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Strontium in PDB 3e5c: Crystal Structure of the Smk Box (Sam-III) Riboswitch with Sam

Protein crystallography data

The structure of Crystal Structure of the Smk Box (Sam-III) Riboswitch with Sam, PDB code: 3e5c was solved by C.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.90 / 2.25
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 97.806, 97.806, 87.138, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 22.7

Strontium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Strontium atom in the Crystal Structure of the Smk Box (Sam-III) Riboswitch with Sam (pdb code 3e5c). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 15 binding sites of Strontium where determined in the Crystal Structure of the Smk Box (Sam-III) Riboswitch with Sam, PDB code: 3e5c:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 15 in 3e5c

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Strontium binding site 1 out of 15 in the Crystal Structure of the Smk Box (Sam-III) Riboswitch with Sam


Mono view


Stereo pair view

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

b:0.3
occ:0.50
OP1 A:A8 4.7 36.9 1.0

Strontium binding site 2 out of 15 in 3e5c

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Strontium binding site 2 out of 15 in the Crystal Structure of the Smk Box (Sam-III) Riboswitch with Sam


Mono view


Stereo pair view

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

b:0.6
occ:1.00
O A:HOH251 2.8 64.8 1.0
O6 A:G50 4.3 32.0 1.0
O A:HOH262 4.4 47.7 1.0
O A:HOH277 4.5 45.6 1.0
O6 A:G49 4.5 31.1 1.0
N7 A:G49 4.7 27.3 1.0
N7 A:G50 4.7 31.1 1.0
O A:HOH265 4.9 60.7 1.0

Strontium binding site 3 out of 15 in 3e5c

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Strontium binding site 3 out of 15 in the Crystal Structure of the Smk Box (Sam-III) Riboswitch with Sam


Mono view


Stereo pair view

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

b:86.7
occ:0.50
N7 A:G11 4.5 53.9 1.0
O6 A:G12 4.5 60.1 1.0
O6 A:G11 4.5 53.1 1.0
O A:HOH259 4.7 47.2 1.0
O6 A:G28 4.8 72.9 1.0
N7 A:G12 5.0 62.4 1.0

Strontium binding site 4 out of 15 in 3e5c

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Strontium binding site 4 out of 15 in the Crystal Structure of the Smk Box (Sam-III) Riboswitch with Sam


Mono view


Stereo pair view

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

b:61.4
occ:1.00
N7 A:G46 2.9 34.6 1.0
O6 A:G46 2.9 33.2 1.0
O A:HOH223 3.0 56.2 1.0
O A:HOH231 3.3 35.7 1.0
C5 A:G46 3.5 34.1 1.0
C6 A:G46 3.5 32.8 1.0
C8 A:G46 4.0 35.4 1.0
O6 A:G42 4.3 35.2 1.0
N1 A:G42 4.6 34.4 1.0
O A:HOH248 4.7 43.5 1.0
OP2 A:A45 4.7 38.4 1.0
C6 A:G42 4.8 34.1 1.0
C4 A:G46 4.8 35.0 1.0
N4 A:C41 4.9 33.1 1.0
N7 A:G47 4.9 33.0 1.0
O6 A:G47 4.9 34.4 1.0
N1 A:G46 4.9 33.0 1.0

Strontium binding site 5 out of 15 in 3e5c

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Strontium binding site 5 out of 15 in the Crystal Structure of the Smk Box (Sam-III) Riboswitch with Sam


Mono view


Stereo pair view

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

b:95.0
occ:1.00
O A:HOH221 3.1 47.7 1.0
N7 A:G42 4.4 33.7 1.0
OP1 A:A44 4.5 41.3 1.0
O6 A:G42 4.8 35.2 1.0

Strontium binding site 6 out of 15 in 3e5c

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Strontium binding site 6 out of 15 in the Crystal Structure of the Smk Box (Sam-III) Riboswitch with Sam


Mono view


Stereo pair view

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

b:78.8
occ:0.50
OP1 A:A21 3.5 77.2 1.0
O6 A:G19 4.4 71.6 1.0
SR A:SR211 4.4 64.3 0.5
P A:A21 4.7 77.4 1.0

Strontium binding site 7 out of 15 in 3e5c

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Strontium binding site 7 out of 15 in the Crystal Structure of the Smk Box (Sam-III) Riboswitch with Sam


Mono view


Stereo pair view

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

b:64.7
occ:1.00
O A:HOH282 2.6 55.4 1.0
OP2 A:C6 2.6 36.7 1.0
O A:HOH219 3.0 39.4 1.0
P A:C6 4.0 37.3 1.0
O A:HOH222 4.0 53.3 1.0
OP2 A:A29 4.4 67.0 1.0
O5' A:C6 4.6 37.6 1.0
O A:HOH260 4.6 52.2 1.0
OP1 A:C6 4.8 39.0 1.0
C5 A:C6 4.8 29.4 1.0
O6 A:G7 4.8 36.6 1.0
N7 A:G7 4.9 30.2 1.0
OP2 A:C5 4.9 41.0 1.0
O A:HOH225 4.9 46.9 1.0
OP1 A:G28 4.9 76.4 1.0
O3' A:C5 5.0 36.9 1.0

Strontium binding site 8 out of 15 in 3e5c

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Strontium binding site 8 out of 15 in the Crystal Structure of the Smk Box (Sam-III) Riboswitch with Sam


Mono view


Stereo pair view

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

b:57.5
occ:1.00
O A:HOH224 2.4 43.8 1.0
O6 A:G36 2.8 40.0 1.0
OP2 A:U34 3.0 64.0 1.0
C6 A:G36 3.9 38.2 1.0
N7 A:G36 4.1 39.4 1.0
P A:U34 4.2 64.0 1.0
OP1 A:U34 4.4 64.3 1.0
C5 A:G36 4.4 39.1 1.0
OP2 A:G31 4.4 67.6 1.0
O A:HOH220 4.5 45.7 1.0
OP2 A:C33 4.6 61.5 1.0
C8 A:G31 4.8 42.3 1.0
C5 A:U34 4.9 56.6 1.0
OP2 A:U35 5.0 62.0 1.0

Strontium binding site 9 out of 15 in 3e5c

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Strontium binding site 9 out of 15 in the Crystal Structure of the Smk Box (Sam-III) Riboswitch with Sam


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of Crystal Structure of the Smk Box (Sam-III) Riboswitch with Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr209

b:86.6
occ:1.00
OP1 A:A38 2.8 41.0 1.0
P A:A38 3.8 37.0 1.0
OP2 A:A38 3.9 40.2 1.0
O2' A:A8 4.4 39.7 1.0
N3 A:A8 4.6 40.5 1.0
C5' A:A38 4.7 37.4 1.0
O5' A:A38 4.8 38.8 1.0

Strontium binding site 10 out of 15 in 3e5c

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Strontium binding site 10 out of 15 in the Crystal Structure of the Smk Box (Sam-III) Riboswitch with Sam


Mono view


Stereo pair view

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

b:0.5
occ:1.00
OP2 A:G46 4.7 38.9 1.0
OP1 A:G36 4.8 54.6 1.0
O A:HOH248 4.8 43.5 1.0
OP1 A:U37 4.8 44.9 1.0
OP2 A:U37 4.9 42.6 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 02:20:41 2020

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