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Strontium in PDB 3e5e: Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah

Protein crystallography data

The structure of Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah, PDB code: 3e5e was solved by C.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.81 / 2.90
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 98.418, 98.418, 86.393, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 25.9

Strontium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Strontium atom in the Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah (pdb code 3e5e). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 12 binding sites of Strontium where determined in the Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah, PDB code: 3e5e:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 12 in 3e5e

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Strontium binding site 1 out of 12 in the Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr201

b:0.9
occ:1.00
N7 A:G49 4.4 27.6 1.0
O6 A:G50 4.4 30.2 1.0
O6 A:G49 4.4 28.4 1.0
N7 A:G50 4.8 32.6 1.0

Strontium binding site 2 out of 12 in 3e5e

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Strontium binding site 2 out of 12 in the Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr202

b:0.1
occ:0.50
O6 A:G11 4.7 65.6 1.0
N7 A:G11 4.7 66.1 1.0
O6 A:G12 4.7 79.4 1.0

Strontium binding site 3 out of 12 in 3e5e

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Strontium binding site 3 out of 12 in the Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr203

b:0.4
occ:1.00
N7 A:G46 2.9 39.3 1.0
O6 A:G46 3.2 41.9 1.0
C5 A:G46 3.6 39.6 1.0
C6 A:G46 3.8 40.4 1.0
CB A:SAH220 3.9 25.7 0.0
C8 A:G46 4.0 38.8 1.0
O6 A:G42 4.2 45.9 1.0
OXT A:SAH220 4.3 25.7 0.0
C A:SAH220 4.3 25.7 0.0
OP2 A:A45 4.3 43.5 1.0
N1 A:G42 4.5 43.9 1.0
O A:SAH220 4.6 25.7 0.0
C6 A:G42 4.7 44.5 1.0
CA A:SAH220 4.8 25.7 0.0
C4 A:G46 4.9 39.8 1.0

Strontium binding site 4 out of 12 in 3e5e

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Strontium binding site 4 out of 12 in the Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr204

b:0.9
occ:1.00
N7 A:G42 4.4 44.5 1.0
OP1 A:A44 4.5 49.0 1.0

Strontium binding site 5 out of 12 in 3e5e

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Strontium binding site 5 out of 12 in the Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr205

b:0.3
occ:0.50
OP1 A:A21 3.5 82.7 1.0
O6 A:G19 4.1 82.1 1.0
P A:A21 4.8 83.1 1.0
C6 A:G19 4.9 81.8 1.0

Strontium binding site 6 out of 12 in 3e5e

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Strontium binding site 6 out of 12 in the Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr206

b:0.2
occ:1.00
O A:HOH222 2.4 49.7 1.0
OP2 A:C6 2.8 38.8 1.0
P A:C6 4.2 39.3 1.0
OP2 A:A29 4.3 88.5 1.0
O6 A:G7 4.7 32.3 1.0
O5' A:C6 4.8 37.9 1.0
N7 A:G7 4.8 27.7 1.0
C5' A:G28 4.9 96.3 1.0
OP2 A:C5 4.9 42.1 1.0

Strontium binding site 7 out of 12 in 3e5e

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Strontium binding site 7 out of 12 in the Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr207

b:83.8
occ:1.00
O6 A:G36 2.8 44.6 1.0
OP2 A:U34 3.6 87.6 1.0
C6 A:G36 3.9 43.1 1.0
OP2 A:G31 4.2 77.1 1.0
N7 A:G36 4.2 44.6 1.0
C5 A:G36 4.4 43.7 1.0
P A:U34 4.7 87.5 1.0
C8 A:G31 4.7 41.8 1.0
OP1 A:U34 4.7 87.5 1.0
O5' A:G31 4.8 73.1 1.0
OP2 A:C33 4.9 82.4 1.0

Strontium binding site 8 out of 12 in 3e5e

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Strontium binding site 8 out of 12 in the Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr208

b:96.2
occ:1.00
OP1 A:A38 2.8 47.9 1.0
P A:A38 3.8 45.2 1.0
OP2 A:A38 3.9 46.3 1.0
O2' A:A8 4.7 47.7 1.0
C5' A:A38 4.7 43.2 1.0
N3 A:A8 4.7 42.0 1.0
O5' A:A38 4.8 43.9 1.0

Strontium binding site 9 out of 12 in 3e5e

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Strontium binding site 9 out of 12 in the Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr219

b:93.0
occ:0.50
SR A:SR211 0.0 87.3 0.5
O4 A:U14 2.8 0.1 1.0
O6 A:G15 3.2 0.5 1.0
C4 A:U14 3.7 0.8 1.0
N4 A:C25 4.2 99.2 1.0
C6 A:G15 4.3 0.5 1.0
C5 A:U14 4.3 0.7 1.0
N4 A:C26 4.5 98.6 1.0
O6 A:G16 4.5 0.9 1.0
N7 A:G15 4.6 0.8 1.0
N3 A:U14 4.7 0.8 1.0
C5 A:G15 4.9 0.6 1.0

Strontium binding site 10 out of 12 in 3e5e

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Strontium binding site 10 out of 12 in the Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of Crystal Structures of the Smk Box (Sam-III) Riboswitch with Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr210

b:89.6
occ:1.00
SR A:SR212 0.0 83.9 1.0
N A:SAH220 2.3 25.7 0.0
OP2 A:A38 2.6 46.3 1.0
CA A:SAH220 2.7 25.7 0.0
C A:SAH220 3.2 25.7 0.0
OP2 A:A39 3.4 48.4 1.0
O A:SAH220 3.6 25.7 0.0
P A:A38 3.7 45.2 1.0
OXT A:SAH220 3.8 25.7 0.0
O5' A:A38 4.0 43.9 1.0
O3' A:U37 4.2 43.7 1.0
CB A:SAH220 4.2 25.7 0.0
C3' A:U37 4.5 41.7 1.0
CG A:SAH220 4.6 25.7 0.0
N7 A:A39 4.7 39.0 1.0
N4 A:C40 4.8 36.5 1.0
P A:A39 4.9 49.5 1.0

Reference:

C.Lu, A.M.Smith, R.T.Fuchs, F.Ding, K.Rajashankar, T.M.Henkin, A.Ke. Crystal Structures of the Sam-III/S(Mk) Riboswitch Reveal the Sam-Dependent Translation Inhibition Mechanism. Nat.Struct.Mol.Biol. V. 15 1076 2008.
ISSN: ISSN 1545-9993
PubMed: 18806797
DOI: 10.1038/NSMB.1494
Page generated: Wed Dec 16 02:20:43 2020

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