.0 59.7 1.0
N3 A:G8 5.0 51.6 1.0

Sodium binding site 6 out of 14 in 6yl5

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Sodium binding site 6 out of 14 in the Crystal Structure of the Sam-Sah Riboswitch with Sah


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 Sam-Sah Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na102

b:0.3
occ:1.00
 O3' B:A51 3.3 45.9 1.0
HO3' B:A51 3.3 55.2 1.0
H3' B:A51 3.9 51.0 1.0
C3' B:A51 4.2 42.5 1.0
H2' B:A51 4.8 61.9 1.0

Sodium binding site 7 out of 14 in 6yl5

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Sodium binding site 7 out of 14 in the Crystal Structure of the Sam-Sah Riboswitch with Sah


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 Sam-Sah Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na103

b:50.6
occ:1.00
 O B:HOH201 2.2 59.0 1.0
OP2 B:G47 2.6 33.4 1.0
H61 B:A48 2.6 38.7 1.0
N7 B:A48 2.8 33.6 1.0
N6 B:A48 3.4 32.2 1.0
H8 B:G47 3.5 36.0 1.0
O B:HOH223 3.5 50.3 1.0
H22 A:G16 3.6 36.6 1.0
H21 A:G16 3.6 36.6 1.0
N7 B:G47 3.6 33.0 1.0
C8 B:G47 3.6 30.0 1.0
C5 B:A48 3.7 28.4 1.0
P B:G47 3.7 44.6 1.0
O5' B:G47 3.7 40.5 1.0
N2 A:G16 3.8 30.5 1.0
C8 B:A48 3.9 34.7 1.0
H3' B:G47 3.9 39.8 1.0
C6 B:A48 4.0 29.1 1.0
O6 B:G49 4.0 33.7 1.0
H8 B:A48 4.1 41.7 1.0
H62 B:A48 4.1 38.7 1.0
OP2 B:A48 4.4 39.6 1.0
C5 B:G47 4.5 32.3 1.0
N7 B:G49 4.5 32.0 1.0
H3' B:G46 4.5 45.9 1.0
N9 B:G47 4.5 32.9 1.0
OP1 B:G47 4.6 47.7 1.0
C6 B:G49 4.7 32.0 1.0
H42 A:C18 4.7 38.0 1.0
C5 B:G49 4.9 31.3 1.0
C3' B:G47 4.9 33.1 1.0
C2 A:G16 4.9 33.5 1.0
C4 B:A48 4.9 31.6 1.0
C4 B:G47 5.0 32.3 1.0

Sodium binding site 8 out of 14 in 6yl5

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Sodium binding site 8 out of 14 in the Crystal Structure of the Sam-Sah Riboswitch with Sah


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 Sam-Sah Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na102

b:64.2
occ:1.00
 O E:HOH280 2.2 59.1 1.0
O E:HOH223 3.5 37.9 1.0
HN41 E:CBV10 3.5 45.1 1.0
O E:HOH267 3.6 53.6 1.0
HN42 E:CBV10 3.7 45.1 1.0
H61 E:A11 3.7 41.9 1.0
O4 E:U28 3.8 37.9 1.0
H62 E:A11 3.9 41.9 1.0
N4 E:CBV10 4.0 37.5 1.0
O E:HOH275 4.0 42.7 1.0
N6 E:A11 4.1 34.9 1.0
O6 E:G29 4.4 36.7 1.0
O E:HOH283 4.5 48.2 1.0
O E:HOH222 4.8 37.9 1.0
C4 E:U28 5.0 33.8 1.0

Sodium binding site 9 out of 14 in 6yl5

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Sodium binding site 9 out of 14 in the Crystal Structure of the Sam-Sah Riboswitch with Sah


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 Sam-Sah Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na103

b:94.8
occ:1.00
 H41 E:C31 3.1 52.2 1.0
H41 E:C32 3.2 59.9 1.0
O E:HOH274 3.5 52.1 1.0
H5 E:C31 3.7 58.9 1.0
N4 E:C32 3.9 49.9 1.0
N4 E:C31 3.9 43.5 1.0
H42 E:C32 4.0 59.9 1.0
H42 E:C31 4.4 52.2 1.0
C5 E:C31 4.4 49.1 1.0
C4 E:C31 4.6 45.6 1.0
H5 E:C32 4.9 65.8 1.0

Sodium binding site 10 out of 14 in 6yl5

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Sodium binding site 10 out of 14 in the Crystal Structure of the Sam-Sah Riboswitch with Sah


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 Sam-Sah Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na104

b:62.7
occ:1.00
 H21 E:G25 2.2 37.3 1.0
H1 E:G25 2.3 39.0 1.0
O E:HOH234 2.6 45.6 1.0
O E:SAH101 2.6 46.4 1.0
N2 E:G25 3.0 31.0 1.0
N1 E:G25 3.1 32.4 1.0
OP2 E:A14 3.1 37.2 1.0
H3' E:A13 3.1 36.6 1.0
H42 E:C15 3.3 35.4 1.0
H2' E:A13 3.4 42.7 1.0
C8 E:A13 3.5 33.8 1.0
C2 E:G25 3.5 30.7 1.0
H8 E:A13 3.6 40.6 1.0
N7 E:A13 3.6 32.0 1.0
H22 E:G25 3.7 37.3 1.0
C E:SAH101 3.7 48.1 1.0
N9 E:A13 3.8 31.5 1.0
N4 E:C15 3.9 29.4 1.0
C5 E:A13 3.9 33.4 1.0
C3' E:A13 4.0 30.4 1.0
C2' E:A13 4.0 35.6 1.0
H41 E:C15 4.0 35.4 1.0
C4 E:A13 4.1 30.0 1.0
C6 E:G25 4.2 34.4 1.0
HB1 E:SAH101 4.3 40.2 1.0
OXT E:SAH101 4.4 38.3 1.0
P E:A14 4.4 39.8 1.0
O6 E:G25 4.5 32.0 1.0
C1' E:A13 4.5 33.8 1.0
HA E:SAH101 4.5 40.8 1.0
O E:HOH243 4.5 58.5 1.0
O5' E:A13 4.6 37.8 1.0
O3' E:A13 4.7 38.0 1.0
CA E:SAH101 4.7 34.0 1.0
C6 E:A13 4.7 37.4 1.0
OP2 E:A13 4.8 40.3 1.0
N3 E:G25 4.8 31.4 1.0
H5 E:C15 4.9 42.1 1.0
N3 E:A13 4.9 31.1 1.0

Reference:

L.Huang, T.W.Liao, J.Wang, T.Ha, D.M.J.Lilley. Crystal Structure and Ligand-Induced Folding of the Sam/Sah Riboswitch. Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
PubMed: 32520325
DOI: 10.1093/NAR/GKAA493
Page generated: Tue Oct 8 15:09:26 2024

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