Zinc in PDB 6x68: Cryo-Em Structure of Piggybac Transposase Synaptic Complex with Hairpin Dna (Snhp)

The structure of Cryo-Em Structure of Piggybac Transposase Synaptic Complex with Hairpin Dna (Snhp) also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Piggybac Transposase Synaptic Complex with Hairpin Dna (Snhp) (pdb code 6x68). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryo-Em Structure of Piggybac Transposase Synaptic Complex with Hairpin Dna (Snhp), PDB code: 6x68:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Structure of Piggybac Transposase Synaptic Complex with Hairpin Dna (Snhp)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Piggybac Transposase Synaptic Complex with Hairpin Dna (Snhp) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn603 b:0.6 occ:1.00 SG C:CYS582 1.9 0.9 1.0 SG C:CYS562 2.1 0.2 1.0 SG C:CYS559 2.1 0.4 1.0 ND1 C:HIS585 2.2 97.3 1.0 CE1 C:HIS585 2.6 97.5 1.0 CB C:CYS582 3.2 0.7 1.0 CB C:CYS559 3.3 94.4 1.0 CB C:CYS562 3.3 85.3 1.0 CG C:HIS585 3.5 92.9 1.0 NE2 C:HIS585 3.9 96.6 1.0 N C:CYS562 3.9 84.2 1.0 OE1 C:GLU584 3.9 0.1 1.0 CA C:CYS562 4.1 81.2 1.0 N C:CYS582 4.1 0.3 1.0 CA C:CYS582 4.2 0.8 1.0 CB C:HIS585 4.3 1.0 1.0 C C:TYR561 4.3 88.3 1.0 CD2 C:HIS585 4.3 95.0 1.0 N C:HIS585 4.5 0.1 1.0 O C:CYS582 4.6 0.1 1.0 CA C:CYS559 4.7 87.3 1.0 C C:CYS582 4.7 0.7 1.0 CD C:ARG568 4.7 80.0 1.0 O C:TYR561 4.7 94.0 1.0 CB C:GLU584 4.9 0.0 1.0 NH1 C:ARG568 4.9 84.3 1.0 N C:TYR561 4.9 92.7 1.0 CB C:TYR561 4.9 95.2 1.0 CA C:TYR561 4.9 91.1 1.0 CA C:HIS585 5.0 0.9 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of Piggybac Transposase Synaptic Complex with Hairpin Dna (Snhp)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Piggybac Transposase Synaptic Complex with Hairpin Dna (Snhp) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn604 b:0.3 occ:1.00 SG C:CYS577 1.7 0.1 1.0 SG C:CYS593 1.9 0.9 1.0 SG C:CYS590 2.0 0.9 1.0 SG C:CYS574 2.0 1.0 1.0 CB C:CYS574 2.9 0.9 1.0 CB C:CYS590 3.0 0.6 1.0 CB C:CYS577 3.1 0.2 1.0 CB C:CYS593 3.2 0.6 1.0 N C:CYS590 3.8 0.3 1.0 N C:CYS577 3.9 0.3 1.0 CA C:CYS590 4.0 0.8 1.0 CA C:CYS577 4.0 0.2 1.0 CA C:CYS593 4.3 0.7 1.0 N C:CYS593 4.3 0.2 1.0 CA C:CYS574 4.3 0.5 1.0 C C:CYS590 4.6 0.8 1.0 O C:CYS590 4.6 0.1 1.0 C C:CYS574 4.7 0.1 1.0 O C:CYS574 4.7 0.6 1.0 C C:CYS577 4.8 0.7 1.0 OH C:TYR561 4.8 0.6 1.0 C C:LYS576 4.9 0.9 1.0 C C:MET589 5.0 0.3 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of Piggybac Transposase Synaptic Complex with Hairpin Dna (Snhp)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Piggybac Transposase Synaptic Complex with Hairpin Dna (Snhp) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:0.2 occ:1.00 SG D:CYS562 1.7 0.6 1.0 SG D:CYS582 2.0 1.0 1.0 SG D:CYS559 2.0 0.0 1.0 ND1 D:HIS585 2.1 0.5 1.0 CE1 D:HIS585 2.7 0.9 1.0 CB D:CYS582 3.0 0.1 1.0 CB D:CYS559 3.0 0.7 1.0 CB D:CYS562 3.2 0.8 1.0 CG D:HIS585 3.3 0.7 1.0 N D:CYS562 3.7 0.7 1.0 CA D:CYS562 3.8 0.6 1.0 NE2 D:HIS585 4.0 0.4 1.0 CB D:HIS585 4.0 0.2 1.0 C D:TYR561 4.1 0.2 1.0 CA D:CYS582 4.1 0.0 1.0 N D:CYS582 4.2 0.2 1.0 CD2 D:HIS585 4.3 0.2 1.0 CA D:CYS559 4.4 0.6 1.0 O D:TYR561 4.4 0.5 1.0 CB D:ARG568 4.5 0.7 1.0 CG D:ARG568 4.6 0.3 1.0 CB D:TYR561 4.7 0.4 1.0 O D:CYS582 4.7 0.7 1.0 N D:HIS585 4.7 0.7 1.0 CA D:TYR561 4.8 0.5 1.0 C D:CYS582 4.8 0.5 1.0 NH1 D:ARG568 4.8 0.1 1.0 N D:TYR561 4.8 0.5 1.0 C D:CYS559 4.8 0.6 1.0 O D:CYS559 5.0 0.1 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of Piggybac Transposase Synaptic Complex with Hairpin Dna (Snhp)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Piggybac Transposase Synaptic Complex with Hairpin Dna (Snhp) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:0.0 occ:1.00 SG D:CYS574 1.8 0.1 1.0 SG D:CYS593 1.8 0.5 1.0 SG D:CYS590 1.9 0.4 1.0 SG D:CYS577 2.1 0.8 1.0 CB D:CYS590 2.9 0.1 1.0 CB D:CYS574 2.9 0.3 1.0 CB D:CYS577 3.1 0.1 1.0 CB D:CYS593 3.1 0.4 1.0 N D:CYS577 3.8 0.0 1.0 CA D:CYS590 4.0 0.6 1.0 CA D:CYS577 4.0 0.0 1.0 N D:CYS590 4.0 0.2 1.0 OG D:SER592 4.2 0.1 1.0 N D:CYS593 4.2 0.5 1.0 CA D:CYS593 4.2 0.7 1.0 CA D:CYS574 4.3 0.1 1.0 C D:LYS576 4.4 0.2 1.0 C D:CYS577 4.6 0.8 1.0 C D:CYS590 4.6 0.1 1.0 CB D:LYS579 4.7 0.6 1.0 O D:CYS590 4.7 1.0 1.0 C D:CYS574 4.7 0.4 1.0 N D:LYS576 4.8 0.8 1.0 N D:LYS578 4.9 0.6 1.0 C D:SER592 5.0 0.4 1.0

Q.Chen, W.Luo, R.A.Veach, A.B.Hickman, M.H.Wilson, F.Dyda. Structural Basis of Seamless Excision and Specific Targeting By Piggybac Transposase Nat Commun V. 11 3446 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-020-17128-1