Atomistry » Caesium » PDB 6dzo-7jhw » 7eoj
Atomistry »
  Caesium »
    PDB 6dzo-7jhw »
      7eoj »

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

Protein crystallography data

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

Other elements in 7eoj:

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

Caesium Binding Sites:

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 7eoj

Go back to Caesium Binding Sites List in 7eoj
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 7eoj

Go back to Caesium Binding Sites List in 7eoj
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 7eoj

Go back to Caesium Binding Sites List in 7eoj
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 7eoj

Go back to Caesium Binding Sites List in 7eoj
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 7eoj

Go back to Caesium Binding Sites List in 7eoj
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 7eoj

Go back to Caesium Binding Sites List in 7eoj
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 7eoj

Go back to Caesium Binding Sites List in 7eoj
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 7eoj

Go back to Caesium Binding Sites List in 7eoj
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

Reference:

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
Page generated: Thu Nov 25 08:59:23 2021

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy