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Barium in PDB 6ymc: 26-Mer Stem-Loop Rna

Protein crystallography data

The structure of 26-Mer Stem-Loop Rna, PDB code: 6ymc was solved by R.Janowski, D.Niessing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 24.27, 52.43, 107.18, 90, 90, 90
R / Rfree (%) 17.5 / 24.1

Barium Binding Sites:

The binding sites of Barium atom in the 26-Mer Stem-Loop Rna (pdb code 6ymc). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 10 binding sites of Barium where determined in the 26-Mer Stem-Loop Rna, PDB code: 6ymc:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 10 in 6ymc

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Barium binding site 1 out of 10 in the 26-Mer Stem-Loop Rna


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of 26-Mer Stem-Loop Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba101

b:42.4
occ:0.50
 O A:HOH238 2.4 39.4 1.0
O A:HOH204 2.5 28.2 1.0
O6 A:G24 2.8 25.2 1.0
O6 A:G23 2.8 23.3 1.0
BA A:BA102 2.9 40.3 0.5
O4 A:U3 2.9 26.5 1.0
O A:HOH231 3.0 27.4 1.0
O6 A:G25 3.2 26.6 1.0
C6 A:G23 3.7 23.5 1.0
N4 A:C2 3.7 27.4 1.0
O A:HOH239 3.8 38.5 1.0
C6 A:G24 3.8 25.0 1.0
C4 A:U3 3.8 28.2 1.0
C6 A:G25 3.9 26.8 1.0
N3 A:U3 4.0 27.0 1.0
N7 A:G24 4.1 24.2 1.0
O A:HOH243 4.2 49.4 1.0
C5 A:G23 4.3 22.8 1.0
N4 A:C4 4.3 24.5 1.0
BA A:BA103 4.3 31.0 0.6
C5 A:G24 4.3 24.8 1.0
N7 A:G23 4.4 24.8 1.0
C5 A:G25 4.5 25.2 1.0
N1 A:G23 4.6 23.6 1.0
N7 A:G25 4.7 26.4 1.0
N1 A:G25 4.7 26.4 1.0
O A:HOH233 4.7 31.2 1.0
C4 A:C2 4.8 29.1 1.0

Barium binding site 2 out of 10 in 6ymc

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Barium binding site 2 out of 10 in the 26-Mer Stem-Loop Rna


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of 26-Mer Stem-Loop Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba102

b:40.3
occ:0.50
 O A:HOH238 2.6 39.4 1.0
O A:HOH233 2.8 31.2 1.0
BA A:BA101 2.9 42.4 0.5
N7 A:G23 2.9 24.8 1.0
O6 A:G23 3.2 23.3 1.0
O A:HOH239 3.6 38.5 1.0
C5 A:G23 3.6 22.8 1.0
O A:HOH204 3.7 28.2 1.0
C6 A:G23 3.7 23.5 1.0
O A:HOH243 3.8 49.4 1.0
C8 A:G23 4.0 25.1 1.0
N7 A:A22 4.1 25.4 1.0
O A:HOH231 4.1 27.4 1.0
N6 A:A22 4.6 24.2 1.0
C5 A:A22 4.6 23.6 1.0
C8 A:A22 4.7 25.7 1.0
OP2 A:G23 4.8 30.5 1.0
C6 A:A22 4.9 22.4 1.0
C4 A:G23 4.9 23.4 1.0
OP2 A:A22 5.0 34.1 1.0
O4 A:U3 5.0 26.5 1.0

Barium binding site 3 out of 10 in 6ymc

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Barium binding site 3 out of 10 in the 26-Mer Stem-Loop Rna


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of 26-Mer Stem-Loop Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba103

b:31.0
occ:0.60
 O A:HOH231 2.4 27.4 1.0
O A:HOH204 2.7 28.2 1.0
N7 A:G25 2.7 26.4 1.0
O A:HOH243 3.1 49.4 1.0
O A:HOH216 3.2 38.7 1.0
O6 A:G25 3.3 26.6 1.0
C5 A:G25 3.6 25.2 1.0
C6 A:G25 3.8 26.8 1.0
C8 A:G25 3.8 28.8 1.0
BA A:BA101 4.3 42.4 0.5
N7 A:G24 4.4 24.2 1.0
C4 A:G25 4.8 26.0 1.0
N6 A:A26 4.9 25.3 1.0
N9 A:G25 4.9 26.6 1.0
O6 A:G24 5.0 25.2 1.0

Barium binding site 4 out of 10 in 6ymc

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Barium binding site 4 out of 10 in the 26-Mer Stem-Loop Rna


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of 26-Mer Stem-Loop Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba104

b:38.6
occ:0.60
 O A:HOH225 2.7 20.6 1.0
O6 A:G12 2.8 25.5 1.0
O A:HOH207 2.9 31.7 1.0
C6 A:G12 3.8 25.6 1.0
N1 A:G12 4.1 26.8 1.0
O A:HOH222 4.7 21.0 1.0
O6 A:G11 4.8 26.5 1.0
OP1 A:A14 4.8 35.3 1.0
O A:HOH228 4.9 28.4 1.0
N4 A:C16 4.9 28.1 1.0
BA A:BA105 4.9 28.9 1.0

Barium binding site 5 out of 10 in 6ymc

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Barium binding site 5 out of 10 in the 26-Mer Stem-Loop Rna


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of 26-Mer Stem-Loop Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba105

b:28.9
occ:1.00
 O A:HOH222 2.6 21.0 1.0
O A:HOH224 2.8 23.1 1.0
O A:HOH212 2.9 41.5 1.0
N7 A:G12 2.9 24.9 1.0
O6 A:G12 3.2 25.5 1.0
C5 A:G12 3.6 26.2 1.0
C6 A:G12 3.7 25.6 1.0
C8 A:G12 4.0 27.3 1.0
O A:HOH235 4.2 41.5 1.0
O A:HOH221 4.4 37.6 1.0
N7 A:G11 4.4 28.2 1.0
O A:HOH225 4.5 20.6 1.0
OP2 A:G11 4.8 29.5 1.0
OP2 A:A14 4.8 36.4 1.0
OP1 A:A14 4.8 35.3 1.0
C4 A:G12 4.9 27.4 1.0
BA A:BA104 4.9 38.6 0.6
C8 A:G11 5.0 28.2 1.0

Barium binding site 6 out of 10 in 6ymc

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Barium binding site 6 out of 10 in the 26-Mer Stem-Loop Rna


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of 26-Mer Stem-Loop Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba101

b:78.8
occ:0.50
 O B:HOH202 2.5 24.2 1.0
O4 B:U5 2.9 36.4 1.0
O4 B:U21 3.3 27.2 1.0
O B:HOH236 3.4 40.2 1.0
O B:HOH250 3.5 43.0 1.0
C4 B:U5 3.9 33.1 1.0
N6 B:A22 4.3 30.1 1.0
C5 B:U5 4.5 34.4 1.0
C4 B:U21 4.5 26.5 1.0
O6 B:G6 4.6 25.8 1.0
N4 B:C4 4.6 38.3 1.0
N4 B:C20 4.7 27.3 1.0

Barium binding site 7 out of 10 in 6ymc

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Barium binding site 7 out of 10 in the 26-Mer Stem-Loop Rna


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of 26-Mer Stem-Loop Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba102

b:76.7
occ:0.80
 O B:HOH238 2.7 21.6 1.0
O B:HOH232 2.9 36.5 1.0
N7 B:G7 3.0 27.3 1.0
O B:HOH242 3.0 35.4 1.0
O6 B:G7 3.1 26.4 1.0
N7 B:G6 3.6 27.6 1.0
C5 B:G7 3.7 26.5 1.0
C6 B:G7 3.7 26.6 1.0
O B:HOH202 3.7 24.2 1.0
O6 B:G6 4.1 25.8 1.0
C5 B:G6 4.1 24.9 1.0
C8 B:G7 4.2 27.9 1.0
C6 B:G6 4.3 24.8 1.0
O4 B:U8 4.3 28.9 1.0
C8 B:G6 4.4 25.8 1.0
OP2 B:G6 4.8 30.6 1.0
N6 B:A19 4.8 29.3 1.0

Barium binding site 8 out of 10 in 6ymc

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Barium binding site 8 out of 10 in the 26-Mer Stem-Loop Rna


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of 26-Mer Stem-Loop Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba103

b:31.9
occ:0.70
 O B:HOH201 2.6 35.5 1.0
O B:HOH240 2.7 38.2 1.0
O B:HOH225 2.8 30.9 1.0
O B:HOH246 2.9 33.5 1.0
N7 B:G25 3.0 33.0 1.0
O B:HOH248 3.0 42.5 1.0
O6 B:G25 3.1 34.5 1.0
C5 B:G25 3.7 34.0 1.0
C6 B:G25 3.7 31.6 1.0
C8 B:G25 4.1 37.5 1.0
N7 B:G24 4.2 39.1 1.0
O B:HOH217 4.3 15.8 1.0
N6 B:A26 4.5 29.7 1.0
OP2 B:G24 4.7 38.7 1.0
C8 B:G24 4.9 39.7 1.0
C5 B:G24 5.0 37.7 1.0
O6 B:G24 5.0 34.6 1.0
C4 B:G25 5.0 34.4 1.0

Barium binding site 9 out of 10 in 6ymc

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Barium binding site 9 out of 10 in the 26-Mer Stem-Loop Rna


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of 26-Mer Stem-Loop Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba104

b:28.9
occ:0.70
 O B:HOH216 2.7 22.0 1.0
O6 B:G12 2.8 27.3 1.0
O B:HOH211 2.8 23.8 1.0
O6 B:G11 2.9 24.0 1.0
C6 B:G12 3.7 28.3 1.0
C6 B:G11 3.9 24.3 1.0
N7 B:G11 4.2 25.5 1.0
N1 B:G12 4.3 29.1 1.0
BA B:BA105 4.4 22.7 0.8
C5 B:G11 4.4 25.0 1.0
N4 B:C16 4.5 30.2 1.0
N6 B:A10 4.5 24.1 1.0
C5 B:G12 4.6 28.0 1.0
N7 B:A10 4.9 26.2 1.0
O B:HOH218 4.9 34.9 1.0

Barium binding site 10 out of 10 in 6ymc

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Barium binding site 10 out of 10 in the 26-Mer Stem-Loop Rna


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of 26-Mer Stem-Loop Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba105

b:22.7
occ:0.80
 O B:HOH220 2.6 23.7 1.0
O B:HOH211 2.8 23.8 1.0
O B:HOH235 2.8 28.1 1.0
O6 B:G12 2.9 27.3 1.0
O B:HOH227 2.9 33.9 1.0
N7 B:G12 3.0 28.0 1.0
C6 B:G12 3.5 28.3 1.0
C5 B:G12 3.6 28.0 1.0
O B:HOH221 4.1 37.2 1.0
C8 B:G12 4.2 28.3 1.0
BA B:BA104 4.4 28.9 0.7
N7 B:G11 4.5 25.5 1.0
O B:HOH209 4.5 27.4 1.0
OP1 B:A14 4.8 34.0 1.0
N1 B:G12 4.9 29.1 1.0
C4 B:G12 4.9 30.1 1.0
OP2 B:A14 4.9 32.6 1.0
OP2 B:G11 4.9 27.6 1.0

Reference:

A.Niedner, J.Hennig, M.Hofweber, T.Monecke, E.Davydova, A.P.Gerber, I.Anosova, M.Mueller, R.Heym, R.Janowski, J.-C.Paillart, D.Dormann, M.Sattler, D.Niessing. Multiple Intrinsically Disordered Rna-Binding Motifs Cooperate As Rna-Folding Catalyst and Mediate Phase Transition To Be Published.
Page generated: Mon Jul 7 02:49:01 2025

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