Strontium in PDB 4tzy: Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+

The structure of Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+, PDB code: 4tzy was solved by J.Zhang, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.38 / 2.57
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	49.283, 152.313, 24.995, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.1

The structure of Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+ also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Strontium atom in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+ (pdb code 4tzy). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 7 binding sites of Strontium where determined in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+, PDB code: 4tzy:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7;

Strontium binding site 1 out of 7 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ X:Sr102 b:84.4 occ:1.00 O4 X:U31 2.7 38.9 1.0 O6 X:G32 2.9 34.5 1.0 O X:HOH214 3.1 40.1 1.0 C4 X:U31 3.7 32.7 1.0 C6 X:G32 4.1 38.7 1.0 C5 X:U31 4.5 30.3 1.0 N3 X:U31 4.7 35.5 1.0 OP2 X:A66 4.8 58.3 1.0 N7 X:G32 4.8 40.5 1.0 C5 X:G32 4.8 41.6 1.0

Strontium binding site 2 out of 7 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ X:Sr103 b:86.5 occ:1.00 O X:HOH218 2.7 52.1 1.0 O X:HOH208 2.7 55.2 1.0 O4 X:U47 2.8 33.4 1.0 O6 X:G46 3.0 32.2 1.0 O X:HOH209 3.4 23.6 1.0 C4 X:U47 3.9 30.1 1.0 C6 X:G46 3.9 30.8 1.0 N7 X:G46 4.1 34.6 1.0 C5 X:G46 4.3 30.9 1.0 N4 X:C53 4.3 25.8 1.0 C5 X:U47 4.4 28.9 1.0 N6 X:A52 4.6 32.8 1.0 OP2 X:C50 4.9 57.9 1.0 N3 X:U47 5.0 29.0 1.0

Strontium binding site 3 out of 7 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ X:Sr104 b:0.5 occ:1.00 O X:HOH216 2.9 34.3 1.0 O6 X:G43 3.7 48.1 1.0 N7 X:G43 3.8 38.5 1.0 O6 X:G44 4.1 42.3 1.0 C6 X:G43 4.3 39.2 1.0 C5 X:G43 4.3 37.6 1.0 N7 X:G44 4.7 36.7 1.0 C8 X:G43 4.8 36.6 1.0 C6 X:G44 5.0 40.1 1.0

Strontium binding site 4 out of 7 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ X:Sr105 b:0.5 occ:1.00 OP2 X:A23 2.6 45.3 1.0 P X:A23 3.9 42.6 1.0 N6 X:A21 4.2 32.4 1.0 N7 X:A21 4.2 38.1 1.0 O3' X:U22 4.2 40.2 1.0 OP1 X:A23 4.6 43.6 1.0 O2' X:U22 4.8 39.9 1.0 C5 X:A21 4.9 34.0 1.0 C6 X:A21 4.9 31.8 1.0 O4 X:U20 5.0 54.9 1.0

Strontium binding site 5 out of 7 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ X:Sr106 b:0.2 occ:1.00 O4 X:U77 3.0 55.5 1.0 N7 X:A76 3.8 41.9 1.0 C4 X:U77 4.1 53.7 1.0 N6 X:A76 4.2 46.7 1.0 C5 X:U77 4.5 52.8 1.0 C5 X:A76 4.6 44.0 1.0 N4 X:C78 4.6 77.7 1.0 C8 X:A76 4.7 39.2 1.0 C5 X:U75 4.7 37.9 1.0 C6 X:A76 4.8 47.3 1.0 C4 X:U75 4.9 37.5 1.0 O4 X:U75 4.9 37.2 1.0 N6 X:A19 5.0 57.0 1.0

Strontium binding site 6 out of 7 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ X:Sr109 b:0.7 occ:1.00 O6 X:G38 3.8 48.9 1.0 O6 X:G37 4.0 55.3 1.0 N4 X:C60 4.2 51.7 1.0 N7 X:G37 4.3 50.0 1.0 C6 X:G37 4.8 53.8 1.0 C6 X:G38 4.9 48.1 1.0 C5 X:G37 5.0 52.2 1.0

Strontium binding site 7 out of 7 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ X:Sr110 b:0.6 occ:1.00 OP1 X:A24 2.8 33.8 1.0 N7 X:G72 3.9 39.7 1.0 N7 X:A24 4.1 37.6 1.0 P X:A24 4.2 31.4 1.0 C8 X:A24 4.5 34.9 1.0 O6 X:G72 4.5 35.9 1.0 OP2 X:A24 4.7 38.8 1.0 O X:HOH213 4.7 28.3 1.0 C8 X:G72 4.8 44.0 1.0 C5 X:G72 4.8 36.9 1.0 C6 X:G72 5.0 37.6 1.0

J.Zhang, A.R.Ferre-D'amare. Dramatic Improvement of Crystals of Large Rnas By Cation Replacement and Dehydration. Structure V. 22 1363 2014.
ISSN: ISSN 0969-2126
PubMed: 25185828
DOI: 10.1016/J.STR.2014.07.011