Bromine in PDB 3kde: Crystal Structure of the Thap Domain From D. Melanogaster P-Element Transposase in Complex with Its Natural Dna Binding Site

The structure of Crystal Structure of the Thap Domain From D. Melanogaster P-Element Transposase in Complex with Its Natural Dna Binding Site, PDB code: 3kde was solved by A.Sabogal, A.Y.Lyubimov, J.M.Berger, D.C.Rio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.09 / 1.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.692, 69.325, 35.126, 90.00, 92.52, 90.00
R / Rfree (%)	17.7 / 21.6

The structure of Crystal Structure of the Thap Domain From D. Melanogaster P-Element Transposase in Complex with Its Natural Dna Binding Site also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Bromine atom in the Crystal Structure of the Thap Domain From D. Melanogaster P-Element Transposase in Complex with Its Natural Dna Binding Site (pdb code 3kde). 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 the Thap Domain From D. Melanogaster P-Element Transposase in Complex with Its Natural Dna Binding Site, PDB code: 3kde:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of the Thap Domain From D. Melanogaster P-Element Transposase in Complex with Its Natural Dna Binding Site


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 the Thap Domain From D. Melanogaster P-Element Transposase in Complex with Its Natural Dna Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Br7 b:26.7 occ:0.50 BR A:BRU7 0.0 26.7 0.5 C5 A:BRU7 1.8 22.3 1.0 C6 A:BRU7 2.8 24.3 1.0 C4 A:BRU7 2.9 22.7 1.0 O C:HOH87 3.1 23.9 1.0 O4 A:BRU7 3.1 20.9 1.0 O A:HOH41 3.7 37.2 1.0 C8 A:DG6 3.7 24.3 1.0 O A:HOH30 3.8 33.6 1.0 N7 A:DG6 3.9 20.7 1.0 O A:HOH40 3.9 28.6 1.0 NE2 C:GLN42 4.0 23.7 1.0 N1 A:BRU7 4.1 26.8 1.0 N3 A:BRU7 4.1 22.3 1.0 CB C:LEU16 4.1 21.7 1.0 CD1 C:LEU16 4.2 23.3 1.0 O A:HOH22 4.2 24.8 1.0 CE C:LYS2 4.3 32.4 1.0 O A:HOH35 4.3 36.1 1.0 N9 A:DG6 4.4 22.2 1.0 CG C:LEU16 4.5 22.2 1.0 C2 A:BRU7 4.6 25.3 1.0 CG C:LYS2 4.6 28.5 1.0 C2' A:DG6 4.6 27.4 1.0 C5 A:DG6 4.6 20.7 1.0 O C:HOH88 4.7 21.8 1.0 CD C:LYS2 4.8 27.8 1.0 N C:LEU16 4.8 23.6 1.0 C4 A:DG6 4.9 23.2 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of the Thap Domain From D. Melanogaster P-Element Transposase in Complex with Its Natural Dna Binding Site


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 the Thap Domain From D. Melanogaster P-Element Transposase in Complex with Its Natural Dna Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Br11 b:32.6 occ:0.50 BR B:BRU11 0.0 32.6 0.5 C5 B:BRU11 1.9 29.8 1.0 C6 B:BRU11 2.9 29.0 1.0 C4 B:BRU11 3.0 29.4 1.0 O4 B:BRU11 3.2 31.6 1.0 CB C:MET1 3.6 27.0 1.0 CG C:MET1 3.7 28.8 1.0 CB C:ALA10 3.9 29.3 1.0 CB C:TYR3 3.9 23.3 1.0 CD1 C:TYR3 3.9 26.7 1.0 O C:MET1 4.0 27.5 1.0 O B:HOH30 4.0 31.6 1.0 N1 B:BRU11 4.1 28.9 1.0 N3 B:BRU11 4.2 29.4 1.0 O C:LYS2 4.3 23.8 1.0 C C:MET1 4.3 27.2 1.0 CG C:TYR3 4.3 24.0 1.0 CA C:ALA10 4.3 30.3 1.0 CA C:MET1 4.4 27.1 1.0 C C:LYS2 4.6 24.7 1.0 CA C:TYR3 4.6 22.6 1.0 N C:ALA10 4.7 30.6 1.0 C2 B:BRU11 4.7 26.6 1.0 N C:TYR3 4.8 24.3 1.0 N C:MET1 4.8 26.6 1.0 CE1 C:TYR3 5.0 28.4 1.0

A.Sabogal, A.Y.Lyubimov, J.E.Corn, J.M.Berger, D.C.Rio. Thap Proteins Target Specific Dna Sites Through Bipartite Recognition of Adjacent Major and Minor Grooves. Nat.Struct.Mol.Biol. V. 17 117 2010.
ISSN: ISSN 1545-9993
PubMed: 20010837
DOI: 10.1038/NSMB.1742