Calcium in PDB 6x67: Cryo-Em Structure of Piggybac Transposase Strand Transfer Complex (Stc)

The structure of Cryo-Em Structure of Piggybac Transposase Strand Transfer Complex (Stc) also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of Piggybac Transposase Strand Transfer Complex (Stc) (pdb code 6x67). 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 Strand Transfer Complex (Stc), PDB code: 6x67:
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 Strand Transfer Complex (Stc)


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 Strand Transfer Complex (Stc) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca603 b:87.0 occ:1.00 OD2 C:ASP346 2.0 73.8 1.0 OP1 K:DT0 2.1 65.0 1.0 OD2 C:ASP268 2.2 77.9 1.0 OD1 C:ASP268 2.3 73.2 1.0 CG C:ASP268 2.6 75.9 1.0 CG C:ASP346 3.1 71.8 1.0 P K:DT0 3.5 60.5 1.0 CB C:ASP346 3.8 68.1 1.0 O3' K:DG-1 4.0 52.2 1.0 OD1 C:ASP346 4.0 67.7 1.0 CB C:ASP268 4.1 64.7 1.0 O3' G:DC-4 4.2 74.9 1.0 OP2 K:DT0 4.4 60.9 1.0 O5' K:DT0 4.5 55.6 1.0 C5' K:DT0 4.5 57.8 1.0 C3' G:DC-4 4.8 76.6 1.0 CG C:GLU269 4.8 69.3 1.0 N C:GLU269 4.9 58.2 1.0 CA C:ASP268 4.9 55.6 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of Piggybac Transposase Strand Transfer Complex (Stc)


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 Strand Transfer Complex (Stc) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca604 b:77.6 occ:1.00 OD2 C:ASP218 2.1 66.2 1.0 OD2 C:ASP197 3.1 77.2 1.0 OD1 C:ASP197 3.2 68.5 1.0 CG C:ASP218 3.4 66.0 1.0 CG C:ASP197 3.6 73.7 1.0 O6 E:DG10 4.0 55.6 1.0 OD1 C:ASP218 4.2 60.6 1.0 CB C:ASP218 4.2 52.0 1.0 N7 E:DG10 4.7 50.2 1.0 OG1 C:THR196 4.7 56.1 1.0 O4 F:DT-11 4.8 53.6 1.0 N7 E:DA9 4.8 45.7 1.0 N6 E:DA11 4.9 51.3 1.0 C6 E:DG10 4.9 48.5 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of Piggybac Transposase Strand Transfer Complex (Stc)


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 Strand Transfer Complex (Stc) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca603 b:0.0 occ:1.00 OD2 D:ASP346 2.0 53.5 1.0 OP1 F:DT0 2.1 46.7 1.0 OD1 D:ASP268 2.3 51.7 1.0 OD2 D:ASP268 2.3 46.0 1.0 CG D:ASP268 2.6 54.0 1.0 CG D:ASP346 3.1 59.1 1.0 P F:DT0 3.5 47.4 1.0 CB D:ASP346 3.9 58.8 1.0 O3' F:DG-1 4.0 44.0 1.0 O3' L:DC-4 4.0 69.1 1.0 O5' F:DT0 4.1 43.0 1.0 OD1 D:ASP346 4.1 58.3 1.0 CB D:ASP268 4.1 50.8 1.0 OE2 D:GLU269 4.5 63.9 1.0 OP2 F:DT0 4.6 48.6 1.0 C3' L:DC-4 4.6 72.0 1.0 N D:GLU269 4.7 45.0 1.0 CG D:GLU269 4.8 56.8 1.0 CA D:ASP268 4.8 45.8 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of Piggybac Transposase Strand Transfer Complex (Stc)


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 Strand Transfer Complex (Stc) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca604 b:68.3 occ:1.00 OD2 D:ASP218 2.2 64.0 1.0 OD2 D:ASP197 2.9 77.7 1.0 OD1 D:ASP197 3.0 69.0 1.0 CG D:ASP197 3.3 75.6 1.0 CG D:ASP218 3.4 64.0 1.0 O6 J:DG10 4.0 56.0 1.0 OD1 D:ASP218 4.2 58.3 1.0 CB D:ASP218 4.3 48.9 1.0 OD1 D:ASP215 4.4 58.5 1.0 OG1 D:THR196 4.7 58.3 1.0 N7 J:DG10 4.7 53.9 1.0 O4 K:DT-11 4.8 56.6 1.0 N7 J:DA9 4.8 50.8 1.0 CB D:ASP197 4.9 62.9 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