Bromine in PDB 3r1e: Crystal Structure of Gc(8BRG)Gcggc Duplex

Protein crystallography data

The structure of Crystal Structure of Gc(8BRG)Gcggc Duplex, PDB code: 3r1e 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) 16.41 / 0.97
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 50.666, 22.538, 44.183, 90.00, 117.82, 90.00
R / Rfree (%) 13.7 / n/a

Other elements in 3r1e:

The structure of Crystal Structure of Gc(8BRG)Gcggc Duplex also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Gc(8BRG)Gcggc Duplex (pdb code 3r1e). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of Gc(8BRG)Gcggc Duplex, PDB code: 3r1e:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 3r1e

Go back to Bromine Binding Sites List in 3r1e
Bromine binding site 1 out of 4 in the Crystal Structure of Gc(8BRG)Gcggc Duplex


Mono view


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)Gcggc Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br3

b:9.6
occ:0.80
BR A:GRB3 0.0 9.6 0.8
BR A:BR11 1.4 22.6 0.2
C8 A:GRB3 1.9 8.9 1.0
N7 A:GRB3 2.8 8.6 1.0
N9 A:GRB3 2.9 8.8 1.0
C1' A:GRB3 3.2 8.8 1.0
C2' A:GRB3 3.6 8.5 1.0
N2 B:G7 3.6 8.9 1.0
O B:HOH12 3.7 12.9 1.0
O4' A:G4 3.7 8.2 1.0
O A:HOH12 3.8 10.2 1.0
C5 A:GRB3 3.9 8.1 1.0
O B:HOH36 4.0 13.6 1.0
C4 A:GRB3 4.0 8.6 1.0
N2 B:G6 4.1 8.2 1.0
C1' A:G4 4.1 8.0 1.0
C2 B:G7 4.1 8.6 1.0
O2' A:GRB3 4.1 9.2 1.0
N3 B:G7 4.2 8.8 1.0
N9 A:G4 4.3 7.8 1.0
C8 A:G4 4.4 8.3 1.0
O4' A:GRB3 4.6 8.6 1.0
O A:HOH51 4.7 16.8 1.0
C3' A:GRB3 4.9 8.2 1.0
C4 A:G4 4.9 7.8 1.0

Bromine binding site 2 out of 4 in 3r1e

Go back to Bromine Binding Sites List in 3r1e
Bromine binding site 2 out of 4 in the Crystal Structure of Gc(8BRG)Gcggc Duplex


Mono view


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)Gcggc Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br3

b:11.8
occ:0.80
BR B:GRB3 0.0 11.8 0.8
BR B:BR10 1.6 23.6 0.2
C8 B:GRB3 1.9 10.3 1.0
N7 B:GRB3 2.8 9.9 1.0
N9 B:GRB3 2.9 10.7 1.0
C1' B:GRB3 3.3 10.7 1.0
C2' B:GRB3 3.4 10.7 1.0
O4' B:G4 3.5 8.9 1.0
O B:HOH42 3.5 16.4 1.0
N2 A:G7 3.7 11.7 1.0
N2 A:G6 3.7 9.9 0.5
N3 A:G7 3.7 11.1 1.0
O A:HOH39 3.7 19.2 1.0
C1' B:G4 3.9 8.5 1.0
N9 B:G4 3.9 8.4 1.0
C5 B:GRB3 3.9 10.0 1.0
C2 A:G7 3.9 11.0 1.0
O2' B:GRB3 3.9 11.4 1.0
C8 B:G4 3.9 9.1 1.0
N2 A:G6 4.0 8.8 0.5
C4 B:GRB3 4.0 10.2 1.0
O A:HOH63 4.1 22.0 1.0
O A:HOH70 4.2 21.7 1.0
C4 B:G4 4.5 7.8 1.0
N7 B:G4 4.6 8.8 1.0
O4' B:GRB3 4.7 11.1 1.0
C4 A:G7 4.7 10.9 1.0
C3' B:GRB3 4.8 10.8 1.0
C4' B:G4 4.9 8.5 1.0
N1 A:G7 4.9 11.0 1.0
C5 B:G4 4.9 8.5 1.0
C2 A:G6 5.0 8.8 0.5

Bromine binding site 3 out of 4 in 3r1e

Go back to Bromine Binding Sites List in 3r1e
Bromine binding site 3 out of 4 in the Crystal Structure of Gc(8BRG)Gcggc Duplex


Mono view


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)Gcggc Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br11

b:22.6
occ:0.20
BR A:GRB3 1.4 9.6 0.8
O B:HOH36 3.0 13.6 1.0
C8 A:GRB3 3.1 8.9 1.0
N2 B:G7 3.4 8.9 1.0
N3 B:G7 3.6 8.8 1.0
O B:HOH12 3.7 12.9 1.0
N7 A:GRB3 3.8 8.6 1.0
C2 B:G7 3.8 8.6 1.0
O A:HOH12 4.0 10.2 1.0
N9 A:GRB3 4.1 8.8 1.0
C1' A:GRB3 4.3 8.8 1.0
N2 B:G6 4.5 8.2 1.0
O4' A:G4 4.7 8.2 1.0
C2' A:GRB3 4.8 8.5 1.0
C4 B:G7 4.8 8.2 1.0
O A:HOH51 4.9 16.8 1.0

Bromine binding site 4 out of 4 in 3r1e

Go back to Bromine Binding Sites List in 3r1e
Bromine binding site 4 out of 4 in the Crystal Structure of Gc(8BRG)Gcggc Duplex


Mono view


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)Gcggc Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br10

b:23.6
occ:0.20
BR B:GRB3 1.6 11.8 0.8
O A:HOH63 2.6 22.0 1.0
C8 B:GRB3 3.4 10.3 1.0
O A:HOH70 3.6 21.7 1.0
O4' B:G4 3.6 8.9 1.0
C1' B:G4 3.7 8.5 1.0
N2 A:G6 3.7 9.9 0.5
O B:HOH42 3.9 16.4 1.0
N7 B:GRB3 4.0 9.9 1.0
N3 A:G7 4.1 11.1 1.0
N2 A:G6 4.1 8.8 0.5
N9 B:G4 4.1 8.4 1.0
C1' A:G7 4.4 12.6 1.0
O A:HOH39 4.4 19.2 1.0
N9 B:GRB3 4.5 10.7 1.0
O2' A:G7 4.5 15.2 1.0
C4 B:G4 4.6 7.8 1.0
C8 B:G4 4.7 9.1 1.0
N2 A:G7 4.7 11.7 1.0
C2 A:G7 4.7 11.0 1.0
C2' B:GRB3 4.7 10.7 1.0
C1' B:GRB3 4.8 10.7 1.0
C4 A:G7 4.8 10.9 1.0
N3 B:G4 4.9 7.9 1.0
O2' B:GRB3 4.9 11.4 1.0
C2' A:G7 4.9 12.7 1.0
C4' B:G4 4.9 8.5 1.0
N9 A:G7 5.0 11.4 1.0
C2 A:G6 5.0 8.8 0.5

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: Sat Dec 12 02:15:10 2020

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