Strontium in PDB 3e5f: Crystal Structures of the Smk Box (Sam-III) Riboswitch with Se-Sam

The structure of Crystal Structures of the Smk Box (Sam-III) Riboswitch with Se-Sam, PDB code: 3e5f was solved by C.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.79 / 2.70
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	96.776, 96.776, 86.765, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 25.5

Pages:

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

Binding sites:

The binding sites of Strontium atom in the Crystal Structures of the Smk Box (Sam-III) Riboswitch with Se-Sam (pdb code 3e5f). 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 Structures of the Smk Box (Sam-III) Riboswitch with Se-Sam, PDB code: 3e5f:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

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


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 Se-Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr201 b:0.0 occ:0.50 OP1 A:A8 4.9 37.1 1.0

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


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 Se-Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr202 b:0.8 occ:1.00 O6 A:G50 4.4 36.9 1.0 O6 A:G49 4.5 35.6 1.0 N7 A:G49 4.6 29.6 1.0 N7 A:G50 4.6 31.9 1.0

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


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 Se-Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr203 b:85.9 occ:0.50 O6 A:G28 4.4 75.8 1.0 O6 A:G12 4.4 60.1 1.0 O6 A:G11 4.6 62.3 1.0 N7 A:G11 4.9 61.2 1.0

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


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 Se-Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr204 b:67.8 occ:1.00 N7 A:G46 2.9 36.2 1.0 O6 A:G46 3.0 39.9 1.0 C5 A:G46 3.6 35.3 1.0 C6 A:G46 3.6 37.3 1.0 C8 A:G46 4.1 37.1 1.0 O6 A:G42 4.2 40.3 1.0 N1 A:G42 4.5 39.8 1.0 OP2 A:A45 4.7 38.3 1.0 C6 A:G42 4.8 40.5 1.0 N4 A:C41 4.8 34.9 1.0 N7 A:G47 4.8 28.9 1.0 C4 A:G46 4.9 37.0 1.0 O6 A:G47 4.9 34.9 1.0 N1 A:G46 5.0 39.1 1.0

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


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 Se-Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr205 b:0.7 occ:1.00 OP1 A:A44 4.5 51.7 1.0 N7 A:G42 4.6 41.4 1.0 O6 A:G42 5.0 40.3 1.0

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


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 Se-Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr206 b:92.5 occ:0.50 OP1 A:A21 3.6 76.9 1.0 SR A:SR211 4.3 68.5 0.5 O6 A:G19 4.4 68.6 1.0 P A:A21 4.8 82.5 1.0

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


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 Se-Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr207 b:64.8 occ:1.00 OP2 A:C6 2.6 40.1 1.0 O A:HOH219 2.9 43.6 1.0 P A:C6 4.0 41.2 1.0 OP2 A:A29 4.4 67.5 1.0 O5' A:C6 4.6 41.8 1.0 OP1 A:G28 4.8 77.0 1.0 OP1 A:C6 4.8 40.7 1.0 OP2 A:C5 4.8 39.9 1.0 C5 A:C6 4.9 33.7 1.0 O6 A:G7 4.9 33.4 1.0 N7 A:G7 4.9 27.8 1.0 C5' A:G28 5.0 78.5 1.0

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


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 Se-Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr208 b:61.1 occ:1.00 O A:HOH217 2.8 48.4 1.0 OP2 A:U34 2.8 64.1 1.0 O6 A:G36 2.9 43.1 1.0 C6 A:G36 4.0 40.6 1.0 P A:U34 4.0 62.1 1.0 N7 A:G36 4.3 44.2 1.0 OP2 A:G31 4.3 57.9 1.0 OP1 A:U34 4.5 61.0 1.0 C5 A:G36 4.5 41.5 1.0 OP2 A:C33 4.6 64.1 1.0 C5 A:U34 4.8 59.0 1.0 O5' A:U34 4.8 62.8 1.0 C8 A:G31 4.8 34.5 1.0

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


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 Se-Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr209 b:90.7 occ:1.00 OP1 A:A38 3.1 47.6 1.0 OP2 A:A38 3.7 45.7 1.0 P A:A38 3.9 43.9 1.0 O2' A:A8 4.5 44.4 1.0 C5' A:A38 4.7 42.1 1.0 N3 A:A8 4.7 42.9 1.0 O5' A:A38 4.8 42.8 1.0

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


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 Se-Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr210 b:0.8 occ:1.00 OP1 A:G36 4.4 57.1 1.0 OP2 A:U37 4.7 46.3 1.0 OP1 A:U37 4.8 47.5 1.0 OP2 A:G46 4.9 41.5 1.0

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