Bromine in PDB 2ao5: Crystal Structure of An Rna Duplex R(Ggcgbrugcgcu)2 with Terminal and Internal Tandem G-U Base Pairs

The structure of Crystal Structure of An Rna Duplex R(Ggcgbrugcgcu)2 with Terminal and Internal Tandem G-U Base Pairs, PDB code: 2ao5 was solved by R.Utsunomiya, K.Suto, D.Balasundaresan, A.Fukamizu, P.K.Kumar, H.Mizuno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.68 / 2.10
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	37.693, 37.693, 96.283, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25

The structure of Crystal Structure of An Rna Duplex R(Ggcgbrugcgcu)2 with Terminal and Internal Tandem G-U Base Pairs also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Bromine atom in the Crystal Structure of An Rna Duplex R(Ggcgbrugcgcu)2 with Terminal and Internal Tandem G-U Base Pairs (pdb code 2ao5). 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 An Rna Duplex R(Ggcgbrugcgcu)2 with Terminal and Internal Tandem G-U Base Pairs, PDB code: 2ao5:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of An Rna Duplex R(Ggcgbrugcgcu)2 with Terminal and Internal Tandem G-U Base Pairs


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 An Rna Duplex R(Ggcgbrugcgcu)2 with Terminal and Internal Tandem G-U Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Br5 b:83.7 occ:1.00 BR A:5BU5 0.0 83.7 1.0 C5 A:5BU5 2.8 29.3 1.0 O A:HOH167 3.4 44.7 1.0 O4 A:5BU5 3.5 25.6 1.0 C4 A:5BU5 3.5 27.3 1.0 OP2 A:5BU5 3.6 41.0 1.0 C6 A:5BU5 3.7 28.7 1.0 O A:HOH249 3.8 60.8 1.0 C8 A:G4 3.9 34.4 1.0 O A:HOH199 3.9 48.0 1.0 N7 A:G4 3.9 33.0 1.0 O5' A:G4 4.3 42.9 1.0 C3' A:G4 4.3 39.0 1.0 O A:HOH250 4.4 59.2 1.0 MG A:MG198 4.4 44.7 1.0 OP2 A:G4 4.4 43.8 1.0 N9 A:G4 4.5 34.4 1.0 C5 A:G4 4.6 32.5 1.0 P A:5BU5 4.7 41.6 1.0 O5' A:5BU5 4.7 40.0 1.0 C2' A:G4 4.8 38.1 1.0 N3 A:5BU5 4.9 27.1 1.0 O A:HOH247 4.9 48.9 1.0 C4 A:G4 4.9 33.7 1.0 N1 A:5BU5 5.0 31.0 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of An Rna Duplex R(Ggcgbrugcgcu)2 with Terminal and Internal Tandem G-U Base Pairs


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 An Rna Duplex R(Ggcgbrugcgcu)2 with Terminal and Internal Tandem G-U Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ B:Br5 b:73.0 occ:1.00 BR B:5BU5 0.0 73.0 1.0 C5 B:5BU5 2.7 30.8 1.0 C4 B:5BU5 3.5 30.4 1.0 O4 B:5BU5 3.5 30.2 1.0 C6 B:5BU5 3.7 29.9 1.0 O B:HOH81 3.8 42.0 1.0 C8 B:G4 3.8 22.9 1.0 OP2 B:5BU5 3.9 32.6 1.0 N7 B:G4 3.9 24.4 1.0 O B:HOH27 4.0 30.0 1.0 C3' B:G4 4.4 28.5 1.0 N9 B:G4 4.5 25.8 1.0 C5 B:G4 4.6 23.0 1.0 O B:HOH42 4.8 33.4 1.0 N3 B:5BU5 4.9 31.2 1.0 O5' B:5BU5 4.9 34.5 1.0 C4 B:G4 4.9 23.2 1.0 P B:5BU5 4.9 33.1 1.0 N1 B:5BU5 5.0 31.1 1.0 C2' B:G4 5.0 27.6 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of An Rna Duplex R(Ggcgbrugcgcu)2 with Terminal and Internal Tandem G-U Base Pairs


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 An Rna Duplex R(Ggcgbrugcgcu)2 with Terminal and Internal Tandem G-U Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ C:Br5 b:69.7 occ:1.00 BR C:5BU5 0.0 69.7 1.0 C5 C:5BU5 2.7 32.2 1.0 C4 C:5BU5 3.6 32.2 1.0 C6 C:5BU5 3.6 33.2 1.0 O C:HOH31 3.6 42.8 1.0 O4 C:5BU5 3.7 34.6 1.0 OP2 C:5BU5 3.7 34.4 1.0 C8 C:G4 3.9 27.1 1.0 N7 C:G4 3.9 28.1 1.0 O C:HOH11 4.0 52.3 1.0 O C:HOH28 4.3 54.6 1.0 C3' C:G4 4.5 31.6 1.0 O C:HOH20 4.5 23.2 1.0 N9 C:G4 4.6 29.3 1.0 C5 C:G4 4.7 25.0 1.0 C5' C:G4 4.8 35.6 1.0 P C:5BU5 4.8 36.7 1.0 O5' C:5BU5 4.9 37.2 1.0 N3 C:5BU5 4.9 33.3 1.0 N1 C:5BU5 4.9 33.6 1.0 O C:HOH12 5.0 68.6 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of An Rna Duplex R(Ggcgbrugcgcu)2 with Terminal and Internal Tandem G-U Base Pairs


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 An Rna Duplex R(Ggcgbrugcgcu)2 with Terminal and Internal Tandem G-U Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ D:Br5 b:70.4 occ:1.00 BR D:5BU5 0.0 70.4 1.0 C5 D:5BU5 2.8 43.9 1.0 O D:HOH15 3.0 58.2 1.0 O D:HOH49 3.3 59.7 1.0 OP2 D:5BU5 3.6 48.9 1.0 C6 D:5BU5 3.6 44.1 1.0 C8 D:G4 3.7 37.8 1.0 C4 D:5BU5 3.7 43.0 1.0 N7 D:G4 3.8 38.1 1.0 O4 D:5BU5 3.9 43.0 1.0 C3' D:G4 4.2 45.5 1.0 N9 D:G4 4.3 40.3 1.0 C5' D:G4 4.4 45.9 1.0 O D:HOH27 4.5 32.7 1.0 C5 D:G4 4.5 37.4 1.0 O D:HOH14 4.5 57.0 1.0 P D:5BU5 4.7 48.1 1.0 C4' D:G4 4.8 45.3 1.0 C4 D:G4 4.8 37.9 1.0 O5' D:5BU5 4.8 48.1 1.0 OP2 D:G4 4.8 47.0 1.0 C2' D:G4 4.9 44.5 1.0 O3' D:G4 4.9 47.1 1.0 O4' D:G4 4.9 44.5 1.0 N1 D:5BU5 5.0 45.0 1.0 C1' D:G4 5.0 42.5 1.0

R.Utsunomiya, K.Suto, D.Balasundaresan, A.Fukamizu, P.K.Kumar, H.Mizuno. Structure of An Rna Duplex R(Ggcgbrugcgcu)2 with Terminal and Internal Tandem G.U Base Pairs. Acta Crystallogr.,Sect.D V. 62 331 2006.
ISSN: ISSN 0907-4449
PubMed: 16510980
DOI: 10.1107/S0907444905043210