Zinc 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:

Bromine

(Br)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total only one binding site of Zinc was 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:

Zinc binding site 1 out of 1 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 Zinc with other atoms in the Zn 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 C:Zn78 b:25.1 occ:1.00 NE2 C:HIS47 2.1 26.6 1.0 SG C:CYS4 2.3 22.5 1.0 SG C:CYS7 2.4 29.8 1.0 SG C:CYS44 2.4 24.8 1.0 CE1 C:HIS47 3.0 28.5 1.0 CD2 C:HIS47 3.1 24.8 1.0 CB C:CYS4 3.2 23.0 1.0 CB C:CYS44 3.2 21.3 1.0 CB C:CYS7 3.3 25.9 1.0 N C:CYS44 3.7 21.4 1.0 N C:CYS7 3.9 26.3 1.0 CA C:CYS44 4.1 21.1 1.0 ND1 C:HIS47 4.1 25.5 1.0 CG C:HIS47 4.2 23.8 1.0 CA C:CYS7 4.2 27.8 1.0 CD2 C:PHE6 4.5 29.0 1.0 CA C:CYS4 4.6 22.2 1.0 CG1 C:VAL11 4.7 29.2 1.0 CB C:PHE6 4.8 26.6 1.0 C C:ILE43 4.8 18.7 1.0 C C:PHE6 5.0 26.9 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