Zinc in PDB 8eb5: Tandem of Hermes Transposase Bed Domain in Complex with the Quasi Palindrome of Its Transposon Left-End

The structure of Tandem of Hermes Transposase Bed Domain in Complex with the Quasi Palindrome of Its Transposon Left-End, PDB code: 8eb5 was solved by L.Lannes, F.Dyda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.64 / 2.50
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.271, 55.271, 212.573, 90, 90, 120
R / Rfree (%)	23.1 / 23.8

The binding sites of Zinc atom in the Tandem of Hermes Transposase Bed Domain in Complex with the Quasi Palindrome of Its Transposon Left-End (pdb code 8eb5). 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 Tandem of Hermes Transposase Bed Domain in Complex with the Quasi Palindrome of Its Transposon Left-End, PDB code: 8eb5:

Zinc binding site 1 out of 1 in the Tandem of Hermes Transposase Bed Domain in Complex with the Quasi Palindrome of Its Transposon Left-End


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tandem of Hermes Transposase Bed Domain in Complex with the Quasi Palindrome of Its Transposon Left-End within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:98.3 occ:1.00 NE2 A:HIS71 2.1 78.6 1.0 SG A:CYS51 2.3 90.8 1.0 SG A:CYS54 2.3 95.7 1.0 SG A:CYS73 2.3 97.5 1.0 CE1 A:HIS71 3.0 79.7 1.0 CB A:CYS51 3.1 87.1 1.0 CB A:CYS54 3.1 96.3 1.0 CB A:CYS73 3.1 93.7 1.0 CD2 A:HIS71 3.2 78.6 1.0 N A:CYS54 3.4 98.0 1.0 CA A:CYS54 3.9 97.1 1.0 ND1 A:HIS71 4.2 80.2 1.0 CG A:HIS71 4.3 79.5 1.0 CB A:LYS53 4.4 101.6 1.0 CA A:CYS73 4.4 92.7 1.0 C A:LYS53 4.5 99.1 1.0 N A:CYS73 4.5 91.4 1.0 CA A:CYS51 4.6 87.1 1.0 CA A:LYS53 4.7 98.5 1.0 C A:CYS54 4.8 97.4 1.0 N A:LYS53 4.8 97.4 1.0 N A:GLU55 4.9 96.5 1.0 C A:CYS51 5.0 91.5 1.0

L.Lannes, C.M.Furman, A.B.Hickman, F.Dyda. Zinc-Finger Bed Domains Drive the Formation of the Active Hermes Transpososome By Asymmetric Dna Binding. Nat Commun V. 14 4470 2023.
ISSN: ESSN 2041-1723
PubMed: 37491363
DOI: 10.1038/S41467-023-40210-3