Strontium in PDB 8amn: Crystal Structure of Auguggcau Duplex with Strontium Ions

The structure of Crystal Structure of Auguggcau Duplex with Strontium Ions, PDB code: 8amn 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)	46.05 / 2.46
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.102, 90.131, 138.182, 90, 91.39, 90
R / Rfree (%)	19.9 / 24.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Strontium atom in the Crystal Structure of Auguggcau Duplex with Strontium Ions (pdb code 8amn). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 22 binding sites of Strontium where determined in the Crystal Structure of Auguggcau Duplex with Strontium Ions, PDB code: 8amn:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 22 in the Crystal Structure of Auguggcau Duplex with Strontium Ions


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Crystal Structure of Auguggcau Duplex with Strontium Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr101 b:134.7 occ:1.00 O6 B:G5 2.3 48.4 0.6 O6 A:G5 2.6 56.0 0.5 O6 A:G5 2.7 57.4 0.6 O4 B:U4 2.7 47.7 1.0 O A:HOH101 2.9 90.7 1.0 O6 B:G5 2.9 48.8 0.5 O B:HOH202 3.4 80.1 1.0 C6 B:G5 3.5 49.2 0.6 O4 A:U4 3.5 61.5 1.0 O B:HOH201 3.7 76.4 1.0 C4 B:U4 3.8 47.8 1.0 C6 A:G5 3.8 56.0 0.5 C6 A:G5 3.8 60.5 0.6 C6 B:G5 3.8 49.7 0.5 N1 B:G5 4.0 50.6 0.5 N1 B:G5 4.1 49.7 0.6 O6 A:G6 4.1 51.7 1.0 N3 B:U4 4.4 48.3 1.0 N1 A:G5 4.4 65.2 0.6 N1 A:G5 4.4 53.1 0.5 C5 B:G5 4.6 50.7 0.6 C4 A:U4 4.6 64.6 1.0 C5 B:U4 4.8 48.8 1.0 O6 B:G6 4.9 54.0 1.0 C5 A:G5 4.9 59.1 0.5 C5 A:G5 5.0 60.0 0.6

Strontium binding site 2 out of 22 in the Crystal Structure of Auguggcau Duplex with Strontium Ions


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Crystal Structure of Auguggcau Duplex with Strontium Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Sr101 b:175.8 occ:1.00 O6 D:G5 2.5 77.5 1.0 O4 C:U4 2.8 61.8 1.0 O6 C:G3 3.1 56.5 1.0 O6 D:G6 3.2 70.6 1.0 C6 D:G5 3.5 77.6 1.0 C4 C:U4 3.8 67.9 1.0 O6 C:G5 4.0 74.9 1.0 N3 C:U4 4.1 69.0 1.0 C6 C:G3 4.1 62.7 1.0 O4 D:U4 4.3 77.7 1.0 N1 D:G5 4.3 74.8 1.0 C6 D:G6 4.3 69.7 1.0 SR C:SR102 4.4 172.5 1.0 N4 D:C7 4.5 68.0 1.0 C5 D:G5 4.5 80.4 1.0 N7 C:G3 4.6 64.4 1.0 C5 C:G3 4.7 67.1 1.0 N7 D:G5 4.8 83.3 1.0 O4 C:U2 4.8 63.0 1.0 N7 D:G6 4.8 75.3 1.0 C6 C:G5 4.9 82.8 1.0 C5 D:G6 5.0 71.9 1.0

Strontium binding site 3 out of 22 in the Crystal Structure of Auguggcau Duplex with Strontium Ions


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Crystal Structure of Auguggcau Duplex with Strontium Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Sr102 b:172.5 occ:1.00 O6 C:G5 2.8 74.9 1.0 O6 C:G6 3.2 59.5 1.0 O4 D:U4 3.2 77.7 1.0 C6 C:G5 3.5 82.8 1.0 O6 D:G3 3.5 69.8 1.0 N1 C:G5 3.5 88.3 1.0 O6 D:G5 3.5 77.5 1.0 O4 C:U4 3.9 61.8 1.0 C4 D:U4 4.2 80.0 1.0 C6 C:G6 4.2 62.5 1.0 C6 D:G5 4.2 77.6 1.0 N3 D:U4 4.3 79.7 1.0 SR C:SR101 4.4 175.8 1.0 N1 D:G5 4.4 74.8 1.0 C6 D:G3 4.5 72.4 1.0 N7 C:G6 4.5 78.5 1.0 N4 C:C7 4.6 65.7 1.0 C4 C:U4 4.7 67.9 1.0 C2 C:G5 4.7 92.1 1.0 C5 C:G6 4.7 70.5 1.0 C5 C:G5 4.7 86.3 1.0

Strontium binding site 4 out of 22 in the Crystal Structure of Auguggcau Duplex with Strontium Ions


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Crystal Structure of Auguggcau Duplex with Strontium Ions within 5.0Å range: probe atom residue distance (Å) B Occ E:Sr101 b:125.2 occ:1.00 O F:HOH101 2.3 53.2 1.0 O6 F:G5 2.5 86.7 1.0 O6 E:G5 2.5 68.4 1.0 O4 E:U4 3.1 67.0 1.0 C6 F:G5 3.5 85.6 1.0 C6 E:G5 3.6 72.9 1.0 O4 F:U4 3.6 74.7 1.0 O E:HOH202 3.7 79.1 1.0 N1 E:G5 3.9 74.1 1.0 N1 F:G5 3.9 84.9 1.0 O F:HOH102 3.9 55.8 1.0 C4 E:U4 4.1 70.0 1.0 O6 F:G6 4.4 84.3 1.0 N3 E:U4 4.5 72.9 1.0 O6 E:G6 4.7 62.8 1.0 O E:HOH201 4.7 85.5 1.0 C4 F:U4 4.7 74.2 1.0 C5 F:G5 4.8 85.0 1.0 C5 E:G5 4.9 76.4 1.0

Strontium binding site 5 out of 22 in the Crystal Structure of Auguggcau Duplex with Strontium Ions


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Crystal Structure of Auguggcau Duplex with Strontium Ions within 5.0Å range: probe atom residue distance (Å) B Occ G:Sr101 b:153.1 occ:1.00 O6 H:G5 2.5 65.9 1.0 O4 G:U4 2.9 70.8 1.0 O4 H:U4 3.0 58.7 1.0 O6 G:G5 3.1 64.4 1.0 SR H:SR101 3.5 92.2 0.3 C6 H:G5 3.5 64.8 1.0 O H:HOH201 3.6 31.7 1.0 O6 G:G6 3.9 54.3 1.0 C4 G:U4 4.0 73.3 1.0 C6 G:G5 4.0 66.3 1.0 N1 H:G5 4.0 62.1 1.0 C4 H:U4 4.1 58.3 1.0 N1 G:G5 4.3 66.7 1.0 N3 H:U4 4.4 56.6 1.0 N3 G:U4 4.7 76.2 1.0 C5 H:G5 4.8 65.4 1.0 C6 G:G6 4.8 54.1 1.0 O6 H:G3 4.9 62.7 1.0 O6 H:G6 5.0 71.4 1.0

Strontium binding site 6 out of 22 in the Crystal Structure of Auguggcau Duplex with Strontium Ions


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Crystal Structure of Auguggcau Duplex with Strontium Ions within 5.0Å range: probe atom residue distance (Å) B Occ H:Sr101 b:92.2 occ:0.30 O6 G:G3 2.7 96.8 1.0 O6 H:G6 2.9 71.4 1.0 O6 H:G5 2.9 65.9 1.0 O4 G:U4 3.1 70.8 1.0 N4 H:C7 3.5 86.3 1.0 SR G:SR101 3.5 153.1 1.0 C6 H:G5 3.6 64.8 1.0 C6 G:G3 3.8 98.4 1.0 C4 G:U4 3.9 73.3 1.0 N3 G:U4 4.0 76.2 1.0 C6 H:G6 4.0 69.5 1.0 N1 H:G5 4.1 62.1 1.0 O4 G:U2 4.2 115.0 1.0 O6 G:G5 4.3 64.4 1.0 N7 H:G6 4.3 73.5 1.0 C5 H:G5 4.5 65.4 1.0 C5 H:G6 4.6 70.2 1.0 C4 H:C7 4.6 84.7 1.0 C5 G:G3 4.7 98.0 1.0 N1 G:G3 4.8 100.5 1.0 N7 G:G3 4.9 96.0 1.0 N7 H:G5 5.0 66.5 1.0

Strontium binding site 7 out of 22 in the Crystal Structure of Auguggcau Duplex with Strontium Ions


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Crystal Structure of Auguggcau Duplex with Strontium Ions within 5.0Å range: probe atom residue distance (Å) B Occ I:Sr101 b:131.1 occ:1.00 O6 J:G5 2.5 89.2 1.0 O6 I:G5 2.8 72.3 1.0 O4 I:U4 3.0 67.5 1.0 C6 J:G5 3.6 88.3 1.0 C6 I:G5 3.7 73.1 1.0 N1 I:G5 3.7 73.8 1.0 O4 J:U4 3.7 91.0 1.0 C4 I:U4 4.1 67.8 1.0 N1 J:G5 4.2 87.5 1.0 O6 I:G6 4.3 75.0 1.0 O6 J:G6 4.4 82.8 1.0 C4 J:U4 4.7 90.1 1.0 N3 I:U4 4.7 68.3 1.0 C5 J:G5 4.8 88.0 1.0

Strontium binding site 8 out of 22 in the Crystal Structure of Auguggcau Duplex with Strontium Ions


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Crystal Structure of Auguggcau Duplex with Strontium Ions within 5.0Å range: probe atom residue distance (Å) B Occ L:Sr101 b:140.3 occ:1.00 O6 K:G5 2.5 78.5 1.0 O6 L:G5 2.5 72.9 1.0 O4 K:U4 2.8 71.4 1.0 O4 L:U4 2.8 58.0 1.0 C6 L:G5 3.4 73.8 1.0 C6 K:G5 3.6 78.3 1.0 N1 L:G5 3.6 72.8 1.0 O K:HOH101 3.7 76.0 1.0 C4 L:U4 3.8 59.2 1.0 C4 K:U4 3.9 73.3 1.0 O6 L:G6 4.1 66.8 1.0 N1 K:G5 4.1 74.8 1.0 N3 L:U4 4.3 61.3 1.0 N3 K:U4 4.4 72.1 1.0 O6 K:G6 4.5 62.9 1.0 C5 K:G5 4.8 80.6 1.0 C5 L:G5 4.8 75.7 1.0 C5 L:U4 4.9 58.6 1.0 O6 K:G3 4.9 68.7 1.0 C2 L:G5 4.9 73.6 1.0

Strontium binding site 9 out of 22 in the Crystal Structure of Auguggcau Duplex with Strontium Ions


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of Crystal Structure of Auguggcau Duplex with Strontium Ions within 5.0Å range: probe atom residue distance (Å) B Occ M:Sr101 b:152.4 occ:1.00 O6 N:G5 2.7 72.2 1.0 O6 M:G5 2.8 78.5 1.0 O4 N:U4 2.8 73.0 1.0 O4 M:U4 3.0 66.1 1.0 O M:HOH201 3.3 76.4 1.0 C6 N:G5 3.7 72.4 1.0 C6 M:G5 3.8 82.4 1.0 C4 N:U4 3.9 75.6 1.0 C4 M:U4 4.0 69.2 1.0 O6 M:G6 4.0 63.7 1.0 SR M:SR102 4.0 125.5 0.5 N1 M:G5 4.1 85.4 1.0 N1 N:G5 4.3 70.0 1.0 N3 N:U4 4.4 75.3 1.0 N3 M:U4 4.7 67.9 1.0 C5 N:G5 4.8 75.6 1.0 C5 M:U4 4.9 73.4 1.0 O6 N:G3 5.0 87.9 1.0

Strontium binding site 10 out of 22 in the Crystal Structure of Auguggcau Duplex with Strontium Ions


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of Crystal Structure of Auguggcau Duplex with Strontium Ions within 5.0Å range: probe atom residue distance (Å) B Occ M:Sr102 b:125.5 occ:0.50 O6 M:G3 2.8 59.1 1.0 O4 M:U4 3.1 66.1 1.0 O6 N:G5 3.2 72.2 1.0 O6 N:G6 3.2 72.5 1.0 C6 M:G3 3.9 61.4 1.0 N4 N:C7 4.0 68.2 1.0 C6 N:G5 4.0 72.4 1.0 C4 M:U4 4.0 69.2 1.0 SR M:SR101 4.0 152.4 1.0 N3 M:U4 4.2 67.9 1.0 C6 N:G6 4.3 72.1 1.0 O4 M:U2 4.6 54.9 1.0 N7 N:G6 4.7 76.5 1.0 N1 N:G5 4.7 70.0 1.0 C5 N:G5 4.7 75.6 1.0 O6 M:G5 4.7 78.5 1.0 N1 M:G3 4.8 60.1 1.0 C5 N:G6 4.9 73.6 1.0 C5 M:G3 4.9 65.5 1.0 N7 N:G5 4.9 79.5 1.0 C4 N:C7 5.0 67.6 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