Calcium 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:

Zinc

(Zn)

4 atoms

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

Calcium 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 Calcium with other atoms in the Ca 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:Ca601 b:44.9 occ:1.00 OD2 C:ASP346 2.1 47.1 1.0 OP1 B:DT-3 2.1 56.1 1.0 OD2 C:ASP268 2.2 43.5 1.0 OD1 C:ASP268 2.3 44.0 1.0 CG C:ASP268 2.5 45.1 1.0 CG C:ASP346 3.3 48.3 1.0 P B:DT-3 3.6 59.4 1.0 CB C:ASP268 4.1 36.9 1.0 OD1 C:ASP346 4.2 58.5 1.0 O3' B:DG-4 4.2 42.8 1.0 CB C:ASP346 4.2 45.6 1.0 O5' B:DT-3 4.5 44.4 1.0 OP2 B:DT-3 4.5 46.2 1.0 CG C:GLU269 4.7 31.8 1.0 C5' B:DT-3 4.7 45.1 1.0 N C:GLU269 4.8 31.1 1.0 CA C:ASP268 4.8 31.3 1.0 OD1 C:ASP447 5.0 37.6 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca602 b:29.1 occ:1.00 OD2 C:ASP218 2.0 19.1 1.0 CG C:ASP218 3.2 20.8 1.0 OD1 C:ASP218 3.8 14.2 1.0 OG1 C:THR196 3.9 17.1 1.0 OD1 C:ASP197 4.4 15.3 1.0 CB C:ASP218 4.4 16.7 1.0 O6 A:DG10 4.4 37.7 1.0 N7 A:DA9 4.8 33.0 1.0 CD C:ARG214 4.9 7.9 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca601 b:43.2 occ:1.00 OD2 D:ASP218 2.2 32.0 1.0 CG D:ASP218 3.5 32.9 1.0 OD1 D:ASP218 4.1 29.4 1.0 OG1 D:THR196 4.1 27.9 1.0 OD1 D:ASP197 4.2 38.0 1.0 O6 B:DG10 4.4 49.7 1.0 CB D:ASP218 4.6 26.3 1.0 N7 B:DA9 4.6 38.1 1.0 CD D:ARG214 4.8 23.3 1.0 N7 B:DG10 4.9 43.6 1.0 O4 B:DT-14 5.0 50.8 1.0

Calcium 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 Calcium with other atoms in the Ca 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 A:Ca101 b:61.6 occ:1.00 OP1 A:DT-3 1.7 44.8 1.0 OD2 D:ASP346 1.9 44.2 1.0 OD1 D:ASP268 2.9 49.0 1.0 OD2 D:ASP268 3.0 40.8 1.0 P A:DT-3 3.1 39.5 1.0 CG D:ASP346 3.1 45.4 1.0 CG D:ASP268 3.3 45.6 1.0 O5' A:DT-3 3.8 39.4 1.0 OP2 A:DT-3 3.8 38.6 1.0 OD1 D:ASP346 4.0 43.1 1.0 CB D:ASP346 4.1 43.3 1.0 O3' A:DG-4 4.1 39.4 1.0 C5' A:DT-3 4.4 39.1 1.0 CB D:ASP268 4.8 28.8 1.0 CG D:GLU269 4.9 31.6 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