Caesium in PDB 3skw: Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak

The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak, PDB code: 3skw was solved by O.Pikovskaya, A.Polonskaia, D.J.Patel, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.65 / 2.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.376, 35.414, 119.269, 90.00, 95.18, 90.00
R / Rfree (%)	21.7 / 28.7

The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Caesium atom in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak (pdb code 3skw). This binding sites where shown within 5.0 Angstroms radius around Caesium atom.
In total 6 binding sites of Caesium where determined in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak, PDB code: 3skw:
Jump to Caesium binding site number: 1; 2; 3; 4; 5; 6;

Caesium binding site 1 out of 6 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, 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 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs201 b:94.6 occ:1.00 O5' A:U72 3.3 40.2 1.0 N7 A:G47 3.4 43.8 1.0 O3' A:A71 3.4 46.9 1.0 OP2 A:G47 3.5 35.0 1.0 O2' A:G46 3.7 42.5 1.0 O3' A:G46 3.7 54.0 1.0 O2' A:A71 4.0 49.9 1.0 P A:U72 4.0 55.1 1.0 O6 A:G47 4.0 45.7 1.0 C5' A:U72 4.2 52.6 1.0 C8 A:G47 4.2 46.0 1.0 P A:G47 4.3 42.8 1.0 C5 A:G47 4.3 32.5 1.0 C1' A:A71 4.3 41.0 1.0 OP2 A:U72 4.4 47.1 1.0 C2' A:A71 4.5 45.0 1.0 C3' A:A71 4.6 45.7 1.0 C6 A:G47 4.6 37.5 1.0 C2' A:G46 4.7 39.1 1.0 C3' A:G46 4.7 38.8 1.0 O5' A:G47 4.9 47.1 1.0

Caesium binding site 2 out of 6 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, 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 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs202 b:0.0 occ:1.00 O3' A:C31 3.0 58.0 1.0 OP2 A:A32 3.1 42.9 1.0 O6 A:GNG120 3.4 38.2 1.0 O2' A:C31 3.5 70.7 1.0 P A:A32 3.5 57.1 1.0 O5' A:A32 3.6 79.2 1.0 N6 A:A79 3.9 74.0 1.0 C2' A:C31 4.2 65.5 1.0 C3' A:C31 4.2 60.7 1.0 C5' A:A32 4.2 69.7 1.0 C1' A:C31 4.3 61.2 1.0 O2 A:C31 4.3 62.6 1.0 C6 A:GNG120 4.5 34.2 1.0 N4 A:C80 4.6 39.9 1.0 OP2 A:G33 4.6 58.6 1.0 O6 A:G78 4.8 67.0 1.0 N4 A:C61 4.9 41.6 1.0 OP1 A:A32 4.9 59.4 1.0

Caesium binding site 3 out of 6 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, 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 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs203 b:0.2 occ:1.00 O2' A:G33 3.5 60.6 1.0 O6 A:G35 3.5 54.5 1.0 N7 A:G35 3.6 50.4 1.0 N7 A:G34 3.7 54.6 1.0 N3 A:G33 3.7 45.2 1.0 O6 A:G34 3.9 62.3 1.0 C5 A:G34 4.1 53.2 1.0 N2 A:G33 4.2 45.5 1.0 C6 A:G35 4.2 52.1 1.0 C5 A:G35 4.2 49.1 1.0 C6 A:G34 4.2 56.5 1.0 C2 A:G33 4.3 43.8 1.0 C8 A:G34 4.5 54.3 1.0 C1' A:G33 4.5 53.9 1.0 C4 A:G33 4.5 49.8 1.0 C2' A:G33 4.6 55.4 1.0 C8 A:G35 4.7 50.1 1.0 N4 A:C51 4.8 41.1 1.0 O4 A:U36 4.8 51.3 1.0 N9 A:G33 4.8 52.4 1.0 N6 A:A50 4.9 52.8 1.0

Caesium binding site 4 out of 6 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, 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 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs204 b:0.4 occ:1.00 O2 A:C48 2.9 51.2 1.0 N2 A:G38 3.4 51.7 1.0 O2 A:C39 3.5 37.3 1.0 N2 A:G47 3.7 37.0 1.0 C1' A:C48 3.8 44.3 1.0 C2 A:C48 3.8 40.7 1.0 O2' A:C48 3.9 48.2 1.0 N1 A:C48 4.2 40.4 1.0 C2' A:C48 4.3 50.0 1.0 C2 A:C39 4.4 27.9 1.0 C2 A:G38 4.4 49.5 1.0 N1 A:G38 4.5 42.7 1.0 O2' A:C39 4.6 29.0 1.0 C2 A:G47 4.7 39.7 1.0 O4' A:C48 4.7 49.0 1.0 O4' A:U49 4.8 63.2 1.0 N3 A:C48 4.9 35.1 1.0 C1' A:C39 4.9 28.9 1.0

Caesium binding site 5 out of 6 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, 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 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs205 b:0.7 occ:1.00 O2' A:C68 3.4 58.7 1.0 O2 A:U72 3.5 31.1 1.0 O2 A:C68 3.6 47.0 1.0 O4' A:U72 3.6 65.1 1.0 C1' A:U72 4.1 54.0 1.0 C1' A:C68 4.2 46.6 1.0 N2 A:G46 4.3 46.2 1.0 C2 A:U72 4.3 34.1 1.0 C2' A:C68 4.3 51.3 1.0 C4' A:U72 4.4 61.5 1.0 O4' A:C69 4.5 46.3 1.0 N1 A:U72 4.6 42.6 1.0 C2 A:C68 4.7 42.8 1.0 O4' A:U73 4.9 56.9 1.0 O3' A:U72 4.9 57.1 1.0

Caesium binding site 6 out of 6 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, 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 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs304 b:0.9 occ:0.50 O4' A:U62 3.7 60.0 1.0 O2' A:C61 3.9 70.3 1.0 O2 A:C61 4.4 44.4 1.0 C1' A:U62 4.5 53.2 1.0 C4' A:U62 4.5 61.0 1.0 C2' A:C61 4.6 68.0 1.0 O2' A:A79 4.8 68.3 1.0 N2 A:G78 4.8 48.9 1.0 C5' A:U62 5.0 60.7 1.0

O.Pikovskaya, A.Polonskaia, D.J.Patel, A.Serganov. Structural Principles of Nucleoside Selectivity in A 2'-Deoxyguanosine Riboswitch. Nat.Chem.Biol. V. 7 748 2011.
ISSN: ISSN 1552-4450
PubMed: 21841796
DOI: 10.1038/NCHEMBIO.631