Strontium in PDB 5tdk: Rna Decamer Duplex with Eight 2'-5'-Linkages

The structure of Rna Decamer Duplex with Eight 2'-5'-Linkages, PDB code: 5tdk was solved by Z.Luo, J.Sheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.70 / 1.43
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	24.820, 47.020, 42.880, 90.00, 96.52, 90.00
R / Rfree (%)	16.8 / 20.6

The binding sites of Strontium atom in the Rna Decamer Duplex with Eight 2'-5'-Linkages (pdb code 5tdk). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 5 binding sites of Strontium where determined in the Rna Decamer Duplex with Eight 2'-5'-Linkages, PDB code: 5tdk:
Jump to Strontium binding site number: 1; 2; 3; 4; 5;

Strontium binding site 1 out of 5 in the Rna Decamer Duplex with Eight 2'-5'-Linkages


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Rna Decamer Duplex with Eight 2'-5'-Linkages within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr101 b:30.9 occ:1.00 O A:HOH232 1.9 27.4 1.0 O A:HOH230 1.9 35.6 1.0 O A:HOH220 2.0 22.9 1.0 O A:HOH237 2.1 27.0 1.0 O A:HOH240 2.2 31.3 1.0 O B:HOH211 3.8 24.5 1.0 O A:HOH221 4.0 36.1 1.0 O B:HOH223 4.0 19.7 1.0 N7 A:G3 4.0 17.9 1.0 O6 A:G3 4.1 16.9 1.0 O6 A:G4 4.2 16.5 1.0 O B:HOH224 4.4 47.8 1.0 O A:HOH223 4.4 27.8 1.0 N7 A:G4 4.5 17.3 1.0 O A:HOH234 4.5 25.9 1.0 C5 A:G3 4.6 19.6 1.0 C6 A:G3 4.6 16.9 1.0 O A:HOH203 4.7 44.6 1.0 C8 A:G3 5.0 18.3 1.0

Strontium binding site 2 out of 5 in the Rna Decamer Duplex with Eight 2'-5'-Linkages


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Rna Decamer Duplex with Eight 2'-5'-Linkages within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr102 b:30.0 occ:1.00 O A:HOH227 2.2 24.2 1.0 O A:HOH224 2.2 28.9 1.0 O A:HOH239 2.3 32.2 1.0 O A:HOH218 2.4 25.2 1.0 N7 A:G9 4.2 17.1 1.0 O6 A:G9 4.3 16.6 1.0 O A:HOH208 4.3 29.0 1.0 O A:HOH229 4.5 30.8 1.0 N7 A:G10 4.7 17.2 1.0 O6 A:G10 4.8 19.3 1.0 C5 A:G9 4.8 14.2 1.0 C6 A:G9 4.8 14.3 1.0

Strontium binding site 3 out of 5 in the Rna Decamer Duplex with Eight 2'-5'-Linkages


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Rna Decamer Duplex with Eight 2'-5'-Linkages within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr103 b:56.2 occ:1.00 O A:HOH233 2.7 56.2 1.0 OP1 A:C7 4.1 30.7 1.0 O A:HOH238 4.7 31.8 0.5

Strontium binding site 4 out of 5 in the Rna Decamer Duplex with Eight 2'-5'-Linkages


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Rna Decamer Duplex with Eight 2'-5'-Linkages within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr104 b:29.8 occ:0.50 O A:HOH216 2.8 19.8 1.0 O B:HOH201 2.8 18.9 1.0 O2 A:C5 3.0 17.2 1.0 O A:HOH231 3.3 16.9 1.0 N2 B:G6 4.0 14.6 1.0 C2 A:C5 4.2 15.0 1.0 C1' A:C5 4.2 15.0 1.0 N2 A:G4 4.6 13.8 1.0 O3' A:C5 4.6 21.0 1.0 O4' A:C5 4.7 17.6 1.0 N1 A:C5 4.7 14.6 1.0 O4' A:G6 4.9 16.3 1.0 O2 B:C7 5.0 15.9 1.0

Strontium binding site 5 out of 5 in the Rna Decamer Duplex with Eight 2'-5'-Linkages


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Rna Decamer Duplex with Eight 2'-5'-Linkages within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr101 b:69.3 occ:1.00 O B:HOH212 2.2 23.1 1.0 O B:HOH203 2.3 28.8 1.0 N7 B:G3 3.8 17.0 1.0 O6 B:G3 3.8 16.9 1.0 O A:HOH215 4.0 23.9 1.0 C6 B:G3 4.4 18.1 1.0 C5 B:G3 4.4 17.3 1.0 O B:HOH221 4.4 34.0 1.0 O6 B:G4 4.5 16.2 1.0 O B:HOH223 4.6 19.7 1.0 N7 B:G4 4.6 16.9 1.0 C8 B:G3 4.8 18.7 1.0 N4 B:C2 4.9 17.4 1.0

F.Shen, Z.Luo, H.Liu, R.Wang, S.Zhang, J.Gan, J.Sheng. Structural Insights Into Rna Duplexes with Multiple 2 -5 -Linkages. Nucleic Acids Res. V. 45 3537 2017.
ISSN: ESSN 1362-4962
PubMed: 28034958
DOI: 10.1093/NAR/GKW1307