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Bromine in PDB 2awe: Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex

Protein crystallography data

The structure of Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex, PDB code: 2awe was solved by B.Pan, K.Shi, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.36 / 2.10
Space group I 41 2 2 1
Cell size a, b, c (Å), α, β, γ (°) 82.667, 82.667, 74.154, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 22.8

Other elements in 2awe:

The structure of Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex also contains other interesting chemical elements:

Strontium (Sr) 1 atom
Potassium (K) 11 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex (pdb code 2awe). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex, PDB code: 2awe:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 2awe

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Bromine binding site 1 out of 8 in the Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2

b:26.3
occ:1.00
BR A:BGM2 0.0 26.3 1.0
C8 A:BGM2 2.0 15.9 1.0
N7 A:BGM2 2.9 14.1 1.0
N9 A:BGM2 2.9 16.9 1.0
O D:HOH49 3.1 37.3 1.0
C1' A:BGM2 3.4 18.3 1.0
O4' A:G3 3.5 11.5 1.0
O D:HOH97 3.5 34.6 1.0
O4' H:U1 3.6 22.6 1.0
C1' H:U1 3.7 20.1 1.0
O A:HOH222 3.8 17.1 1.0
O D:HOH105 3.9 32.8 1.0
O D:HOH17 3.9 14.1 1.0
N2 D:BGM2 4.0 13.0 1.0
C5 A:BGM2 4.0 14.8 1.0
C4 A:BGM2 4.1 15.4 1.0
N1 H:U1 4.1 18.9 1.0
C1' A:G3 4.1 11.5 1.0
N9 A:G3 4.2 10.6 1.0
N3 A:G3 4.2 6.3 1.0
C4 A:G3 4.3 9.0 1.0
O4' A:BGM2 4.3 21.5 1.0
C4' A:G3 4.4 12.9 1.0
O H:HOH165 4.5 55.9 1.0
C6 H:U1 4.6 15.6 1.0
C2' A:BGM2 4.6 18.8 1.0
C2 H:U1 4.6 17.3 1.0
C4' H:U1 4.6 25.1 1.0
O2 H:U1 4.8 19.5 1.0
C5' A:G3 4.8 12.1 1.0
C2 A:G3 4.9 7.2 1.0
C8 A:G3 4.9 11.8 1.0
C5 A:G3 5.0 8.4 1.0

Bromine binding site 2 out of 8 in 2awe

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Bromine binding site 2 out of 8 in the Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br2

b:29.2
occ:1.00
BR B:BGM2 0.0 29.2 1.0
C8 B:BGM2 2.0 19.7 1.0
N7 B:BGM2 3.0 18.4 1.0
N9 B:BGM2 3.0 18.7 1.0
O4' G:U1 3.4 22.9 1.0
C1' B:BGM2 3.4 17.4 1.0
O4' B:G3 3.4 19.8 1.0
O B:HOH23 3.8 17.8 1.0
C5' G:U1 4.0 23.9 1.0
C1' B:G3 4.0 16.2 1.0
N3 B:G3 4.0 12.6 1.0
O C:HOH232 4.1 33.9 1.0
C5 B:BGM2 4.1 17.0 1.0
C4 B:BGM2 4.1 17.5 1.0
O4' B:BGM2 4.1 18.3 1.0
O5' G:U1 4.1 27.6 1.0
N2 C:BGM2 4.1 19.9 1.0
N9 B:G3 4.1 15.7 1.0
C4 B:G3 4.2 13.3 1.0
C4' G:U1 4.2 25.4 1.0
C4' B:G3 4.4 21.3 1.0
C6 G:U1 4.4 15.8 1.0
C1' G:U1 4.5 21.3 1.0
N1 G:U1 4.7 18.6 1.0
C2' B:BGM2 4.7 18.8 1.0
C2 B:G3 4.8 11.1 1.0
C5' B:G3 4.9 21.1 1.0
C8 B:G3 5.0 12.8 1.0
C5 B:G3 5.0 11.1 1.0

Bromine binding site 3 out of 8 in 2awe

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Bromine binding site 3 out of 8 in the Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br2

b:31.8
occ:1.00
BR C:BGM2 0.0 31.8 1.0
C8 C:BGM2 2.0 20.9 1.0
N9 C:BGM2 2.9 19.3 1.0
N7 C:BGM2 2.9 19.1 1.0
O C:HOH236 3.2 32.8 1.0
C1' C:BGM2 3.3 20.5 1.0
O4' C:G3 3.6 18.5 1.0
C1' F:U1 3.7 34.8 1.0
O C:HOH240 3.8 29.8 1.0
O C:HOH229 3.9 17.4 1.0
N2 A:BGM2 4.0 17.0 1.0
C4 C:BGM2 4.0 17.9 1.0
C5 C:BGM2 4.0 17.2 1.0
O4' C:BGM2 4.1 23.1 1.0
O4' F:U1 4.1 38.0 1.0
O A:HOH237 4.1 29.6 1.0
C1' C:G3 4.2 16.4 1.0
N1 F:U1 4.2 30.7 1.0
O2 F:U1 4.3 28.2 1.0
O2' F:U1 4.4 45.3 1.0
C4' C:G3 4.4 18.0 1.0
N9 C:G3 4.4 13.6 1.0
C2 F:U1 4.4 29.3 1.0
C4' F:U1 4.4 38.7 1.0
N3 C:G3 4.5 11.1 1.0
C4 C:G3 4.5 12.8 1.0
C2' C:BGM2 4.6 20.4 1.0
C2' F:U1 4.7 39.0 1.0
C5' C:G3 4.9 19.3 1.0

Bromine binding site 4 out of 8 in 2awe

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Bromine binding site 4 out of 8 in the Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br2

b:25.6
occ:1.00
BR D:BGM2 0.0 25.6 1.0
C8 D:BGM2 2.0 13.5 1.0
N7 D:BGM2 2.9 13.8 1.0
N9 D:BGM2 3.0 13.0 1.0
O4' E:U1 3.4 19.3 1.0
C1' D:BGM2 3.4 13.8 1.0
O4' D:G3 3.5 13.8 1.0
O B:HOH40 3.8 23.1 1.0
N3 D:G3 3.9 9.9 1.0
O D:HOH45 3.9 24.3 1.0
N2 B:BGM2 4.0 18.3 1.0
C4 D:G3 4.0 11.8 1.0
O4' D:BGM2 4.0 14.2 1.0
C5 D:BGM2 4.1 12.4 1.0
C1' D:G3 4.1 12.7 1.0
N9 D:G3 4.1 12.0 1.0
C4 D:BGM2 4.1 12.7 1.0
C1' E:U1 4.2 16.7 1.0
C4' E:U1 4.4 17.7 1.0
C4' D:G3 4.5 14.7 1.0
N1 E:U1 4.5 15.2 1.0
C5' E:U1 4.6 20.2 1.0
C6 E:U1 4.6 13.2 1.0
C2 D:G3 4.6 11.9 1.0
C2' D:BGM2 4.7 11.5 1.0
O5' E:U1 4.8 20.0 1.0
C5 D:G3 4.8 10.2 1.0
C8 D:G3 4.9 9.4 1.0
C5' D:G3 5.0 16.4 1.0

Bromine binding site 5 out of 8 in 2awe

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Bromine binding site 5 out of 8 in the Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br2

b:27.2
occ:1.00
BR E:BGM2 0.0 27.2 1.0
C8 E:BGM2 2.0 16.5 1.0
N7 E:BGM2 2.9 16.6 1.0
N9 E:BGM2 3.0 15.6 1.0
O E:HOH112 3.1 41.1 1.0
O4' D:U1 3.3 18.3 1.0
C1' E:BGM2 3.4 15.8 1.0
O E:HOH73 3.4 25.6 1.0
O4' E:G3 3.6 18.1 1.0
O H:HOH86 3.8 25.0 1.0
N3 E:G3 3.9 14.8 1.0
N2 H:BGM2 4.0 20.5 1.0
C4 E:G3 4.0 14.8 1.0
C1' E:G3 4.0 16.8 1.0
N9 E:G3 4.0 16.5 1.0
C5 E:BGM2 4.1 14.1 1.0
C4 E:BGM2 4.1 15.5 1.0
O4' E:BGM2 4.1 17.1 1.0
O E:HOH67 4.2 25.8 1.0
C5' D:U1 4.3 18.9 1.0
C4' D:U1 4.3 18.9 1.0
C1' D:U1 4.3 16.5 1.0
O5' D:U1 4.4 21.1 1.0
O E:HOH179 4.5 48.7 1.0
O E:HOH172 4.5 37.5 1.0
C4' E:G3 4.5 19.9 1.0
C2 E:G3 4.6 15.7 1.0
C6 D:U1 4.6 15.0 1.0
N1 D:U1 4.7 14.7 1.0
C2' E:BGM2 4.7 13.6 1.0
C5 E:G3 4.7 14.7 1.0
C8 E:G3 4.8 14.9 1.0

Bromine binding site 6 out of 8 in 2awe

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Bromine binding site 6 out of 8 in the Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Br2

b:30.5
occ:1.00
BR F:BGM2 0.0 30.5 1.0
C8 F:BGM2 2.0 20.8 1.0
N7 F:BGM2 2.9 17.9 1.0
N9 F:BGM2 3.0 20.3 1.0
O G:HOH41 3.1 24.7 1.0
C1' F:BGM2 3.4 21.4 1.0
O4' F:G3 3.4 16.7 1.0
C1' C:U1 3.6 31.2 1.0
O F:HOH240 3.7 48.2 1.0
O4' C:U1 4.0 30.6 1.0
O G:HOH35 4.0 20.4 1.0
O F:HOH222 4.0 13.8 1.0
C5 F:BGM2 4.0 17.8 1.0
N1 C:U1 4.1 26.2 1.0
O2 C:U1 4.1 28.0 1.0
N2 G:BGM2 4.1 21.9 1.0
C4 F:BGM2 4.1 17.7 1.0
C1' F:G3 4.1 16.0 1.0
C2 C:U1 4.2 26.5 1.0
C4' F:G3 4.2 19.3 1.0
O4' F:BGM2 4.3 23.8 1.0
N9 F:G3 4.3 15.4 1.0
C4' C:U1 4.4 32.3 1.0
O2' C:U1 4.4 39.7 1.0
C4 F:G3 4.5 12.4 1.0
N3 F:G3 4.5 12.8 1.0
C2' C:U1 4.6 35.5 1.0
C2' F:BGM2 4.6 21.6 1.0
C5' F:G3 4.8 18.6 1.0
C6 C:U1 4.8 24.6 1.0

Bromine binding site 7 out of 8 in 2awe

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Bromine binding site 7 out of 8 in the Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Br2

b:31.6
occ:1.00
BR G:BGM2 0.0 31.6 1.0
C8 G:BGM2 2.0 19.1 1.0
N7 G:BGM2 2.9 18.8 1.0
N9 G:BGM2 3.0 18.6 1.0
O E:HOH61 3.1 34.3 1.0
C1' G:BGM2 3.3 19.4 1.0
O4' G:G3 3.4 18.3 1.0
O4' B:U1 3.5 24.6 1.0
O G:HOH74 3.7 37.6 1.0
C1' B:U1 3.9 21.0 1.0
O E:HOH22 3.9 15.1 1.0
O4' G:BGM2 4.0 18.6 1.0
N2 E:BGM2 4.0 16.9 1.0
C1' G:G3 4.0 16.2 1.0
N3 G:G3 4.0 11.9 1.0
C4 G:G3 4.1 12.2 1.0
C5 G:BGM2 4.1 17.0 1.0
N9 G:G3 4.1 15.3 1.0
C4 G:BGM2 4.1 17.7 1.0
N1 B:U1 4.2 18.4 1.0
O G:HOH32 4.3 29.1 1.0
C4' G:G3 4.3 19.7 1.0
O G:HOH161 4.3 32.3 1.0
C6 B:U1 4.5 13.1 1.0
C4' B:U1 4.7 25.7 1.0
C2' G:BGM2 4.7 18.5 1.0
C2 G:G3 4.8 12.5 1.0
C8 G:G3 4.8 13.5 1.0
C5 G:G3 4.9 11.8 1.0
C5' G:G3 4.9 20.2 1.0
C2 B:U1 4.9 15.7 1.0

Bromine binding site 8 out of 8 in 2awe

Go back to Bromine Binding Sites List in 2awe
Bromine binding site 8 out of 8 in the Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of I-Motif Rna Octaplex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br2

b:33.3
occ:1.00
BR H:BGM2 0.0 33.3 1.0
C8 H:BGM2 2.0 21.5 1.0
N9 H:BGM2 2.9 21.3 1.0
N7 H:BGM2 2.9 18.9 1.0
C1' H:BGM2 3.3 21.5 1.0
O4' A:U1 3.4 24.0 1.0
O4' H:G3 3.4 19.2 1.0
O H:HOH129 3.8 29.6 1.0
O F:HOH227 3.9 22.7 1.0
C5' A:U1 3.9 25.1 1.0
C1' H:G3 4.0 16.5 1.0
C4 H:BGM2 4.1 20.4 1.0
C5 H:BGM2 4.1 19.8 1.0
N2 F:BGM2 4.1 19.8 1.0
O4' H:BGM2 4.1 23.0 1.0
N3 H:G3 4.1 13.5 1.0
N9 H:G3 4.1 15.0 1.0
C4 H:G3 4.2 13.4 1.0
C4' A:U1 4.2 25.4 1.0
C4' H:G3 4.3 20.7 1.0
O5' A:U1 4.3 25.1 1.0
O H:HOH148 4.4 44.3 1.0
O H:HOH139 4.5 36.9 1.0
C6 A:U1 4.5 19.9 1.0
C1' A:U1 4.6 22.3 1.0
C2' H:BGM2 4.6 21.3 1.0
N1 A:U1 4.8 20.4 1.0
C5' H:G3 4.8 19.5 1.0
C2 H:G3 4.8 13.9 1.0
C8 H:G3 4.9 15.3 1.0
C5 H:G3 5.0 13.0 1.0

Reference:

B.Pan, K.Shi, M.Sundaralingam. Base-Tetrad Swapping Results in Dimerization of Rna Quadruplexes: Implications For Formation of the I-Motif Rna Octaplex. Proc.Natl.Acad.Sci.Usa V. 103 3130 2006.
ISSN: ISSN 0027-8424
PubMed: 16492787
DOI: 10.1073/PNAS.0507730103
Page generated: Sat Dec 12 02:05:12 2020

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