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Barium in PDB 7ecm: Rna Duplex Containing C-A Base Pair

Protein crystallography data

The structure of Rna Duplex Containing C-A Base Pair, PDB code: 7ecm was solved by J.Kondo, A.Tsudura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.54 / 1.51
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 26.475, 27.909, 46.665, 100.08, 93.54, 110.47
R / Rfree (%) 15.7 / 19.6

Barium Binding Sites:

The binding sites of Barium atom in the Rna Duplex Containing C-A Base Pair (pdb code 7ecm). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 9 binding sites of Barium where determined in the Rna Duplex Containing C-A Base Pair, PDB code: 7ecm:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Barium binding site 1 out of 9 in 7ecm

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Barium binding site 1 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba101

b:18.5
occ:0.34
 O A:HOH242 2.1 28.8 1.0
O B:HOH247 2.6 28.8 1.0
O A:HOH261 2.7 31.8 1.0
O A:HOH224 2.8 24.1 1.0
O A:HOH219 2.9 21.1 1.0
N7 A:G8 2.9 13.6 1.0
O6 A:G8 2.9 10.9 1.0
O A:HOH239 3.0 26.4 1.0
C5 A:G8 3.6 10.8 1.0
C6 A:G8 3.6 9.2 1.0
O B:HOH256 3.7 15.1 1.0
C8 A:G8 4.1 13.1 1.0
O6 A:G7 4.2 12.3 1.0
O B:HOH239 4.4 8.6 1.0
N7 A:G7 4.5 15.1 1.0
C6 A:G7 4.7 10.3 1.0
C5 A:G7 4.9 12.9 1.0
C4 A:G8 4.9 10.7 1.0
N1 A:G8 4.9 10.7 1.0

Barium binding site 2 out of 9 in 7ecm

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Barium binding site 2 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba102

b:14.7
occ:0.44
 O A:HOH234 2.7 25.0 1.0
O A:HOH215 2.8 20.1 1.0
O A:HOH212 2.8 32.9 1.0
OP2 A:G2 2.8 20.0 1.0
O A:HOH210 2.9 23.1 1.0
O A:HOH254 3.8 29.7 1.0
O B:HOH259 3.9 21.9 1.0
P A:G2 4.3 17.7 1.0
N4 A:C4 4.4 11.8 1.0
O A:HOH255 4.5 26.5 1.0
N7 A:G2 4.5 12.9 1.0
O A:HOH232 4.7 21.1 1.0
O5' A:G2 4.8 17.2 1.0
O A:HOH206 4.8 29.0 1.0
O5' A:G1 4.9 23.2 1.0
C8 A:G2 4.9 10.0 1.0
O B:HOH244 4.9 26.8 1.0
BA B:BA101 5.0 39.0 0.4

Barium binding site 3 out of 9 in 7ecm

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Barium binding site 3 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba103

b:25.4
occ:0.34
 O A:HOH232 2.5 21.1 1.0
O B:HOH258 2.7 35.1 1.0
O A:HOH252 2.9 31.1 1.0
O6 A:G1 3.2 15.9 1.0
O B:HOH241 3.2 24.9 1.0
O A:HOH254 3.3 29.7 1.0
N7 A:G1 3.7 14.1 1.0
C6 A:G1 4.0 9.9 1.0
C5 A:G1 4.2 11.8 1.0
O B:HOH242 4.4 19.5 1.0
O6 A:G2 4.8 12.4 1.0
O A:HOH215 4.8 20.1 1.0
C8 A:G1 4.9 13.3 1.0

Barium binding site 4 out of 9 in 7ecm

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Barium binding site 4 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba101

b:39.0
occ:0.44
 O B:HOH259 2.6 21.9 1.0
O6 B:G8 2.6 14.1 1.0
O B:HOH225 2.7 23.1 1.0
O B:HOH224 2.9 16.4 1.0
O6 B:G7 3.0 12.1 1.0
N7 B:G8 3.3 12.6 1.0
C6 B:G8 3.4 8.4 1.0
O B:HOH244 3.5 26.8 1.0
C5 B:G8 3.7 11.5 1.0
C6 B:G7 3.7 10.9 1.0
O B:HOH248 4.0 22.4 1.0
N7 B:G7 4.1 11.8 1.0
C5 B:G7 4.2 10.2 1.0
N4 A:C5 4.4 12.3 1.0
C8 B:G8 4.5 12.4 1.0
N4 A:C6 4.8 13.9 1.0
N1 B:G8 4.8 10.2 1.0
O B:HOH258 4.8 35.1 1.0
N1 B:G7 4.8 10.9 1.0
BA A:BA102 5.0 14.7 0.4

Barium binding site 5 out of 9 in 7ecm

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Barium binding site 5 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba101

b:29.7
occ:0.44
 N7 C:G8 2.7 19.0 1.0
O C:HOH247 2.7 31.3 1.0
O C:HOH237 2.8 27.6 1.0
O C:HOH229 2.9 26.2 1.0
O D:HOH257 2.9 23.1 1.0
O6 C:G8 3.2 15.9 1.0
O C:HOH252 3.3 20.9 1.0
O D:HOH262 3.5 24.4 1.0
C5 C:G8 3.5 14.4 1.0
O C:HOH215 3.5 18.1 1.0
C6 C:G8 3.7 11.4 1.0
N7 C:G7 3.7 17.2 1.0
C8 C:G8 3.8 17.6 1.0
C5 C:G7 4.1 13.9 1.0
O C:HOH223 4.3 26.9 1.0
C8 C:G7 4.3 20.4 1.0
O6 C:G7 4.4 12.7 1.0
C6 C:G7 4.4 11.4 1.0
C4 C:G8 4.8 14.2 1.0
O D:HOH260 4.8 13.2 1.0
O D:HOH210 4.9 24.5 1.0
O C:HOH218 4.9 24.3 1.0
N9 C:G8 4.9 18.5 1.0
OP2 C:G8 4.9 25.8 1.0
C4 C:G7 4.9 15.4 1.0
O D:HOH261 4.9 27.6 1.0

Barium binding site 6 out of 9 in 7ecm

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Barium binding site 6 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba102

b:50.1
occ:0.42
 O C:HOH207 2.3 28.7 1.0
O C:HOH227 2.7 27.6 1.0
N7 C:G2 2.8 14.9 1.0
O C:HOH201 2.8 31.7 1.0
O6 C:G2 2.9 13.4 1.0
O C:HOH234 3.2 22.6 1.0
C5 C:G2 3.4 9.7 1.0
C6 C:G2 3.5 8.2 1.0
N7 C:G1 3.6 19.2 1.0
C5 C:G1 3.7 13.4 1.0
O6 C:G1 3.8 16.8 1.0
C6 C:G1 3.8 12.0 1.0
C8 C:G2 3.9 13.5 1.0
O C:HOH249 3.9 26.1 1.0
O C:HOH253 4.2 40.4 1.0
C8 C:G1 4.2 15.0 1.0
C4 C:G1 4.5 11.2 1.0
N1 C:G1 4.7 14.8 1.0
O6 C:G3 4.7 11.6 1.0
N9 C:G1 4.8 15.8 1.0
C4 C:G2 4.8 12.4 1.0
O C:HOH222 4.8 25.8 1.0
N7 C:G3 4.8 14.1 1.0
N1 C:G2 4.9 11.9 1.0
N9 C:G2 5.0 15.1 1.0

Barium binding site 7 out of 9 in 7ecm

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Barium binding site 7 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ba101

b:12.4
occ:0.88
 O D:HOH232 2.6 15.4 1.0
O D:HOH241 2.8 13.5 1.0
O C:HOH249 2.8 26.1 1.0
O C:HOH230 2.8 21.7 1.0
O D:HOH217 2.8 13.2 1.0
O C:HOH210 2.8 15.3 1.0
O D:HOH234 2.9 13.9 1.0
O6 D:G8 2.9 10.9 1.0
C6 D:G8 3.9 8.5 1.0
N7 D:G8 4.1 10.6 1.0
O C:HOH201 4.2 31.7 1.0
O6 D:G7 4.4 12.3 1.0
C5 D:G8 4.4 8.4 1.0
N4 C:C5 4.5 10.2 1.0
N7 D:G7 4.7 11.9 1.0
N4 C:C4 4.7 17.7 1.0
O D:HOH258 4.8 24.0 1.0
N6 D:A9 4.9 10.1 1.0
O D:HOH231 5.0 19.6 1.0
C6 D:G7 5.0 12.8 1.0
O C:HOH234 5.0 22.6 1.0
O6 C:G3 5.0 11.6 1.0

Barium binding site 8 out of 9 in 7ecm

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Barium binding site 8 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ba102

b:11.6
occ:0.75
 O D:HOH253 2.8 22.2 1.0
O D:HOH252 2.9 20.0 1.0
O D:HOH226 2.9 15.0 1.0
O D:HOH213 3.0 15.7 1.0
OP1 D:C11 4.6 16.9 1.0
OP1 D:C12 4.8 12.1 1.0

Barium binding site 9 out of 9 in 7ecm

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Barium binding site 9 out of 9 in the Rna Duplex Containing C-A Base Pair


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Rna Duplex Containing C-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ba103

b:123.7
occ:1.00
 O D:HOH246 2.2 30.9 1.0
O D:HOH261 2.8 27.6 1.0
N7 D:G1 2.9 15.1 1.0
O6 D:G1 3.1 14.7 1.0
O D:HOH214 3.3 30.8 1.0
C5 D:G1 3.6 9.7 1.0
C6 D:G1 3.7 10.9 1.0
C8 D:G1 4.1 13.5 1.0
O6 D:G2 4.6 14.2 1.0
O C:HOH217 4.8 28.6 1.0
C4 D:G1 4.9 10.5 1.0
N7 D:G2 4.9 13.7 1.0

Reference:

J.Kondo, A.Tsudura. Rna Duplex Containing C-A Base Pair To Be Published.
Page generated: Tue Apr 4 17:22:57 2023

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