Caesium in PDB 8amm: Crystal Structure of Auguggcau Duplex with Cesium Ions

The structure of Crystal Structure of Auguggcau Duplex with Cesium Ions, PDB code: 8amm was solved by A.Kiliszek, W.Rypniewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.31 / 2.86
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.231, 90.612, 139.933, 90, 91.43, 90
R / Rfree (%)	22.1 / 26.9

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Caesium atom in the Crystal Structure of Auguggcau Duplex with Cesium Ions (pdb code 8amm). This binding sites where shown within 5.0 Angstroms radius around Caesium atom.
In total 28 binding sites of Caesium where determined in the Crystal Structure of Auguggcau Duplex with Cesium Ions, PDB code: 8amm:
Jump to Caesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Caesium binding site 1 out of 28 in the Crystal Structure of Auguggcau Duplex with Cesium Ions


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 Auguggcau Duplex with Cesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs101 b:117.5 occ:1.00 O6 B:G5 3.1 76.8 1.0 O4 A:U4 3.2 74.0 1.0 O6 A:G3 3.4 73.8 1.0 O6 B:G6 3.5 71.4 1.0 O6 A:G5 3.6 77.8 1.0 C6 B:G5 3.9 73.3 1.0 C4 A:U4 4.2 73.0 1.0 N4 B:C7 4.3 61.9 1.0 N3 A:U4 4.3 73.0 1.0 C6 A:G3 4.4 66.7 1.0 C6 A:G5 4.5 79.8 1.0 N1 B:G5 4.5 71.4 1.0 C6 B:G6 4.6 69.7 1.0 N7 B:G6 4.7 62.0 1.0 C5 B:G5 4.7 62.8 1.0

Caesium binding site 2 out of 28 in the Crystal Structure of Auguggcau Duplex with Cesium Ions


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 Auguggcau Duplex with Cesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs102 b:110.1 occ:1.00 O4 B:U4 3.1 70.4 1.0 O6 A:G6 3.2 66.0 1.0 O6 B:G3 3.2 56.3 1.0 O6 A:G5 3.3 77.8 1.0 O6 B:G5 3.7 76.8 1.0 C6 A:G5 4.0 79.8 1.0 C4 B:U4 4.0 59.9 1.0 N4 A:C7 4.0 62.6 1.0 N3 B:U4 4.1 60.2 1.0 N1 A:G5 4.2 77.5 1.0 C6 A:G6 4.2 61.8 1.0 C6 B:G3 4.3 56.6 1.0 C6 B:G5 4.4 73.3 1.0 N7 A:G6 4.6 63.9 1.0 N1 B:G5 4.8 71.4 1.0 C5 A:G6 4.8 59.9 1.0 C5 A:G5 5.0 73.3 1.0

Caesium binding site 3 out of 28 in the Crystal Structure of Auguggcau Duplex with Cesium Ions


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 Auguggcau Duplex with Cesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Cs101 b:153.2 occ:1.00 O6 C:G5 3.1 63.9 1.0 O6 C:G6 3.2 75.5 1.0 N1 C:G5 3.4 75.5 1.0 O4 D:U4 3.4 97.6 1.0 C6 C:G5 3.4 70.0 1.0 O6 D:G3 3.5 84.9 1.0 N4 C:C7 3.9 71.2 1.0 O6 D:G5 4.1 60.8 1.0 C6 C:G6 4.3 69.8 1.0 C4 D:U4 4.4 87.0 1.0 C2 C:G5 4.4 79.2 1.0 N7 C:G6 4.4 64.5 1.0 C6 D:G3 4.5 84.0 1.0 N3 D:U4 4.5 80.0 1.0 C5 C:G5 4.6 64.2 1.0 C5 C:G6 4.7 62.9 1.0 O4 C:U4 4.8 79.1 1.0 C6 D:G5 4.8 72.3 1.0 N2 C:G5 4.8 79.5 1.0 C4 C:C7 4.9 67.6 1.0

Caesium binding site 4 out of 28 in the Crystal Structure of Auguggcau Duplex with Cesium Ions


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 Auguggcau Duplex with Cesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Cs102 b:155.9 occ:1.00 O6 D:G5 3.1 60.8 1.0 O4 C:U4 3.1 79.1 1.0 O6 C:G3 3.2 72.8 1.0 O6 D:G6 3.4 71.3 1.0 O6 C:G5 4.0 63.9 1.0 C6 D:G5 4.0 72.3 1.0 C4 C:U4 4.1 72.9 1.0 C6 C:G3 4.2 70.4 1.0 N3 C:U4 4.4 70.3 1.0 N4 D:C7 4.4 68.2 1.0 C6 D:G6 4.5 65.1 1.0 O4 D:U4 4.6 97.6 1.0 O4 C:U2 4.7 81.2 1.0 C5 D:G5 4.7 76.9 1.0 N7 D:G5 4.7 78.7 1.0 N7 C:G3 4.9 75.5 1.0 C5 C:G3 4.9 72.9 1.0 C6 C:G5 4.9 70.0 1.0 N7 D:G6 5.0 68.8 1.0 N1 D:G5 5.0 68.2 1.0

Caesium binding site 5 out of 28 in the Crystal Structure of Auguggcau Duplex with Cesium Ions


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 Auguggcau Duplex with Cesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ E:Cs101 b:123.9 occ:1.00 O6 F:G5 3.1 88.5 1.0 O4 E:U4 3.2 93.3 1.0 O6 E:G3 3.2 93.8 1.0 O6 F:G6 3.3 95.7 1.0 N4 F:C7 3.9 88.0 1.0 O6 E:G5 4.0 92.8 1.0 C6 F:G5 4.1 88.5 1.0 C4 E:U4 4.1 93.7 1.0 C6 E:G3 4.2 91.4 1.0 N3 E:U4 4.3 93.6 1.0 C6 F:G6 4.5 90.8 1.0 O4 E:U2 4.6 99.7 1.0 N1 F:G5 4.8 88.2 1.0 N7 F:G6 4.9 90.3 1.0 C4 F:C7 5.0 83.2 1.0 C5 F:G5 5.0 85.3 1.0

Caesium binding site 6 out of 28 in the Crystal Structure of Auguggcau Duplex with Cesium Ions


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 Auguggcau Duplex with Cesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ E:Cs102 b:140.1 occ:1.00 O6 E:G6 3.1 83.4 1.0 O4 F:U4 3.2 78.4 1.0 O6 F:G5 3.2 88.5 1.0 O6 E:G5 3.5 92.8 1.0 O6 F:G3 3.9 67.1 1.0 C6 F:G5 3.9 88.5 1.0 C6 E:G5 4.1 91.5 1.0 N1 E:G5 4.2 94.9 1.0 C4 F:U4 4.2 66.3 1.0 N1 F:G5 4.2 88.2 1.0 C6 E:G6 4.3 82.5 1.0 N3 F:U4 4.4 68.3 1.0 N4 E:C7 4.5 79.7 1.0 N7 E:G6 4.7 88.7 1.0 O4 E:U4 4.9 93.3 1.0 C5 E:G6 4.9 82.7 1.0 C6 F:G3 4.9 64.8 1.0

Caesium binding site 7 out of 28 in the Crystal Structure of Auguggcau Duplex with Cesium Ions


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 Auguggcau Duplex with Cesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ G:Cs101 b:128.7 occ:1.00 O6 G:G3 3.1 87.8 1.0 O6 H:G5 3.2 75.2 1.0 O4 G:U4 3.3 83.1 1.0 O6 H:G6 3.4 79.0 1.0 C6 H:G5 4.0 71.1 1.0 N4 H:C7 4.1 82.5 1.0 C6 G:G3 4.2 85.2 1.0 C4 G:U4 4.2 81.3 1.0 O6 G:G5 4.3 75.9 1.0 O4 G:U2 4.3 93.9 1.0 N3 G:U4 4.4 79.1 1.0 C6 H:G6 4.4 77.6 1.0 N7 H:G6 4.7 73.5 1.0 C5 H:G5 4.8 70.7 1.0 N1 H:G5 4.8 70.8 1.0 CS G:CS102 4.8 127.4 1.0 N7 G:G3 5.0 83.4 1.0 C5 G:G3 5.0 83.1 1.0 N7 H:G5 5.0 69.6 1.0 C5 H:G6 5.0 76.2 1.0

Caesium binding site 8 out of 28 in the Crystal Structure of Auguggcau Duplex with Cesium Ions


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 Auguggcau Duplex with Cesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ G:Cs102 b:127.4 occ:1.00 O6 G:G5 3.2 75.9 1.0 O6 G:G6 3.3 74.3 1.0 O6 H:G5 3.3 75.2 1.0 O4 H:U4 3.3 71.1 1.0 N1 G:G5 3.8 78.8 1.0 O4 G:U4 3.9 83.1 1.0 C6 G:G5 3.9 75.9 1.0 O6 H:G3 4.1 69.2 1.0 C6 H:G5 4.3 71.1 1.0 C4 H:U4 4.3 66.7 1.0 C6 G:G6 4.3 69.3 1.0 N3 H:U4 4.4 66.9 1.0 N7 G:G6 4.7 67.7 1.0 N1 H:G5 4.7 70.8 1.0 C4 G:U4 4.7 81.3 1.0 CS G:CS101 4.8 128.7 1.0 N4 G:C7 4.8 65.0 1.0 C5 G:G6 4.9 65.8 1.0

Caesium binding site 9 out of 28 in the Crystal Structure of Auguggcau Duplex with Cesium Ions


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 9 of Crystal Structure of Auguggcau Duplex with Cesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ I:Cs101 b:109.6 occ:1.00 O6 J:G5 3.0 85.7 1.0 O4 I:U4 3.1 77.4 1.0 O6 I:G3 3.3 71.6 1.0 O6 J:G6 3.4 70.9 1.0 O6 I:G5 3.5 75.6 1.0 C6 J:G5 3.8 74.4 1.0 N4 J:C7 4.0 64.9 1.0 C4 I:U4 4.1 70.0 1.0 N3 I:U4 4.3 66.0 1.0 N1 J:G5 4.3 74.0 1.0 C6 I:G3 4.3 71.2 1.0 C6 J:G6 4.5 67.6 1.0 N7 J:G6 4.5 70.4 1.0 C6 I:G5 4.5 77.9 1.0 C5 J:G5 4.8 69.2 1.0 C5 J:G6 4.9 64.4 1.0 CS I:CS102 4.9 139.2 1.0

Caesium binding site 10 out of 28 in the Crystal Structure of Auguggcau Duplex with Cesium Ions


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 10 of Crystal Structure of Auguggcau Duplex with Cesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ I:Cs102 b:139.2 occ:1.00 O6 I:G6 3.1 73.0 1.0 O4 J:U4 3.2 77.8 1.0 O6 I:G5 3.2 75.6 1.0 O6 J:G5 3.4 85.7 1.0 C6 I:G5 3.9 77.9 1.0 N1 I:G5 4.1 79.1 1.0 C6 I:G6 4.2 72.7 1.0 C6 J:G5 4.2 74.4 1.0 C4 J:U4 4.3 71.6 1.0 O6 J:G3 4.4 68.7 1.0 N1 J:G5 4.5 74.0 1.0 N7 I:G6 4.5 72.3 1.0 O4 I:U4 4.7 77.4 1.0 N3 J:U4 4.7 69.8 1.0 C5 I:G6 4.8 70.5 1.0 CS I:CS101 4.9 109.6 1.0

A.Kiliszek, M.Pluta, M.Bejger, W.Rypniewski. Structure and Thermodynamics of A Ugg Motif Interacting with BA2+ and Other Metal Ions: Accommodating Changes in the Rna Structure and the Presence of A G(Syn)-G(Syn) Pair. Rna 2022.
ISSN: ESSN 1469-9001
PubMed: 36319090
DOI: 10.1261/RNA.079414.122