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Bromine in PDB 7ecl: Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair

Protein crystallography data

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

Resolution Low / High (Å) 42.11 / 3.01
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 43.252, 43.252, 378.967, 90, 90, 120
R / Rfree (%) 21.8 / 29.3

Other elements in 7ecl:

The structure of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair also contains other interesting chemical elements:

Silver (Ag) 23 atoms

Bromine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Bromine atom in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair (pdb code 7ecl). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 12 binding sites of Bromine where determined in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair, PDB code: 7ecl:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 12 in 7ecl

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Bromine binding site 1 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br6

b:73.8
occ:1.00
BR A:CBR6 0.0 73.8 1.0
C5 A:CBR6 1.9 47.5 1.0
C4 A:CBR6 2.9 48.5 1.0
C6 A:CBR6 2.9 44.1 1.0
N4 A:CBR6 3.0 51.6 1.0
C5 A:U5 3.5 54.3 1.0
C6 A:U5 3.7 54.2 1.0
C4 A:U5 3.8 53.8 1.0
OP2 A:CBR6 4.1 58.0 1.0
N3 A:CBR6 4.1 44.0 1.0
N1 A:CBR6 4.1 48.9 1.0
N1 A:U5 4.2 55.7 1.0
N3 A:U5 4.2 50.5 1.0
O4 A:U5 4.3 47.2 1.0
C2 A:U5 4.4 51.0 1.0
C3' A:U5 4.6 50.3 1.0
C2 A:CBR6 4.7 47.6 1.0
O5' A:U5 4.8 62.6 1.0
O5' A:CBR6 4.8 46.7 1.0
C2' A:U5 4.9 58.0 1.0
N7 A:G7 5.0 47.4 1.0

Bromine binding site 2 out of 12 in 7ecl

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Bromine binding site 2 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br6

b:80.2
occ:1.00
BR B:CBR6 0.0 80.2 1.0
C5 B:CBR6 1.9 53.1 1.0
C6 B:CBR6 2.9 54.5 1.0
C4 B:CBR6 2.9 53.0 1.0
N4 B:CBR6 3.2 58.6 1.0
C4 B:U5 3.6 59.6 1.0
N3 B:U5 3.6 48.7 1.0
C5 B:U5 3.6 66.5 1.0
C6 B:U5 3.8 65.9 1.0
C2 B:U5 3.8 55.0 1.0
N1 B:U5 3.9 63.8 1.0
OP2 B:CBR6 3.9 47.7 1.0
O4 B:U5 4.0 68.2 1.0
N1 B:CBR6 4.2 54.7 1.0
N3 B:CBR6 4.2 52.8 1.0
C2' B:U5 4.3 55.9 1.0
O2 B:U5 4.5 54.2 1.0
AG B:AG102 4.6 72.5 1.0
C3' B:U5 4.6 53.4 1.0
C2 B:CBR6 4.7 50.6 1.0
C1' B:U5 4.7 56.8 1.0
C5' B:CBR6 4.8 39.6 1.0

Bromine binding site 3 out of 12 in 7ecl

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Bromine binding site 3 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br6

b:67.1
occ:1.00
BR C:CBR6 0.0 67.1 1.0
C5 C:CBR6 2.0 59.0 1.0
C4 C:CBR6 2.9 64.8 1.0
C6 C:CBR6 3.0 54.7 1.0
N4 C:CBR6 3.1 60.9 1.0
C5 C:U5 3.5 62.5 1.0
C4 C:U5 3.5 61.5 1.0
C6 C:U5 3.7 61.5 1.0
N3 C:U5 3.7 64.5 1.0
OP2 C:CBR6 3.8 57.5 1.0
N1 C:U5 4.0 67.9 1.0
C2 C:U5 4.0 71.1 1.0
O4 C:U5 4.0 66.1 1.0
N3 C:CBR6 4.2 64.7 1.0
N1 C:CBR6 4.2 60.4 1.0
C3' C:U5 4.5 57.9 1.0
O6 C:G7 4.6 59.9 1.0
C2' C:U5 4.6 60.9 1.0
O5' C:CBR6 4.7 61.0 1.0
O2 C:U5 4.7 70.9 1.0
C2 C:CBR6 4.8 62.2 1.0
P C:CBR6 4.8 61.0 1.0
C1' C:U5 4.9 65.6 1.0
O5' C:U5 4.9 51.3 1.0

Bromine binding site 4 out of 12 in 7ecl

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Bromine binding site 4 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br6

b:77.1
occ:1.00
BR D:CBR6 0.0 77.1 1.0
C5 D:CBR6 1.9 50.9 1.0
C6 D:CBR6 2.8 56.7 1.0
C4 D:CBR6 3.0 54.1 1.0
N4 D:CBR6 3.3 56.8 1.0
OP2 D:CBR6 3.3 53.4 1.0
C2 D:U5 3.6 50.3 1.0
C2' D:U5 3.7 44.4 1.0
N1 D:U5 3.7 56.3 1.0
N3 D:U5 3.7 46.0 1.0
C6 D:U5 4.0 53.9 1.0
O2 D:U5 4.0 47.0 1.0
C4 D:U5 4.0 46.3 1.0
N1 D:CBR6 4.1 56.4 1.0
C5 D:U5 4.1 46.3 1.0
C3' D:U5 4.2 46.1 1.0
N3 D:CBR6 4.2 56.1 1.0
C1' D:U5 4.3 47.2 1.0
P D:CBR6 4.5 52.5 1.0
O2' D:U5 4.7 41.8 1.0
O5' D:CBR6 4.7 35.1 1.0
C2 D:CBR6 4.7 55.9 1.0
O4 D:U5 4.7 52.6 1.0
C5' D:CBR6 4.8 40.2 1.0
O3' D:U5 4.9 49.3 1.0
O4' D:CBR6 4.9 53.7 1.0
AG C:AG101 4.9 69.0 0.7

Bromine binding site 5 out of 12 in 7ecl

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Bromine binding site 5 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br6

b:57.2
occ:1.00
BR E:CBR6 0.0 57.2 1.0
C5 E:CBR6 1.9 33.8 1.0
C6 E:CBR6 2.9 39.4 1.0
C4 E:CBR6 2.9 40.3 1.0
N4 E:CBR6 3.1 42.6 1.0
C5 E:U5 3.4 40.8 1.0
C6 E:U5 3.5 39.5 1.0
C4 E:U5 3.5 42.0 1.0
N3 E:U5 3.7 39.7 1.0
N1 E:U5 3.7 41.4 1.0
C2 E:U5 3.8 45.4 1.0
OP2 E:CBR6 3.9 60.8 1.0
O4 E:U5 4.1 43.0 1.0
N1 E:CBR6 4.1 46.5 1.0
N3 E:CBR6 4.2 41.8 1.0
C2' E:U5 4.3 48.3 1.0
O5' E:CBR6 4.3 37.8 1.0
C3' E:U5 4.4 50.8 1.0
O2 E:U5 4.5 49.0 1.0
N7 E:G7 4.6 43.7 1.0
C1' E:U5 4.6 46.6 1.0
C2 E:CBR6 4.7 45.9 1.0
P E:CBR6 4.8 55.5 1.0

Bromine binding site 6 out of 12 in 7ecl

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Bromine binding site 6 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Br6

b:75.7
occ:1.00
BR F:CBR6 0.0 75.7 1.0
C5 F:CBR6 1.9 55.7 1.0
C6 F:CBR6 2.9 52.5 1.0
C4 F:CBR6 2.9 57.4 1.0
N4 F:CBR6 3.1 57.5 1.0
C5 F:U5 3.6 66.9 1.0
C4 F:U5 3.6 61.2 1.0
C6 F:U5 3.8 71.7 1.0
N3 F:U5 3.8 61.4 1.0
OP2 F:CBR6 3.9 69.3 1.0
O4 F:U5 4.0 64.4 1.0
N1 F:U5 4.1 71.5 1.0
C2 F:U5 4.1 67.8 1.0
N1 F:CBR6 4.1 45.6 1.0
N3 F:CBR6 4.2 52.1 1.0
C2' F:U5 4.7 57.9 1.0
AG E:AG102 4.7 71.5 0.6
C2 F:CBR6 4.7 49.1 1.0
O5' F:CBR6 4.7 53.2 1.0
C3' F:U5 4.8 59.5 1.0
O2 F:U5 4.9 64.4 1.0
P F:CBR6 4.9 62.7 1.0

Bromine binding site 7 out of 12 in 7ecl

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Bromine binding site 7 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Br6

b:64.3
occ:1.00
BR G:CBR6 0.0 64.3 1.0
C5 G:CBR6 1.9 50.4 1.0
C6 G:CBR6 2.9 52.5 1.0
C4 G:CBR6 2.9 52.7 1.0
N4 G:CBR6 3.1 49.5 1.0
C5 G:U5 3.7 59.0 1.0
OP2 G:CBR6 3.7 60.8 1.0
C4 G:U5 3.8 57.2 1.0
C6 G:U5 3.8 62.2 1.0
N3 G:U5 3.9 58.4 1.0
N1 G:U5 4.0 60.4 1.0
C2 G:U5 4.1 61.9 1.0
N1 G:CBR6 4.1 57.2 1.0
N3 G:CBR6 4.1 58.0 1.0
O4 G:U5 4.3 58.2 1.0
C2' G:U5 4.4 54.5 1.0
C3' G:U5 4.5 55.6 1.0
O5' G:CBR6 4.6 53.6 1.0
C2 G:CBR6 4.7 51.8 1.0
P G:CBR6 4.7 64.7 1.0
O2 G:U5 4.8 67.1 1.0
C1' G:U5 4.8 57.5 1.0
AG H:AG103 4.9 65.5 0.7

Bromine binding site 8 out of 12 in 7ecl

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Bromine binding site 8 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br6

b:73.4
occ:1.00
BR H:CBR6 0.0 73.4 1.0
C5 H:CBR6 2.0 44.2 1.0
C6 H:CBR6 2.9 42.1 1.0
C4 H:CBR6 2.9 52.3 1.0
N4 H:CBR6 3.2 57.8 1.0
C5 H:U5 3.6 47.4 1.0
C6 H:U5 3.6 44.6 1.0
OP2 H:CBR6 3.7 61.6 1.0
C4 H:U5 3.7 47.7 1.0
N1 H:U5 3.8 43.4 1.0
N3 H:U5 3.8 45.9 1.0
C2 H:U5 3.9 46.6 1.0
C3' H:U5 4.1 45.0 1.0
O5' H:CBR6 4.1 45.9 1.0
N1 H:CBR6 4.2 52.4 1.0
N3 H:CBR6 4.2 49.8 1.0
C2' H:U5 4.2 44.9 1.0
O4 H:U5 4.3 49.5 1.0
P H:CBR6 4.5 48.2 1.0
C1' H:U5 4.6 44.9 1.0
O2 H:U5 4.6 45.4 1.0
C2 H:CBR6 4.8 48.7 1.0
O3' H:U5 4.8 39.0 1.0

Bromine binding site 9 out of 12 in 7ecl

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Bromine binding site 9 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Br6

b:57.6
occ:1.00
BR I:CBR6 0.0 57.6 1.0
C5 I:CBR6 1.9 46.4 1.0
C6 I:CBR6 2.8 51.7 1.0
C4 I:CBR6 2.9 51.5 1.0
N4 I:CBR6 3.2 55.2 1.0
C5 I:U5 3.7 52.7 1.0
C4 I:U5 3.7 53.2 1.0
N3 I:U5 3.7 47.9 1.0
C6 I:U5 3.8 46.2 1.0
N1 I:U5 3.9 47.2 1.0
C2 I:U5 3.9 46.1 1.0
N1 I:CBR6 4.1 53.5 1.0
N3 I:CBR6 4.2 51.6 1.0
OP2 I:CBR6 4.2 44.8 1.0
O4 I:U5 4.2 50.6 1.0
O5' I:CBR6 4.3 34.3 1.0
C2' I:U5 4.3 48.2 1.0
N7 I:G7 4.4 54.0 1.0
C3' I:U5 4.5 46.4 1.0
O2 I:U5 4.6 44.6 1.0
C2 I:CBR6 4.7 51.0 1.0
C1' I:U5 4.7 54.1 1.0
P I:CBR6 4.9 42.5 1.0

Bromine binding site 10 out of 12 in 7ecl

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Bromine binding site 10 out of 12 in the Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Br6

b:81.1
occ:1.00
BR J:CBR6 0.0 81.1 1.0
C5 J:CBR6 2.0 51.1 1.0
C6 J:CBR6 3.0 51.0 1.0
C4 J:CBR6 3.0 54.6 1.0
N4 J:CBR6 3.2 52.4 1.0
C6 J:U5 3.5 49.8 1.0
C5 J:U5 3.6 48.4 1.0
N1 J:U5 3.8 50.4 1.0
OP2 J:CBR6 3.8 34.7 1.0
C4 J:U5 4.0 48.5 1.0
C2 J:U5 4.2 56.1 1.0
N3 J:U5 4.2 50.1 1.0
N3 J:CBR6 4.2 50.6 1.0
N1 J:CBR6 4.3 52.0 1.0
C3' J:U5 4.3 49.5 1.0
C2' J:U5 4.3 51.2 1.0
C1' J:U5 4.6 48.3 1.0
O4 J:U5 4.7 51.5 1.0
O5' J:CBR6 4.7 45.0 1.0
C2 J:CBR6 4.8 47.0 1.0
P J:CBR6 4.8 55.0 1.0
O2 J:U5 4.9 58.7 1.0
O4' J:U5 5.0 48.4 1.0

Reference:

J.Kondo, Y.Uchida. Rna Duplex Containing C-Ag-A and U-Ag-A Base Pair To Be Published.
Page generated: Thu Jul 11 03:44:58 2024

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