Bromine in PDB 2got: Crystal Structure of D(Gcgaacgc): Two Types of Bulge- Containing Duplexes

The structure of Crystal Structure of D(Gcgaacgc): Two Types of Bulge- Containing Duplexes, PDB code: 2got was solved by J.Kondo, T.Sunami, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.15 / 2.60
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	26.830, 26.830, 226.325, 90.00, 90.00, 120.00
R / Rfree (%)	25.3 / 26.9

The binding sites of Bromine atom in the Crystal Structure of D(Gcgaacgc): Two Types of Bulge- Containing Duplexes (pdb code 2got). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of D(Gcgaacgc): Two Types of Bulge- Containing Duplexes, PDB code: 2got:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of D(Gcgaacgc): Two Types of Bulge- Containing Duplexes


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 D(Gcgaacgc): Two Types of Bulge- Containing Duplexes within 5.0Å range: probe atom residue distance (Å) B Occ A:Br2 b:50.8 occ:1.00 BR A:CBR2 0.0 50.8 1.0 C5 A:CBR2 1.8 35.9 1.0 C6 A:CBR2 2.7 35.7 1.0 C4 A:CBR2 2.9 34.6 1.0 N4 A:CBR2 3.2 28.9 1.0 C8 A:DG1 3.6 24.7 1.0 N9 A:DG1 3.8 27.5 1.0 C2' A:DG1 3.8 40.7 1.0 N1 A:CBR2 4.0 38.1 1.0 N7 A:DG1 4.0 20.8 1.0 O6 A:DG3 4.0 30.4 1.0 N3 A:CBR2 4.1 32.0 1.0 C1' A:DG1 4.2 36.6 1.0 C4 A:DG1 4.3 23.0 1.0 C5 A:DG1 4.3 20.6 1.0 C2 A:CBR2 4.6 34.5 1.0 C6 A:DG3 4.9 30.5 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of D(Gcgaacgc): Two Types of Bulge- Containing Duplexes


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 D(Gcgaacgc): Two Types of Bulge- Containing Duplexes within 5.0Å range: probe atom residue distance (Å) B Occ B:Br2 b:46.9 occ:1.00 BR B:CBR2 0.0 46.9 1.0 C5 B:CBR2 1.8 34.8 1.0 C6 B:CBR2 2.7 36.9 1.0 C4 B:CBR2 2.9 31.7 1.0 N4 B:CBR2 3.2 29.6 1.0 O B:HOH9 3.5 43.7 1.0 C2' B:DG1 3.6 30.8 1.0 N9 B:DG1 3.7 21.7 1.0 C8 B:DG1 3.8 21.8 1.0 N1 B:CBR2 3.9 37.9 1.0 C1' B:DG1 4.0 27.9 1.0 C4 B:DG1 4.1 18.2 1.0 N3 B:CBR2 4.1 29.8 1.0 N7 B:DG1 4.2 19.1 1.0 O6 B:DG3 4.3 19.3 1.0 C5 B:DG1 4.4 16.6 1.0 C2 B:CBR2 4.6 34.5 1.0 N3 B:DG1 4.7 15.4 1.0 N7 B:DG3 4.8 17.5 1.0 C6 B:DG3 5.0 13.0 1.0

J.Kondo, T.Sunami, A.Takenaka. The Structure of A D(Gcgaacgc) Duplex Containing Two Consecutive Bulged A Residues in Both Strands Suggests A Molecular Switch Acta Crystallogr.,Sect.D V. 63 673 2007.
ISSN: ISSN 0907-4449
PubMed: 17505105
DOI: 10.1107/S0907444907012607