Barium in PDB 8amg: Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1)

The structure of Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1), PDB code: 8amg 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)	42.01 / 2.26
Space group	P 65 2 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.014, 84.014, 138.966, 90, 90, 120
R / Rfree (%)	19.1 / 24

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Barium atom in the Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1) (pdb code 8amg). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 12 binding sites of Barium where determined in the Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1), PDB code: 8amg:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 12 in the Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba101 b:44.5 occ:1.00 O B:HOH202 2.6 34.9 1.0 O B:HOH204 2.6 35.6 1.0 O6 A:G3 2.7 37.1 1.0 O6 B:G6 2.7 36.5 1.0 O6 B:G5 2.7 43.5 1.0 O A:HOH206 2.7 37.7 1.0 O B:HOH207 2.7 30.3 0.5 O A:HOH203 3.0 35.9 1.0 O4 A:U4 3.0 36.0 1.0 C6 B:G5 3.7 42.8 1.0 C6 A:G3 3.8 36.8 1.0 C6 B:G6 3.9 37.6 1.0 C4 A:U4 3.9 34.7 1.0 O A:HOH202 4.0 38.1 1.0 O6 A:G5 4.0 41.2 1.0 N3 A:U4 4.1 31.2 1.0 N4 B:C7 4.1 37.0 1.0 N1 B:G5 4.4 38.9 1.0 O4 B:U4 4.4 47.4 1.0 C5 A:G3 4.6 30.7 1.0 C5 B:G5 4.6 44.6 1.0 N7 A:G3 4.6 38.1 1.0 C5 B:G6 4.7 38.6 1.0 N7 B:G6 4.7 36.4 1.0 N1 A:G3 4.7 36.0 1.0 O4 A:U2 4.7 40.4 1.0 BA B:BA101 4.8 46.5 1.0 N1 B:G6 5.0 32.5 1.0 N7 B:G5 5.0 41.5 1.0 O A:HOH205 5.0 34.4 1.0

Barium binding site 2 out of 12 in the Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ba101 b:46.5 occ:1.00 O A:HOH205 2.5 34.4 1.0 O A:HOH201 2.7 33.7 1.0 O B:HOH205 2.8 44.8 1.0 O B:HOH203 2.8 41.6 1.0 O6 A:G6 2.8 36.7 1.0 O B:HOH204 2.8 35.6 1.0 O6 B:G3 2.9 46.0 1.0 O4 B:U4 2.9 47.4 1.0 O6 A:G5 3.0 41.2 1.0 O6 B:G5 3.3 43.5 1.0 C6 A:G5 3.8 34.5 1.0 C4 B:U4 3.9 48.9 1.0 C6 A:G6 3.9 37.0 1.0 C6 B:G3 3.9 47.6 1.0 O A:HOH202 4.0 38.1 1.0 C6 B:G5 4.0 42.8 1.0 N1 A:G5 4.1 36.2 1.0 N3 B:U4 4.1 46.9 1.0 N4 A:C7 4.2 37.1 1.0 N1 B:G5 4.4 38.9 1.0 O4 A:U4 4.4 36.0 1.0 N7 A:G6 4.4 34.8 1.0 C5 A:G6 4.5 40.4 1.0 BA A:BA101 4.8 44.5 1.0 C5 B:G3 4.8 53.2 1.0 N1 B:G3 4.8 46.1 1.0 N7 B:G3 4.9 54.6 1.0

Barium binding site 3 out of 12 in the Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ba101 b:60.1 occ:1.00 O D:HOH102 2.3 30.4 1.0 O C:HOH203 2.6 30.4 1.0 O D:HOH101 2.8 44.8 1.0 O6 D:G5 2.9 51.6 1.0 O4 C:U4 3.0 38.9 1.0 O6 D:G6 3.1 35.5 1.0 O6 C:G3 3.1 38.2 1.0 O C:HOH204 3.6 48.7 1.0 O6 C:G5 3.7 40.9 1.0 C6 D:G5 3.7 50.4 1.0 C4 C:U4 3.8 36.0 1.0 N3 C:U4 3.9 32.6 1.0 N1 D:G5 3.9 52.4 1.0 C6 D:G6 4.1 35.7 1.0 C6 C:G3 4.2 35.6 1.0 O4 D:U4 4.3 48.7 1.0 N7 D:G6 4.4 42.1 1.0 C6 C:G5 4.4 42.5 1.0 N4 D:C7 4.5 37.9 1.0 N1 C:G5 4.6 40.6 1.0 C5 D:G6 4.7 38.1 1.0 N7 C:G3 4.8 33.4 1.0 C5 C:G3 4.8 36.1 1.0 O4 C:U2 4.9 40.8 1.0 BA C:BA102 4.9 56.6 1.0

Barium binding site 4 out of 12 in the Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ba102 b:56.6 occ:1.00 O D:HOH105 2.6 31.9 1.0 O6 C:G5 2.6 40.9 1.0 O6 D:G3 2.8 48.5 1.0 O D:HOH102 2.8 30.4 1.0 O4 D:U4 2.8 48.7 1.0 O C:HOH202 2.9 34.9 1.0 O D:HOH104 3.0 49.2 1.0 O C:HOH205 3.0 48.4 1.0 O6 C:G6 3.1 44.4 1.0 O C:HOH204 3.4 48.7 1.0 C6 C:G5 3.5 42.5 1.0 C4 D:U4 3.7 44.2 1.0 C6 D:G3 3.8 45.8 1.0 N3 D:U4 3.9 47.6 1.0 O6 D:G5 3.9 51.6 1.0 N1 C:G5 4.1 40.6 1.0 N4 C:C7 4.2 39.9 1.0 C6 C:G6 4.2 44.2 1.0 C5 D:G3 4.5 44.6 1.0 N7 D:G3 4.5 49.0 1.0 C5 C:G5 4.6 39.6 1.0 O4 C:U4 4.6 38.9 1.0 N7 C:G6 4.8 38.8 1.0 O4 D:U2 4.8 50.0 1.0 N1 D:G3 4.8 40.8 1.0 C6 D:G5 4.9 50.4 1.0 C5 C:G6 4.9 40.3 1.0 BA C:BA101 4.9 60.1 1.0

Barium binding site 5 out of 12 in the Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ba101 b:46.7 occ:1.00 O6 E:G5 2.6 41.6 1.0 O F:HOH106 2.6 36.0 1.0 O6 F:G3 2.6 45.3 1.0 O F:HOH102 2.7 36.9 1.0 O4 F:U4 2.8 42.5 1.0 O E:HOH201 2.8 30.4 1.0 O6 E:G6 2.9 41.0 1.0 O E:HOH206 3.0 34.8 1.0 O F:HOH103 3.0 34.7 1.0 C6 E:G5 3.6 37.5 1.0 C4 F:U4 3.7 43.6 1.0 C6 F:G3 3.7 40.8 1.0 N3 F:U4 3.9 37.8 1.0 O6 F:G5 3.9 48.4 1.0 C6 E:G6 4.1 40.8 1.0 N4 E:C7 4.1 43.0 1.0 N1 E:G5 4.3 40.8 1.0 C5 F:G3 4.4 45.2 1.0 N7 F:G3 4.5 42.3 1.0 O4 E:U4 4.5 32.9 1.0 C5 E:G5 4.6 34.8 1.0 N7 E:G6 4.7 39.3 1.0 N1 F:G3 4.7 44.0 1.0 C6 F:G5 4.7 42.7 1.0 O4 F:U2 4.7 48.5 1.0 C5 E:G6 4.8 36.0 1.0 BA E:BA102 4.9 45.9 1.0 N7 E:G5 4.9 35.1 1.0 C5 F:U4 5.0 43.3 1.0

Barium binding site 6 out of 12 in the Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ba102 b:45.9 occ:1.00 O F:HOH105 2.5 43.5 1.0 O6 E:G3 2.7 42.2 1.0 O6 F:G6 2.7 33.3 1.0 O F:HOH101 2.8 30.4 1.0 O E:HOH203 2.8 30.4 1.0 O F:HOH103 2.9 34.7 1.0 O6 F:G5 2.9 48.4 1.0 O4 E:U4 2.9 32.9 1.0 O E:HOH202 3.0 30.4 1.0 O6 E:G5 3.5 41.6 1.0 C6 E:G3 3.7 33.4 1.0 C6 F:G5 3.7 42.7 1.0 C4 E:U4 3.8 31.3 1.0 C6 F:G6 3.8 36.0 1.0 N3 E:U4 3.9 32.4 1.0 N1 F:G5 3.9 43.5 1.0 C6 E:G5 4.2 37.5 1.0 N4 F:C7 4.2 34.2 1.0 O4 F:U4 4.4 42.5 1.0 C5 E:G3 4.5 35.1 1.0 N1 E:G5 4.5 40.8 1.0 N7 F:G6 4.5 35.2 1.0 N7 E:G3 4.5 34.5 1.0 C5 F:G6 4.6 39.7 1.0 N1 E:G3 4.7 32.5 1.0 O4 E:U2 4.9 41.7 1.0 BA E:BA101 4.9 46.7 1.0 N1 F:G6 5.0 40.0 1.0

Barium binding site 7 out of 12 in the Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1) within 5.0Å range: probe atom residue distance (Å) B Occ H:Ba101 b:47.3 occ:1.00 O6 H:G5 2.6 44.6 0.7 O G:HOH104 2.6 32.9 1.0 O G:HOH101 2.7 33.1 1.0 O4 G:U4 2.7 39.3 1.0 O H:HOH202 2.7 33.7 1.0 O6 G:G3 2.7 38.9 1.0 O6 H:G5 2.9 44.6 0.3 O6 H:G6 3.0 37.1 1.0 O G:HOH105 3.0 29.6 1.0 O H:HOH201 3.0 29.6 1.0 C6 H:G5 3.5 46.0 0.7 C4 G:U4 3.7 37.8 1.0 C6 H:G5 3.7 46.0 0.3 C6 G:G3 3.8 38.2 1.0 N3 G:U4 4.0 34.4 1.0 N1 H:G5 4.1 45.8 0.3 O6 G:G5 4.1 41.6 1.0 C6 H:G6 4.1 39.5 1.0 N1 H:G5 4.2 45.8 0.7 N4 H:C7 4.2 30.6 1.0 C5 H:G5 4.5 42.3 0.7 C5 G:G3 4.5 37.6 1.0 N7 G:G3 4.6 38.3 1.0 O4 H:U4 4.7 42.9 1.0 N7 H:G6 4.7 39.4 1.0 BA H:BA102 4.8 51.4 1.0 O4 G:U2 4.8 40.3 1.0 C5 H:G5 4.8 42.3 0.3 C5 H:G6 4.8 39.3 1.0 N1 G:G3 4.8 35.6 1.0 N7 H:G5 4.9 39.4 0.7 C6 G:G5 4.9 43.6 1.0 C5 G:U4 5.0 36.6 1.0 O H:HOH205 5.0 41.2 1.0

Barium binding site 8 out of 12 in the Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1) within 5.0Å range: probe atom residue distance (Å) B Occ H:Ba102 b:51.4 occ:1.00 O H:HOH203 2.7 42.9 1.0 O4 H:U4 2.7 42.9 1.0 O G:HOH102 2.7 44.0 1.0 O H:HOH204 2.8 49.4 1.0 O6 H:G3 2.9 41.1 1.0 O G:HOH101 3.0 33.1 1.0 O G:HOH106 3.1 30.4 1.0 O6 G:G6 3.1 39.4 1.0 O6 G:G5 3.1 41.6 1.0 O6 H:G5 3.5 44.6 0.7 O6 H:G5 3.5 44.6 0.3 C4 H:U4 3.7 38.0 1.0 C6 G:G5 3.9 43.6 1.0 C6 H:G3 4.0 42.1 1.0 N1 G:G5 4.0 48.2 1.0 N3 H:U4 4.0 37.7 1.0 O4 G:U4 4.1 39.3 1.0 C6 G:G6 4.2 44.0 1.0 C6 H:G5 4.2 46.0 0.7 N4 G:C7 4.3 41.6 1.0 N7 G:G6 4.4 45.0 1.0 N1 H:G5 4.5 45.8 0.7 C6 H:G5 4.6 46.0 0.3 C5 G:G6 4.7 44.2 1.0 C5 H:G3 4.8 38.7 1.0 BA H:BA101 4.8 47.3 1.0 N1 H:G3 4.9 42.9 1.0 N7 H:G3 4.9 41.7 1.0 O4 H:U2 4.9 41.6 1.0 C4 G:U4 5.0 37.8 1.0 C5 H:U4 5.0 40.4 1.0

Barium binding site 9 out of 12 in the Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1) within 5.0Å range: probe atom residue distance (Å) B Occ I:Ba101 b:52.2 occ:1.00 O I:HOH202 2.5 44.6 1.0 O6 I:G5 2.5 49.4 1.0 O J:HOH204 2.6 46.4 1.0 O J:HOH203 2.7 45.3 1.0 O J:HOH202 2.8 43.4 1.0 O4 J:U4 2.8 45.9 1.0 O6 I:G6 2.8 54.1 1.0 O6 J:G3 2.9 54.6 1.0 O I:HOH201 2.9 56.8 1.0 C6 I:G5 3.5 58.5 1.0 O6 J:G5 3.5 55.8 0.6 O6 J:G5 3.5 55.6 0.4 N1 I:G5 3.8 61.7 1.0 C4 J:U4 3.8 55.9 1.0 C6 J:G3 3.9 50.9 1.0 C6 I:G6 4.0 57.5 1.0 N3 J:U4 4.0 57.3 1.0 C6 J:G5 4.1 55.4 0.6 N4 I:C7 4.2 47.8 1.0 N1 J:G5 4.3 55.3 0.6 N7 J:G3 4.5 54.5 1.0 C6 J:G5 4.5 55.3 0.4 C5 J:G3 4.5 50.1 1.0 N7 I:G6 4.6 55.7 1.0 O4 J:U2 4.7 47.2 1.0 C5 I:G6 4.7 57.8 1.0 C5 I:G5 4.7 56.7 1.0 BA J:BA101 4.8 55.3 1.0 O4 I:U4 4.8 56.4 1.0 N1 J:G3 4.9 53.5 1.0

Barium binding site 10 out of 12 in the Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of Crystal Structure of Auguggcau Duplex with Barium Ions (Model 1) within 5.0Å range: probe atom residue distance (Å) B Occ J:Ba101 b:55.3 occ:1.00 O6 I:G3 2.6 40.0 1.0 O J:HOH203 2.6 45.3 1.0 O J:HOH201 2.7 60.4 1.0 O I:HOH203 2.7 30.3 0.5 O6 J:G5 2.7 55.8 0.6 O4 I:U4 2.8 56.4 1.0 O6 J:G6 2.8 56.3 1.0 O J:HOH205 2.9 30.4 1.0 O6 J:G5 3.2 55.6 0.4 C6 J:G5 3.7 55.4 0.6 C6 I:G3 3.7 52.2 1.0 O6 I:G5 3.8 49.4 1.0 C4 I:U4 3.8 55.3 1.0 C6 J:G6 4.0 53.9 1.0 C6 J:G5 4.0 55.3 0.4 N3 I:U4 4.1 53.7 1.0 N1 J:G5 4.2 54.4 0.4 N1 J:G5 4.3 55.3 0.6 N4 J:C7 4.3 41.3 1.0 C5 I:G3 4.6 52.6 1.0 N7 J:G6 4.6 56.2 1.0 C6 I:G5 4.6 58.5 1.0 N7 I:G3 4.6 55.5 1.0 C5 J:G6 4.7 53.2 1.0 C5 J:G5 4.7 54.6 0.6 N1 I:G3 4.8 48.5 1.0 O4 J:U4 4.8 45.9 1.0 O4 I:U2 4.8 56.1 1.0 BA I:BA101 4.8 52.2 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