Calcium in PDB 6zp9: Cyanophage S-2L Primase-Polymerase (Primpol), Aep Domain (Pp-N190)

The structure of Cyanophage S-2L Primase-Polymerase (Primpol), Aep Domain (Pp-N190), PDB code: 6zp9 was solved by D.Czernecki, P.Legrand, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.30 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.177, 47.686, 66.155, 90, 97.11, 90
R / Rfree (%)	16.6 / 17.3

The binding sites of Calcium atom in the Cyanophage S-2L Primase-Polymerase (Primpol), Aep Domain (Pp-N190) (pdb code 6zp9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Cyanophage S-2L Primase-Polymerase (Primpol), Aep Domain (Pp-N190), PDB code: 6zp9:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Cyanophage S-2L Primase-Polymerase (Primpol), Aep Domain (Pp-N190)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cyanophage S-2L Primase-Polymerase (Primpol), Aep Domain (Pp-N190) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:21.5 occ:1.00 O A:LEU179 2.3 18.4 1.0 O A:HOH505 2.4 31.4 1.0 O A:HOH546 2.4 28.1 1.0 O B:HOH309 2.4 26.6 1.0 O A:HOH483 2.5 26.5 1.0 O B:HOH323 2.6 19.1 1.0 O A:HOH435 2.6 29.9 1.0 C A:LEU179 3.5 16.5 1.0 OE1 A:GLU178 4.0 29.8 1.0 N A:LEU179 4.0 16.0 1.0 CA A:LEU179 4.3 16.0 1.0 O A:HOH332 4.4 51.3 1.0 OD2 B:ASP23 4.4 24.4 1.0 O A:HOH453 4.5 35.0 1.0 N A:TYR180 4.6 13.4 1.0 CB B:ALA25 4.7 16.3 1.0 OD1 B:ASP23 4.7 18.5 1.0 CB A:LEU179 4.7 16.8 1.0 CA A:TYR180 4.7 14.2 1.0 O A:HOH339 4.9 29.0 1.0 O A:HOH508 5.0 38.4 1.0

Calcium binding site 2 out of 3 in the Cyanophage S-2L Primase-Polymerase (Primpol), Aep Domain (Pp-N190)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cyanophage S-2L Primase-Polymerase (Primpol), Aep Domain (Pp-N190) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:19.2 occ:1.00 O A:HOH330 2.2 25.4 1.0 O B:HOH500 2.3 28.9 1.0 O B:HOH542 2.3 23.3 1.0 O B:LEU179 2.4 15.3 1.0 O B:HOH477 2.5 25.7 1.0 O B:HOH317 2.5 23.2 1.0 O B:HOH339 2.5 17.1 1.0 O B:HOH540 3.4 33.7 1.0 C B:LEU179 3.6 13.3 1.0 O B:HOH527 3.7 55.7 1.0 OE1 B:GLU178 4.1 22.2 1.0 N B:LEU179 4.1 15.2 1.0 OD2 A:ASP23 4.4 24.2 1.0 O B:HOH431 4.4 39.7 1.0 CA B:LEU179 4.4 15.0 1.0 N B:TYR180 4.6 15.8 1.0 CB A:ALA25 4.7 18.9 1.0 OD1 A:ASP23 4.8 17.9 1.0 CA B:TYR180 4.8 16.3 1.0 O A:HOH575 4.8 50.9 1.0 O B:HOH555 4.8 46.0 1.0 CB B:LEU179 4.9 15.0 1.0 O B:HOH468 4.9 25.4 1.0

Calcium binding site 3 out of 3 in the Cyanophage S-2L Primase-Polymerase (Primpol), Aep Domain (Pp-N190)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cyanophage S-2L Primase-Polymerase (Primpol), Aep Domain (Pp-N190) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:27.2 occ:1.00 O B:HOH560 2.3 41.6 1.0 O B:HOH460 2.4 25.3 1.0 O B:HOH483 2.4 33.7 1.0 O B:HOH381 2.4 30.9 1.0 OD2 B:ASP71 2.5 21.3 1.0 O B:HOH313 2.6 24.8 1.0 O B:HOH501 2.6 38.4 1.0 CG B:ASP71 3.4 21.4 1.0 CB B:ASP71 3.7 20.1 1.0 O B:HOH506 3.8 35.3 1.0 O B:HOH514 4.1 43.3 1.0 NH2 B:ARG28 4.1 18.6 1.0 OG1 B:THR44 4.5 18.4 1.0 OD1 B:ASP71 4.5 17.4 1.0 OE1 B:GLU75 4.6 25.0 1.0 OE2 B:GLU75 4.7 30.4 1.0 O B:HOH551 4.7 37.2 1.0 N B:ASP71 4.7 18.1 1.0 CA B:ASP71 4.9 18.3 1.0 CZ B:ARG28 5.0 19.5 1.0

D.Czernecki, P.Legrand, M.Tekpinar, S.Rosario, P.A.Kaminski, M.Delarue. How Cyanophage S-2L Rejects Adenine and Incorporates 2-Aminoadenine to Saturate Hydrogen Bonding in Its Dna Nat Commun 2021.
ISSN: ESSN 2041-1723