Caesium in PDB 7eoj: Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak

The structure of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak, PDB code: 7eoj was solved by K.Y.Huang, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.85 / 1.77
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.277, 34.749, 58.124, 90, 127.93, 90
R / Rfree (%)	20.7 / 21.6

The structure of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak also contains other interesting chemical elements:

Magnesium

(Mg)

9 atoms

The binding sites of Caesium atom in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak (pdb code 7eoj). This binding sites where shown within 5.0 Angstroms radius around Caesium atom.
In total 8 binding sites of Caesium where determined in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak, PDB code: 7eoj:
Jump to Caesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Caesium binding site 1 out of 8 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 1 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs111 b:35.4 occ:1.00 O6 A:G41 3.1 15.8 1.0 O A:HOH225 3.2 22.0 1.0 N7 A:A6 3.2 15.9 1.0 OP2 A:C5 3.3 13.0 1.0 O A:HOH268 3.3 19.2 1.0 N7 A:G41 3.5 15.4 1.0 C6 A:G41 3.7 16.1 1.0 C5 A:G41 3.8 16.3 1.0 O23 A:J8F101 3.8 29.4 1.0 OP1 A:C5 3.9 15.1 1.0 P A:C5 4.0 15.6 1.0 C8 A:A6 4.1 14.9 1.0 O A:HOH262 4.2 25.3 1.0 O A:HOH243 4.2 26.4 1.0 N6 A:A6 4.2 12.3 1.0 C5 A:A6 4.2 14.2 1.0 OP2 A:A6 4.5 16.3 1.0 O5' A:C5 4.5 16.4 1.0 C8 A:G41 4.6 17.1 1.0 C6 A:A6 4.7 15.1 1.0 C21 A:J8F101 4.7 20.6 1.0 N1 A:G41 4.8 14.2 1.0

Caesium binding site 2 out of 8 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 2 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs112 b:34.2 occ:1.00 O2 A:C48 2.7 17.1 1.0 O A:HOH286 3.0 19.4 1.0 O2 A:C3 3.1 14.8 1.0 O2' A:C48 3.8 23.0 1.0 N2 A:G47 3.8 16.6 1.0 C2 A:C48 3.8 18.4 1.0 C1' A:C48 3.9 22.4 1.0 N2 A:G2 3.9 16.6 1.0 C2' A:C48 4.3 21.1 1.0 C2 A:C3 4.3 15.2 1.0 N1 A:C48 4.4 17.4 1.0 O2' A:C3 4.5 17.0 1.0 C1' A:C3 4.5 14.4 1.0 O A:HOH308 4.7 23.9 1.0 N3 A:C48 4.9 18.9 1.0 C2 A:G2 4.9 16.4 1.0 C2 A:G47 4.9 18.8 1.0 C2' A:C3 4.9 12.5 1.0 N1 A:C3 5.0 12.4 1.0 O4' A:C48 5.0 20.4 1.0

Caesium binding site 3 out of 8 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 3 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs113 b:31.4 occ:1.00 O2 A:C5 3.1 15.7 1.0 O2 A:C46 3.1 17.9 1.0 O A:HOH207 3.4 25.9 1.0 O A:HOH331 3.4 18.8 1.0 O A:HOH326 3.5 22.4 1.0 O A:HOH253 3.8 23.9 1.0 N2 A:G45 3.9 17.3 1.0 O2' A:C5 4.0 18.4 1.0 N2 A:G4 4.1 14.6 1.0 C2 A:C5 4.2 16.1 1.0 C2 A:C46 4.3 17.5 1.0 C1' A:C5 4.3 14.9 1.0 O2' A:C46 4.4 18.4 1.0 C1' A:C46 4.4 18.3 1.0 C2' A:C5 4.7 14.9 1.0 N1 A:C5 4.7 14.9 1.0 C2' A:C46 4.8 18.7 1.0 C2 A:G45 4.9 15.9 1.0 N1 A:C46 4.9 18.0 1.0

Caesium binding site 4 out of 8 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 4 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs114 b:40.5 occ:1.00 OP2 A:G9 3.0 14.4 1.0 OP1 A:U8 3.0 14.4 1.0 O A:HOH223 3.6 17.2 1.0 P A:U8 4.3 14.9 1.0 P A:G9 4.3 19.0 1.0 C5' A:U8 4.3 16.1 1.0 O5' A:U8 4.5 14.5 1.0 OP1 A:G9 4.8 17.8 1.0

Caesium binding site 5 out of 8 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 5 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs115 b:66.0 occ:1.00 O2 A:C13 3.0 26.7 1.0 O A:HOH235 3.1 34.5 1.0 O2 A:C38 3.2 22.1 1.0 O A:HOH334 3.5 28.3 1.0 O2' A:C13 3.7 31.7 1.0 N2 A:G12 3.9 20.8 1.0 C1' A:C13 4.1 25.4 1.0 C2 A:C13 4.2 23.1 1.0 N2 A:G37 4.2 26.2 1.0 C2' A:C13 4.3 29.3 1.0 C2 A:C38 4.3 22.3 1.0 C1' A:C38 4.5 21.5 1.0 N1 A:C13 4.7 24.1 1.0 O4' A:U14 4.7 40.2 1.0 O2' A:C38 4.7 20.6 1.0 N1 A:C38 4.9 20.8 1.0 C2 A:G12 5.0 22.7 1.0

Caesium binding site 6 out of 8 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 6 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs116 b:50.9 occ:1.00 O2 A:C28 3.0 23.1 1.0 O2 A:C16 3.4 35.7 1.0 O2' A:C28 3.4 21.7 1.0 O A:HOH337 3.6 37.6 1.0 N2 A:G15 3.7 29.0 1.0 C1' A:C28 4.0 24.4 1.0 C2 A:C28 4.1 26.1 1.0 C2' A:C28 4.1 21.5 1.0 O2' A:C16 4.1 51.6 1.0 N2 A:G27 4.2 31.6 1.0 C2 A:C16 4.4 37.1 1.0 C1' A:C16 4.5 44.0 1.0 C2' A:C16 4.6 48.6 1.0 N1 A:C28 4.6 21.9 1.0 N1 A:C16 4.9 36.6 1.0 C2 A:G15 4.9 28.9 1.0

Caesium binding site 7 out of 8 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 7 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs117 b:31.1 occ:1.00 O6 A:G34 3.1 15.7 1.0 O2 A:U32 3.1 18.4 1.0 OP2 A:C38 3.1 19.5 1.0 OP1 A:C38 3.2 21.4 1.0 O4 A:U35 3.3 18.7 1.0 O A:HOH259 3.3 20.5 1.0 O A:HOH233 3.3 16.1 1.0 P A:C38 3.6 19.9 1.0 C2 A:U32 4.1 15.7 1.0 C4 A:U35 4.1 16.7 1.0 C6 A:G34 4.2 18.6 1.0 N3 A:U35 4.3 17.4 1.0 N3 A:U32 4.4 16.2 1.0 N1 A:A31 4.7 21.2 1.0 O A:HOH234 4.7 17.6 1.0 O5' A:C38 4.8 20.8 1.0 O3' A:G37 4.8 19.9 1.0

Caesium binding site 8 out of 8 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 8 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Cesium Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs118 b:39.9 occ:1.00 O2' A:C49 3.2 21.5 1.0 O2 A:C49 3.3 18.4 1.0 O A:HOH324 3.6 30.4 1.0 N2 A:GDP1 3.9 17.9 1.0 C2' A:C49 4.1 18.7 1.0 C1' A:C49 4.4 18.1 1.0 C2 A:C49 4.4 17.4 1.0 O A:HOH335 4.4 27.4 1.0 O A:HOH201 4.5 23.9 1.0 N1 A:C49 5.0 16.9 1.0

K.Huang, X.Chen, C.Li, Q.Song, H.Li, L.Zhu, Y.Yang, A.Ren. Structure-Based Investigation of Fluorogenic Pepper Aptamer. Nat.Chem.Biol. 2021.
ISSN: ESSN 1552-4469
PubMed: 34725509
DOI: 10.1038/S41589-021-00884-6