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Strontium in PDB 5t83: Structure of A Guanidine-I Riboswitch From S. Acidophilus

Protein crystallography data

The structure of Structure of A Guanidine-I Riboswitch From S. Acidophilus, PDB code: 5t83 was solved by C.W.Reiss, Y.Xiong, S.A.Strobel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.71
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 49.091, 49.091, 246.341, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 22.6

Other elements in 5t83:

The structure of Structure of A Guanidine-I Riboswitch From S. Acidophilus also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iridium (Ir) 3 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the Structure of A Guanidine-I Riboswitch From S. Acidophilus (pdb code 5t83). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 9 binding sites of Strontium where determined in the Structure of A Guanidine-I Riboswitch From S. Acidophilus, PDB code: 5t83:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Strontium binding site 1 out of 9 in 5t83

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Strontium binding site 1 out of 9 in the Structure of A Guanidine-I Riboswitch From S. Acidophilus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Structure of A Guanidine-I Riboswitch From S. Acidophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr101

b:82.8
occ:1.00
 O A:HOH205 2.4 64.0 1.0
OP2 A:A14 2.5 54.5 1.0
O A:HOH209 2.6 92.9 1.0
N7 A:G15 2.6 64.9 1.0
O A:HOH204 2.7 67.2 1.0
O6 A:G15 2.8 61.9 1.0
C5 A:G15 3.3 54.1 1.0
C6 A:G15 3.3 61.5 1.0
N14 A:SPK110 3.7 0.4 1.0
C8 A:G15 3.8 58.7 1.0
P A:A14 3.9 63.3 1.0
C13 A:SPK110 4.4 0.8 1.0
OP1 A:A14 4.5 60.2 1.0
N1 A:A43 4.6 66.9 1.0
C4 A:G15 4.6 50.7 1.0
N7 A:G16 4.6 56.5 1.0
O6 A:G16 4.7 64.5 1.0
C12 A:SPK110 4.7 0.1 1.0
N1 A:G15 4.7 56.3 1.0
O5' A:A14 4.8 59.6 1.0
C2 A:A43 4.8 63.2 1.0
N9 A:G15 4.9 53.8 1.0
O3' A:U13 5.0 71.3 1.0

Strontium binding site 2 out of 9 in 5t83

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Strontium binding site 2 out of 9 in the Structure of A Guanidine-I Riboswitch From S. Acidophilus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Structure of A Guanidine-I Riboswitch From S. Acidophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr102

b:0.3
occ:1.00
 O6 A:G76 2.5 0.6 1.0
C6 A:G76 3.5 0.4 1.0
N7 A:G76 3.7 0.5 1.0
C5 A:G76 3.9 0.3 1.0
O6 A:G77 4.7 88.5 1.0
N1 A:G76 4.7 0.7 1.0
OP2 A:G84 4.9 55.4 1.0
N7 A:A75 4.9 0.7 1.0
C8 A:G76 4.9 0.8 1.0
OP2 A:A83 5.0 51.7 1.0

Strontium binding site 3 out of 9 in 5t83

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Strontium binding site 3 out of 9 in the Structure of A Guanidine-I Riboswitch From S. Acidophilus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Structure of A Guanidine-I Riboswitch From S. Acidophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr103

b:0.6
occ:1.00
 OP1 A:C86 2.2 0.8 1.0
OP2 A:G45 2.3 67.9 1.0
OP1 A:A44 3.3 60.7 1.0
P A:C86 3.4 78.0 1.0
O3' A:C85 3.5 75.5 1.0
P A:G45 3.7 70.5 1.0
OP1 A:G45 4.3 85.4 1.0
O5' A:C86 4.4 65.8 1.0
OP2 A:C86 4.4 63.3 1.0
C5' A:C86 4.5 82.3 1.0
O3' A:A44 4.6 64.3 1.0
C5' A:G45 4.7 53.7 1.0
P A:A44 4.7 68.2 1.0
C3' A:C85 4.8 67.7 1.0
O5' A:G45 4.8 64.2 1.0
C4' A:A44 4.9 61.9 1.0
C4' A:C85 5.0 79.6 1.0
C3' A:A44 5.0 56.4 1.0

Strontium binding site 4 out of 9 in 5t83

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Strontium binding site 4 out of 9 in the Structure of A Guanidine-I Riboswitch From S. Acidophilus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Structure of A Guanidine-I Riboswitch From S. Acidophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr104

b:0.3
occ:1.00
 O6 A:G17 2.8 77.1 1.0
O4 A:U18 3.2 68.3 1.0
C11 A:SPK110 3.5 0.2 1.0
N10 A:SPK110 3.5 0.8 1.0
N7 A:G38 3.7 99.2 1.0
C12 A:SPK110 3.7 0.1 1.0
C6 A:G17 3.9 67.4 1.0
C8 A:G38 4.1 0.4 1.0
C9 A:SPK110 4.1 1.0 1.0
N2 A:G34 4.2 66.5 1.0
C4 A:U18 4.2 67.4 1.0
OP2 A:G38 4.3 0.4 1.0
C5 A:G38 4.5 97.8 1.0
N3 A:U18 4.5 67.0 1.0
C2 A:G34 4.6 64.2 1.0
N1 A:G17 4.7 68.2 1.0
N1 A:G34 4.7 62.5 1.0
OP2 A:U37 4.8 99.7 1.0
C13 A:SPK110 4.8 0.8 1.0
OP2 A:G39 4.8 93.5 1.0
C5 A:G17 4.8 65.1 1.0
O4 A:U40 4.8 82.8 1.0
C5' A:G38 5.0 0.3 1.0
O6 A:G38 5.0 76.8 1.0

Strontium binding site 5 out of 9 in 5t83

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Strontium binding site 5 out of 9 in the Structure of A Guanidine-I Riboswitch From S. Acidophilus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Structure of A Guanidine-I Riboswitch From S. Acidophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr105

b:0.0
occ:1.00
 O6 A:G54 4.8 75.2 1.0
O6 A:G65 4.8 74.9 1.0
N4 A:C66 4.9 62.7 1.0

Strontium binding site 6 out of 9 in 5t83

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Strontium binding site 6 out of 9 in the Structure of A Guanidine-I Riboswitch From S. Acidophilus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Structure of A Guanidine-I Riboswitch From S. Acidophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr106

b:0.2
occ:1.00
 OP2 A:A91 2.3 84.7 1.0
O6 A:G92 2.6 80.2 1.0
N7 A:G92 2.8 97.7 1.0
O A:HOH201 2.8 74.9 1.0
OP2 A:G90 3.1 93.0 1.0
C6 A:G92 3.3 92.5 1.0
C5 A:G92 3.3 93.3 1.0
P A:A91 3.7 1.0 1.0
P A:G90 3.9 89.3 1.0
OP1 A:G90 3.9 0.7 1.0
C8 A:G92 4.0 0.3 1.0
OP1 A:A91 4.4 0.9 1.0
O5' A:G90 4.4 76.5 1.0
O3' A:G90 4.5 0.3 1.0
O5' A:A91 4.6 0.4 1.0
N1 A:G92 4.6 87.3 1.0
N2 A:G72 4.6 77.8 1.0
C4 A:G92 4.7 97.0 1.0
N6 A:A93 4.8 90.4 1.0
OP2 A:G92 4.9 0.2 1.0
C3' A:G90 5.0 0.1 1.0
N9 A:G92 5.0 0.5 1.0

Strontium binding site 7 out of 9 in 5t83

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Strontium binding site 7 out of 9 in the Structure of A Guanidine-I Riboswitch From S. Acidophilus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Structure of A Guanidine-I Riboswitch From S. Acidophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr107

b:0.3
occ:1.00
 OP2 A:C86 2.3 63.3 1.0
OP1 A:G45 2.3 85.4 1.0
OP1 A:C85 2.3 86.6 1.0
P A:C85 3.5 72.7 1.0
P A:C86 3.7 78.0 1.0
P A:G45 3.7 70.5 1.0
OP2 A:C85 3.8 86.4 1.0
N7 A:G45 3.8 68.8 1.0
O3' A:A44 4.2 64.3 1.0
OP1 A:C86 4.2 0.8 1.0
C8 A:G45 4.2 67.4 1.0
O2' A:G88 4.4 71.4 1.0
O3' A:G84 4.5 60.1 1.0
O5' A:G45 4.6 64.2 1.0
O5' A:C86 4.6 65.8 1.0
O4 A:U87 4.6 1.0 1.0
O5' A:C85 4.6 65.3 1.0
N3 A:G88 4.7 94.2 1.0
OP2 A:G45 4.7 67.9 1.0
O3' A:C85 4.7 75.5 1.0
N2 A:G88 4.7 79.9 1.0
C3' A:C85 4.9 67.7 1.0
C5' A:C85 5.0 82.1 1.0

Strontium binding site 8 out of 9 in 5t83

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Strontium binding site 8 out of 9 in the Structure of A Guanidine-I Riboswitch From S. Acidophilus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Structure of A Guanidine-I Riboswitch From S. Acidophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr108

b:0.8
occ:1.00
 OP1 A:G84 2.5 69.5 1.0
P A:G84 4.0 59.8 1.0
O3' A:A83 4.5 61.5 1.0
OP2 A:A74 4.6 91.5 1.0
OP1 A:G73 4.6 69.8 1.0
OP1 A:A74 4.7 84.2 1.0
O5' A:G84 4.8 71.8 1.0
C5' A:G84 4.8 67.8 1.0

Strontium binding site 9 out of 9 in 5t83

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Strontium binding site 9 out of 9 in the Structure of A Guanidine-I Riboswitch From S. Acidophilus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of Structure of A Guanidine-I Riboswitch From S. Acidophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr109

b:0.1
occ:1.00
 OP1 A:G7 2.5 0.7 1.0
P A:G7 3.8 88.0 1.0
N7 A:G89 3.9 90.3 1.0
O5' A:G7 3.9 81.4 1.0
O6 A:G89 4.2 90.8 1.0
O2' A:G45 4.2 58.4 1.0
C3' A:A6 4.4 0.1 1.0
C5' A:G7 4.6 77.5 1.0
O4' A:G45 4.6 60.5 1.0
O3' A:A6 4.6 0.8 1.0
OP2 A:U8 4.6 76.9 1.0
C5 A:G89 4.7 82.5 1.0
C2' A:A6 4.8 94.5 1.0
C6 A:G89 4.8 82.8 1.0
C8 A:G89 4.9 84.5 1.0
OP2 A:G7 4.9 92.5 1.0
C1' A:G45 5.0 68.1 1.0

Reference:

C.W.Reiss, Y.Xiong, S.A.Strobel. Structural Basis For Ligand Binding to the Guanidine-I Riboswitch. Structure V. 25 195 2017.
ISSN: ISSN 1878-4186
PubMed: 28017522
DOI: 10.1016/J.STR.2016.11.020
Page generated: Fri Oct 11 06:25:53 2024

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