Caesium in PDB 9e9o: Sars-Cov-2 SL5 Crystal Structure Cesium Derivative

The structure of Sars-Cov-2 SL5 Crystal Structure Cesium Derivative, PDB code: 9e9o was solved by C.P.Jones, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 3.51
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	95.991, 95.991, 114.351, 90, 90, 120
R / Rfree (%)	16.7 / 21

The structure of Sars-Cov-2 SL5 Crystal Structure Cesium Derivative also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Caesium atom in the Sars-Cov-2 SL5 Crystal Structure Cesium Derivative (pdb code 9e9o). This binding sites where shown within 5.0 Angstroms radius around Caesium atom.
In total 7 binding sites of Caesium where determined in the Sars-Cov-2 SL5 Crystal Structure Cesium Derivative, PDB code: 9e9o:
Jump to Caesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Caesium binding site 1 out of 7 in the Sars-Cov-2 SL5 Crystal Structure Cesium Derivative


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 1 of Sars-Cov-2 SL5 Crystal Structure Cesium Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs201 b:291.2 occ:0.41 O4 A:U95 3.4 244.6 1.0 O6 A:G96 3.4 194.7 1.0 O4 A:U7 3.7 185.0 1.0 C4 A:U95 4.1 222.1 1.0 C5 A:U95 4.3 206.1 1.0 C6 A:G96 4.5 204.9 1.0 O6 A:G97 4.5 189.3 1.0 N4 A:C6 4.7 209.6 1.0 N7 A:G96 4.7 210.1 1.0 C4 A:U7 4.8 185.5 1.0 C5 A:G96 5.0 210.4 1.0

Caesium binding site 2 out of 7 in the Sars-Cov-2 SL5 Crystal Structure Cesium Derivative


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 2 of Sars-Cov-2 SL5 Crystal Structure Cesium Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs202 b:321.9 occ:0.24 C2' A:U68 4.0 358.9 1.0 O2' A:U68 4.1 327.7 1.0 N2 A:G70 4.1 276.4 1.0 N1 A:U68 4.1 360.3 1.0 C1' A:U68 4.7 371.2 1.0 O2' A:U66 4.8 359.4 1.0 O2' A:C72 4.9 275.6 1.0 O2 A:U66 4.9 336.9 1.0

Caesium binding site 3 out of 7 in the Sars-Cov-2 SL5 Crystal Structure Cesium Derivative


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 3 of Sars-Cov-2 SL5 Crystal Structure Cesium Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs203 b:316.1 occ:0.32 O6 A:G75 3.3 207.6 1.0 O6 A:G74 4.0 181.9 1.0 N4 A:C61 4.0 233.6 1.0 C6 A:G75 4.5 200.9 1.0 N7 A:G74 4.5 213.6 1.0 O4 A:U62 4.6 203.8 1.0 OP2 A:C73 4.6 240.9 1.0 C6 A:G74 4.7 203.5 1.0 O4 A:U60 4.8 190.3 1.0 N7 A:G75 4.9 168.7 1.0 C5 A:G74 4.9 207.0 1.0

Caesium binding site 4 out of 7 in the Sars-Cov-2 SL5 Crystal Structure Cesium Derivative


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 4 of Sars-Cov-2 SL5 Crystal Structure Cesium Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs204 b:333.6 occ:0.64 OP1 A:C13 2.9 183.7 1.0 O3' A:U12 3.4 189.1 1.0 P A:C13 3.4 195.5 1.0 OP2 A:C13 3.6 213.7 1.0 O4' A:A81 3.7 196.8 1.0 O2' A:U12 3.9 189.3 1.0 C5' A:A81 4.1 180.5 1.0 C4' A:A81 4.2 190.8 1.0 C3' A:U12 4.6 191.4 1.0 C2' A:U12 4.7 171.7 1.0 O5' A:A81 4.9 179.3 1.0 C1' A:A81 4.9 188.4 1.0 O5' A:C13 4.9 131.6 1.0

Caesium binding site 5 out of 7 in the Sars-Cov-2 SL5 Crystal Structure Cesium Derivative


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 5 of Sars-Cov-2 SL5 Crystal Structure Cesium Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs205 b:249.7 occ:0.25 O3' A:A81 2.9 128.2 1.0 OP1 A:C82 2.9 174.3 1.0 P A:C82 3.4 175.2 1.0 C5' A:C82 3.5 157.8 1.0 O2 A:U79 3.6 156.0 1.0 O5' A:C82 3.9 161.2 1.0 O2 A:C58 4.0 186.7 1.0 O2' A:A81 4.1 185.0 1.0 C3' A:A81 4.1 157.1 1.0 C1' A:C58 4.5 181.9 1.0 C4' A:A81 4.6 190.8 1.0 O2' A:C58 4.6 172.1 1.0 O2' A:U79 4.6 158.4 1.0 N2 A:G78 4.7 166.0 1.0 C2 A:U79 4.7 166.1 1.0 C1' A:U79 4.7 147.5 1.0 C2' A:A81 4.7 177.3 1.0 OP2 A:C82 4.8 153.4 1.0 C2 A:C58 4.8 168.7 1.0 C4' A:C82 4.9 166.3 1.0 C2 A:A57 5.0 169.1 1.0

Caesium binding site 6 out of 7 in the Sars-Cov-2 SL5 Crystal Structure Cesium Derivative


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 6 of Sars-Cov-2 SL5 Crystal Structure Cesium Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs206 b:236.7 occ:0.25 O2 A:C53 3.8 160.1 1.0 O2 A:C16 4.1 208.9 1.0 C1' A:A54 4.2 170.6 1.0 O4' A:A54 4.2 144.8 1.0 N2 A:G15 4.2 190.0 1.0 O2' A:A54 4.4 177.7 1.0 O2' A:C53 4.5 163.3 1.0 C2 A:C16 4.9 173.6 1.0 C2' A:A54 5.0 168.0 1.0

Caesium binding site 7 out of 7 in the Sars-Cov-2 SL5 Crystal Structure Cesium Derivative


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 7 of Sars-Cov-2 SL5 Crystal Structure Cesium Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs207 b:220.8 occ:0.20 OP1 A:U52 3.3 203.3 1.0 O2' A:A51 3.4 198.8 1.0 O3' A:A51 3.4 185.9 1.0 P A:U52 3.9 202.6 1.0 C2' A:A51 4.2 177.5 1.0 C1' A:A51 4.3 186.2 1.0 C3' A:A51 4.4 159.2 1.0 O5' A:U52 4.7 186.8 1.0

C.P.Jones, A.R.Ferre-D'amare. Crystallographic and Cryoem Analyses Reveal Sars-Cov-2 SL5 Is A Mobile T-Shaped Four-Way Junction with Deep Pockets. Rna V. 31 949 2025.
ISSN: ESSN 1469-9001
PubMed: 40527531
DOI: 10.1261/RNA.080413.125