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Bromine in PDB 3r1d: Crystal Structure of Gc(8BRG)Gcggcggc Duplex

Protein crystallography data

The structure of Crystal Structure of Gc(8BRG)Gcggcggc Duplex, PDB code: 3r1d was solved by A.Kiliszek, R.Kierzek, W.J.Krzyzosiak, W.Rypniewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 118.565, 28.612, 61.833, 90.00, 117.98, 90.00
R / Rfree (%) 23.2 / 27

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Gc(8BRG)Gcggcggc Duplex (pdb code 3r1d). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 10 binding sites of Bromine where determined in the Crystal Structure of Gc(8BRG)Gcggcggc Duplex, PDB code: 3r1d:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 10 in 3r1d

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Bromine binding site 1 out of 10 in the Crystal Structure of Gc(8BRG)Gcggcggc Duplex


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Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Gc(8BRG)Gcggcggc Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br3

b:22.9
occ:0.35
 BR A:GRB3 0.0 22.9 0.3
BR A:GRB3 1.4 22.5 0.2
C8 A:GRB3 1.9 18.4 0.7
N7 A:GRB3 2.8 21.6 0.7
N9 A:GRB3 2.9 19.9 0.7
C8 A:GRB3 3.0 22.1 0.3
C1' A:GRB3 3.2 16.9 0.7
BR A:BR12 3.3 38.8 0.4
C2' A:GRB3 3.4 19.3 0.7
O4' A:G4 3.5 21.7 0.7
N2 B:G10 3.6 27.0 1.0
N7 A:GRB3 3.7 20.9 0.3
N3 B:G10 3.7 22.0 1.0
N2 B:G9 3.7 23.7 1.0
O4' A:G4 3.9 16.7 0.3
O2' A:GRB3 3.9 20.9 0.7
C2 B:G10 3.9 22.4 1.0
C1' A:G4 3.9 21.8 0.7
C5 A:GRB3 4.0 20.1 0.7
C4 A:GRB3 4.0 19.7 0.7
C1' A:G4 4.0 21.2 0.3
N9 A:G4 4.1 18.9 0.7
N9 A:GRB3 4.1 19.1 0.3
C8 A:G4 4.3 20.4 0.7
N9 A:G4 4.5 18.4 0.3
C1' A:GRB3 4.5 21.8 0.3
O4' A:GRB3 4.6 22.5 0.7
C4 B:G10 4.7 23.7 1.0
C2' A:GRB3 4.7 21.0 0.3
C3' A:GRB3 4.7 20.2 0.7
C4' A:G4 4.8 20.0 0.7
C4 A:G4 4.9 18.8 0.7
C8 A:G4 4.9 18.4 0.3
N1 B:G10 4.9 25.4 1.0
C5 A:GRB3 4.9 19.9 0.3
O2' A:GRB3 5.0 21.0 0.3

Bromine binding site 2 out of 10 in 3r1d

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Bromine binding site 2 out of 10 in the Crystal Structure of Gc(8BRG)Gcggcggc Duplex


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Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Gc(8BRG)Gcggcggc Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br3

b:22.5
occ:0.25
 BR A:GRB3 0.0 22.5 0.2
C8 A:GRB3 1.2 18.4 0.7
BR A:GRB3 1.4 22.9 0.3
N9 A:GRB3 1.8 19.9 0.7
C8 A:GRB3 1.9 22.1 0.3
C1' A:GRB3 2.2 16.9 0.7
C2' A:GRB3 2.3 19.3 0.7
N7 A:GRB3 2.4 21.6 0.7
N7 A:GRB3 2.8 20.9 0.3
N9 A:GRB3 2.9 19.1 0.3
C4 A:GRB3 3.0 19.7 0.7
O4' A:G4 3.1 21.7 0.7
O4' A:G4 3.1 16.7 0.3
C5 A:GRB3 3.2 20.1 0.7
O2' A:GRB3 3.2 20.9 0.7
C1' A:GRB3 3.3 21.8 0.3
C2' A:GRB3 3.4 21.0 0.3
C8 A:G4 3.4 20.4 0.7
C3' A:GRB3 3.5 20.2 0.7
C1' A:G4 3.6 21.2 0.3
O4' A:GRB3 3.6 22.5 0.7
N9 A:G4 3.6 18.9 0.7
C1' A:G4 3.7 21.8 0.7
N9 A:G4 3.8 18.4 0.3
N2 B:G10 3.8 27.0 1.0
C8 A:G4 3.9 18.4 0.3
O2' A:GRB3 3.9 21.0 0.3
N2 B:G9 4.0 23.7 1.0
C5 A:GRB3 4.0 19.9 0.3
C4 A:GRB3 4.0 21.8 0.3
N3 A:GRB3 4.2 22.6 0.7
N7 A:G4 4.2 17.8 0.7
C4' A:GRB3 4.2 17.3 0.7
C2 B:G10 4.3 22.4 1.0
C4' A:G4 4.3 20.0 0.7
BR A:BR12 4.3 38.8 0.4
O5' A:G4 4.3 19.4 0.7
C4' A:G4 4.4 21.9 0.3
C5' A:G4 4.4 20.4 0.7
N3 B:G10 4.5 22.0 1.0
C4 A:G4 4.5 18.8 0.7
O3' A:GRB3 4.5 21.0 0.7
C6 A:GRB3 4.6 20.0 0.7
O4' A:GRB3 4.7 22.4 0.3
C3' A:GRB3 4.7 19.8 0.3
C4 A:G4 4.8 19.0 0.3
N7 A:G4 4.8 16.2 0.3
C5 A:G4 4.8 16.2 0.7
C5' A:G4 5.0 20.0 0.3

Bromine binding site 3 out of 10 in 3r1d

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Bromine binding site 3 out of 10 in the Crystal Structure of Gc(8BRG)Gcggcggc Duplex


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Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Gc(8BRG)Gcggcggc Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br3

b:27.1
occ:0.40
 BR B:GRB3 0.0 27.1 0.4
BR B:BR12 0.8 47.8 0.3
C8 B:GRB3 1.9 29.1 1.0
N7 B:GRB3 2.9 20.9 1.0
N9 B:GRB3 2.9 23.3 1.0
C1' B:GRB3 3.3 30.7 1.0
C2' B:GRB3 3.5 29.2 1.0
O4' B:G4 3.5 21.9 1.0
O A:HOH244 3.7 40.1 1.0
N2 A:G10 3.7 24.1 1.0
N3 A:G10 3.7 28.8 1.0
N2 A:G9 3.8 21.3 1.0
C1' B:G4 3.9 20.7 1.0
O B:HOH108 3.9 29.7 1.0
C2 A:G10 3.9 23.4 1.0
O2' B:GRB3 4.0 31.6 1.0
N9 B:G4 4.0 17.5 1.0
C5 B:GRB3 4.0 24.4 1.0
C4 B:GRB3 4.1 24.5 1.0
C8 B:G4 4.1 17.8 1.0
C4 A:G10 4.7 23.3 1.0
O4' B:GRB3 4.7 29.5 1.0
C4 B:G4 4.7 17.3 1.0
C3' B:GRB3 4.8 22.4 1.0
C4' B:G4 4.9 20.6 1.0
N7 B:G4 4.9 18.9 1.0
N1 A:G10 4.9 22.0 1.0

Bromine binding site 4 out of 10 in 3r1d

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Bromine binding site 4 out of 10 in the Crystal Structure of Gc(8BRG)Gcggcggc Duplex


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Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Gc(8BRG)Gcggcggc Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br3

b:35.8
occ:0.60
 BR C:GRB3 0.0 35.8 0.6
BR C:GRB3 1.4 33.5 0.4
C8 C:GRB3 1.9 28.5 0.6
N7 C:GRB3 2.9 25.9 0.6
N9 C:GRB3 2.9 27.9 0.6
C8 C:GRB3 3.2 27.1 0.4
C1' C:GRB3 3.3 30.4 0.6
C2' C:GRB3 3.5 27.2 0.6
O4' C:G4 3.6 28.5 0.6
N2 D:G10 3.6 30.6 1.0
N3 D:G10 3.8 24.6 1.0
O4' C:G4 4.0 25.2 0.4
C2 D:G10 4.0 21.9 1.0
C5 C:GRB3 4.0 27.0 0.6
C4 C:GRB3 4.1 28.4 0.6
O2' C:GRB3 4.1 31.9 0.6
N7 C:GRB3 4.1 24.2 0.4
N9 C:GRB3 4.1 27.0 0.4
N2 D:G9 4.1 22.0 1.0
C1' C:G4 4.1 23.4 0.6
C1' C:GRB3 4.2 27.2 0.4
C8 C:G4 4.2 24.3 0.6
N9 C:G4 4.3 22.9 0.6
C1' C:G4 4.3 24.2 0.4
C2' C:GRB3 4.4 27.5 0.4
O2' C:GRB3 4.6 28.2 0.4
O4' C:GRB3 4.7 28.8 0.6
N9 C:G4 4.8 23.0 0.4
C3' C:GRB3 4.8 28.4 0.6
C4 D:G10 4.8 22.4 1.0
C4' C:G4 4.9 25.2 0.6

Bromine binding site 5 out of 10 in 3r1d

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Bromine binding site 5 out of 10 in the Crystal Structure of Gc(8BRG)Gcggcggc Duplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of Gc(8BRG)Gcggcggc Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br3

b:33.5
occ:0.40
 BR C:GRB3 0.0 33.5 0.4
C8 C:GRB3 0.8 28.5 0.6
BR C:GRB3 1.4 35.8 0.6
N7 C:GRB3 1.7 25.9 0.6
C8 C:GRB3 1.9 27.1 0.4
N9 C:GRB3 2.0 27.9 0.6
C5 C:GRB3 2.7 27.0 0.6
N7 C:GRB3 2.8 24.2 0.4
C1' C:GRB3 2.9 30.4 0.6
N9 C:GRB3 2.9 27.0 0.4
C4 C:GRB3 2.9 28.4 0.6
C2' C:GRB3 3.1 27.2 0.6
C8 C:G4 3.2 24.3 0.6
C1' C:GRB3 3.3 27.2 0.4
O4' C:G4 3.4 25.2 0.4
N2 D:G9 3.5 22.0 1.0
O4' C:G4 3.5 28.5 0.6
C2' C:GRB3 3.5 27.5 0.4
N2 D:G10 3.5 30.6 1.0
N9 C:G4 3.6 22.9 0.6
C1' C:G4 3.7 24.2 0.4
C2 D:G10 3.8 21.9 1.0
N7 C:G4 3.8 22.5 0.6
N9 C:G4 3.8 23.0 0.4
C8 C:G4 3.9 23.1 0.4
C1' C:G4 3.9 23.4 0.6
N3 D:G10 3.9 24.6 1.0
C5 C:GRB3 4.0 26.4 0.4
C4 C:GRB3 4.0 25.1 0.4
C3' C:GRB3 4.1 28.4 0.6
C6 C:GRB3 4.1 26.1 0.6
O2' C:GRB3 4.1 28.2 0.4
O2' C:GRB3 4.1 31.9 0.6
O4' C:GRB3 4.2 28.8 0.6
N3 C:GRB3 4.2 28.2 0.6
C4 C:G4 4.4 21.6 0.6
C5 C:G4 4.5 22.3 0.6
N1 D:G10 4.6 26.8 1.0
C4 C:G4 4.6 21.5 0.4
N7 C:G4 4.7 22.7 0.4
O5' C:G4 4.7 26.8 0.6
O4' C:GRB3 4.7 26.6 0.4
O6 C:GRB3 4.8 26.2 0.6
C2 D:G9 4.8 19.9 1.0
C4 D:G10 4.8 22.4 1.0
C4' C:G4 4.8 25.2 0.6
C4' C:G4 4.8 24.9 0.4
C3' C:GRB3 4.8 26.8 0.4
C4' C:GRB3 4.9 28.9 0.6
C5' C:G4 4.9 26.4 0.6

Bromine binding site 6 out of 10 in 3r1d

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Bromine binding site 6 out of 10 in the Crystal Structure of Gc(8BRG)Gcggcggc Duplex


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Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of Gc(8BRG)Gcggcggc Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br3

b:18.4
occ:0.61
 BR D:GRB3 0.0 18.4 0.6
C8 D:GRB3 1.9 15.6 1.0
O D:HOH249 2.6 26.6 1.0
N7 D:GRB3 2.8 14.7 1.0
N9 D:GRB3 2.9 16.3 1.0
C1' D:GRB3 3.3 18.4 1.0
C2' D:GRB3 3.4 20.4 1.0
O D:HOH251 3.5 26.1 0.5
N2 C:G10 3.5 16.7 1.0
O C:HOH14 3.6 20.2 1.0
O4' D:G4 3.6 17.7 1.0
N3 C:G10 3.7 14.4 1.0
C2 C:G10 3.8 14.2 1.0
O C:HOH46 3.9 23.4 1.0
N2 C:G9 3.9 13.9 1.0
O2' D:GRB3 3.9 19.9 1.0
C5 D:GRB3 3.9 15.7 1.0
C4 D:GRB3 4.0 16.7 1.0
N9 D:G4 4.1 12.3 1.0
C1' D:G4 4.1 16.9 1.0
C8 D:G4 4.1 12.9 1.0
C4 C:G10 4.7 13.3 1.0
O4' D:GRB3 4.7 19.6 1.0
C4 D:G4 4.7 13.6 1.0
N7 D:G4 4.8 15.4 1.0
C3' D:GRB3 4.8 20.6 1.0
N1 C:G10 4.8 13.1 1.0
C4' D:G4 5.0 17.8 1.0

Bromine binding site 7 out of 10 in 3r1d

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Bromine binding site 7 out of 10 in the Crystal Structure of Gc(8BRG)Gcggcggc Duplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of Gc(8BRG)Gcggcggc Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br3

b:32.7
occ:0.50
 BR E:GRB3 0.0 32.7 0.5
BR E:GRB3 1.2 27.1 0.5
C8 E:GRB3 1.2 21.7 0.5
C8 E:GRB3 1.9 23.0 0.5
N7 E:GRB3 2.1 22.5 0.5
N9 E:GRB3 2.3 22.2 0.5
N7 E:GRB3 2.8 21.3 0.5
N9 E:GRB3 2.9 21.6 0.5
O4' E:G4 3.0 24.2 0.5
C1' E:GRB3 3.0 18.9 0.5
O4' E:G4 3.1 24.6 0.5
C2' E:GRB3 3.1 22.6 0.5
C5 E:GRB3 3.1 22.1 0.5
C8 E:G4 3.3 23.9 0.5
C4 E:GRB3 3.3 20.8 0.5
C1' E:G4 3.3 23.4 0.5
C1' E:GRB3 3.3 22.0 0.5
N9 E:G4 3.3 21.4 0.5
C1' E:G4 3.4 23.9 0.5
N9 E:G4 3.5 21.5 0.5
C2' E:GRB3 3.5 24.5 0.5
C8 E:G4 3.7 22.9 0.5
C5 E:GRB3 4.0 21.3 0.5
N7 E:G4 4.0 22.0 0.5
C4 E:GRB3 4.0 23.5 0.5
O E:HOH158 4.0 32.2 1.0
O2' E:GRB3 4.0 21.4 0.5
C4 E:G4 4.1 22.1 0.5
O2' E:GRB3 4.1 25.6 0.5
C3' E:GRB3 4.2 22.5 0.5
O4' E:GRB3 4.4 18.3 0.5
C4' E:G4 4.4 23.2 0.5
C4 E:G4 4.4 22.4 0.5
C4' E:G4 4.4 23.5 0.5
O E:HOH216 4.4 30.2 1.0
C6 E:GRB3 4.4 22.5 0.5
C5 E:G4 4.5 21.8 0.5
N7 E:G4 4.5 22.1 0.5
N3 E:GRB3 4.6 22.2 0.5
O5' E:G4 4.7 20.9 0.5
O4' E:GRB3 4.7 23.4 0.5
C2' E:G4 4.8 23.1 0.5
C5' E:G4 4.8 23.2 0.5
C3' E:GRB3 4.8 23.5 0.5
C5 E:G4 4.9 22.2 0.5
C2' E:G4 4.9 23.2 0.5
N3 E:G4 4.9 22.9 0.5

Bromine binding site 8 out of 10 in 3r1d

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Bromine binding site 8 out of 10 in the Crystal Structure of Gc(8BRG)Gcggcggc Duplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of Gc(8BRG)Gcggcggc Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br3

b:27.1
occ:0.50
 BR E:GRB3 0.0 27.1 0.5
BR E:GRB3 1.2 32.7 0.5
C8 E:GRB3 1.9 21.7 0.5
N7 E:GRB3 2.8 22.5 0.5
N9 E:GRB3 2.9 22.2 0.5
C8 E:GRB3 2.9 23.0 0.5
C1' E:GRB3 3.3 18.9 0.5
O E:HOH158 3.3 32.2 1.0
O4' E:G4 3.4 24.2 0.5
C2' E:GRB3 3.5 22.6 0.5
O4' E:G4 3.7 24.6 0.5
N7 E:GRB3 3.8 21.3 0.5
N9 E:GRB3 3.8 21.6 0.5
C1' E:G4 3.9 23.9 0.5
C1' E:G4 3.9 23.4 0.5
O E:HOH216 4.0 30.2 1.0
C5 E:GRB3 4.0 22.1 0.5
C4 E:GRB3 4.0 20.8 0.5
C1' E:GRB3 4.0 22.0 0.5
O2' E:GRB3 4.1 21.4 0.5
N9 E:G4 4.1 21.4 0.5
C2' E:GRB3 4.3 24.5 0.5
C8 E:G4 4.3 23.9 0.5
N9 E:G4 4.4 21.5 0.5
O2' E:GRB3 4.6 25.6 0.5
O4' E:GRB3 4.7 18.3 0.5
C8 E:G4 4.7 22.9 0.5
C4' E:G4 4.7 23.2 0.5
C3' E:GRB3 4.8 22.5 0.5
C4 E:G4 4.9 22.1 0.5
C4' E:G4 4.9 23.5 0.5
C5 E:GRB3 4.9 21.3 0.5

Bromine binding site 9 out of 10 in 3r1d

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Bromine binding site 9 out of 10 in the Crystal Structure of Gc(8BRG)Gcggcggc Duplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Crystal Structure of Gc(8BRG)Gcggcggc Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br12

b:38.8
occ:0.40
 O B:HOH60 3.0 31.0 0.8
BR A:GRB3 3.3 22.9 0.3
N2 B:G9 3.6 23.7 1.0
C1' A:G4 3.9 21.8 0.7
C1' B:G10 3.9 29.4 1.0
N3 A:G4 4.2 16.8 0.7
O4' B:G10 4.2 28.2 1.0
O4' A:G4 4.3 21.7 0.7
BR A:GRB3 4.3 22.5 0.2
N9 A:G4 4.4 18.9 0.7
C1' A:G4 4.4 21.2 0.3
O2' B:G10 4.5 26.7 1.0
C4 A:G4 4.5 18.8 0.7
C2 B:G9 4.6 20.7 1.0
N3 B:G9 4.6 22.4 1.0
N9 B:G10 4.6 21.6 1.0
N3 B:G10 4.7 22.0 1.0
C8 A:GRB3 4.7 18.4 0.7
O2' A:G4 4.7 21.7 0.7
N3 A:G4 4.7 17.5 0.3
O2' A:G4 4.7 22.6 0.3
N7 A:GRB3 4.9 21.6 0.7
C2' B:G10 4.9 23.6 1.0
C4 B:G10 4.9 23.7 1.0
C2' A:G4 4.9 22.0 0.7

Bromine binding site 10 out of 10 in 3r1d

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Bromine binding site 10 out of 10 in the Crystal Structure of Gc(8BRG)Gcggcggc Duplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Crystal Structure of Gc(8BRG)Gcggcggc Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br12

b:47.8
occ:0.30
 BR B:GRB3 0.8 27.1 0.4
C8 B:GRB3 2.7 29.1 1.0
O A:HOH244 3.3 40.1 1.0
O B:HOH108 3.4 29.7 1.0
N9 B:GRB3 3.6 23.3 1.0
N7 B:GRB3 3.7 20.9 1.0
O4' B:G4 3.7 21.9 1.0
C1' B:GRB3 3.8 30.7 1.0
N3 A:G10 3.9 28.8 1.0
C2' B:GRB3 3.9 29.2 1.0
N2 A:G10 4.0 24.1 1.0
C1' B:G4 4.1 20.7 1.0
O2' B:GRB3 4.2 31.6 1.0
C2 A:G10 4.2 23.4 1.0
N2 A:G9 4.3 21.3 1.0
N9 B:G4 4.5 17.5 1.0
O B:HOH205 4.6 31.4 1.0
C8 B:G4 4.8 17.8 1.0
C5 B:GRB3 4.8 24.4 1.0
C4 A:G10 4.8 23.3 1.0
C4 B:GRB3 4.9 24.5 1.0
C4' B:G4 5.0 20.6 1.0

Reference:

A.Kiliszek, R.Kierzek, W.J.Krzyzosiak, W.Rypniewski. Crystal Structures of Cgg Rna Repeats with Implications For Fragile X-Associated Tremor Ataxia Syndrome. Nucleic Acids Res. V. 39 7308 2011.
ISSN: ISSN 0305-1048
PubMed: 21596781
DOI: 10.1093/NAR/GKR368
Page generated: Wed Jul 10 20:16:41 2024

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