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Bromine in PDB 5lqt: Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs

Protein crystallography data

The structure of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs, PDB code: 5lqt was solved by L.Huang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.58 / 1.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 34.340, 34.340, 103.170, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 22.7

Other elements in 5lqt:

The structure of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Calcium (Ca) 1 atom
Sodium (Na) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs (pdb code 5lqt). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs, PDB code: 5lqt:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 5lqt

Go back to Bromine Binding Sites List in 5lqt
Bromine binding site 1 out of 2 in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2

b:35.5
occ:1.00
BR A:CBV2 0.0 35.5 1.0
C5 A:CBV2 1.9 29.1 1.0
C4 A:CBV2 2.9 29.0 1.0
C6 A:CBV2 2.9 28.1 1.0
N4 A:CBV2 3.2 30.8 1.0
O3P A:CBV2 3.5 45.3 1.0
C5 A:G1 3.6 30.1 1.0
O A:HOH204 3.6 46.2 1.0
N7 A:G1 3.7 36.5 1.0
O A:HOH202 3.7 35.9 1.0
C4 A:G1 3.8 32.9 1.0
C8 A:G1 3.8 34.2 1.0
N9 A:G1 3.9 34.1 1.0
C6 A:G1 4.1 33.0 1.0
C3' A:G1 4.2 35.8 1.0
N3 A:CBV2 4.3 28.4 1.0
N1 A:CBV2 4.3 25.8 1.0
N3 A:G1 4.4 31.1 1.0
C2' A:G1 4.4 35.3 1.0
O5' A:CBV2 4.4 34.2 1.0
O5' A:G1 4.5 40.7 1.0
P A:CBV2 4.6 34.8 1.0
N1 A:G1 4.6 30.3 1.0
O6 A:G1 4.6 34.2 1.0
C2 A:G1 4.7 32.7 1.0
C1' A:G1 4.8 31.8 1.0
N4 A:C3 4.8 28.4 1.0
C2 A:CBV2 4.8 30.7 1.0
O2P A:CBV2 4.8 56.6 1.0
O3' A:G1 4.9 36.9 1.0
C5 A:C3 5.0 29.6 1.0

Bromine binding site 2 out of 2 in 5lqt

Go back to Bromine Binding Sites List in 5lqt
Bromine binding site 2 out of 2 in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br2

b:37.1
occ:1.00
BR B:CBV2 0.0 37.1 1.0
C5 B:CBV2 1.9 31.9 1.0
C4 B:CBV2 2.9 29.9 1.0
C6 B:CBV2 2.9 35.6 1.0
N4 B:CBV2 3.2 31.9 1.0
O B:HOH202 3.4 40.7 1.0
O2P B:CBV2 3.6 45.8 1.0
O B:HOH217 3.6 39.8 1.0
N7 B:G1 3.6 34.0 1.0
C5 B:G1 3.6 30.2 1.0
O B:HOH212 3.6 39.8 1.0
O B:HOH206 3.7 40.8 1.0
C8 B:G1 3.7 31.5 1.0
C4 B:G1 3.8 29.1 1.0
N9 B:G1 3.8 30.7 1.0
C3' B:G1 4.1 32.0 1.0
C6 B:G1 4.2 32.8 1.0
N3 B:CBV2 4.3 32.9 1.0
N1 B:CBV2 4.3 33.3 1.0
C2' B:G1 4.3 32.7 1.0
O5' B:G1 4.4 36.9 1.0
O5' B:CBV2 4.5 39.3 1.0
N3 B:G1 4.5 30.0 1.0
P B:CBV2 4.6 38.3 1.0
N4 B:C3 4.6 38.2 1.0
C1' B:G1 4.6 31.5 1.0
O6 B:G1 4.8 33.4 1.0
N1 B:G1 4.8 30.9 1.0
C5 B:C3 4.8 35.6 1.0
C2 B:CBV2 4.8 33.2 1.0
O3' B:G1 4.8 35.8 1.0
C2 B:G1 4.9 28.5 1.0
O3P B:CBV2 4.9 62.0 1.0

Reference:

L.Huang, S.Ashraf, J.Wang, D.M.Lilley. Control of Box C/D Snornp Assembly By N(6)-Methylation of Adenine. Embo Rep. V. 18 1631 2017.
ISSN: ESSN 1469-3178
PubMed: 28623187
DOI: 10.15252/EMBR.201743967
Page generated: Thu Jul 11 00:12:12 2024

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