Calcium in PDB 7jk1: Human Primpol Inserting Correct Dctp Opposite the 8-Oxoguanine Lesion

The structure of Human Primpol Inserting Correct Dctp Opposite the 8-Oxoguanine Lesion, PDB code: 7jk1 was solved by O.Rechkoblit, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.88 / 2.62
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	52.558, 65.732, 75.179, 69.66, 82.83, 88.54
R / Rfree (%)	23.9 / 28.6

The binding sites of Calcium atom in the Human Primpol Inserting Correct Dctp Opposite the 8-Oxoguanine Lesion (pdb code 7jk1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Human Primpol Inserting Correct Dctp Opposite the 8-Oxoguanine Lesion, PDB code: 7jk1:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human Primpol Inserting Correct Dctp Opposite the 8-Oxoguanine Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Primpol Inserting Correct Dctp Opposite the 8-Oxoguanine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:49.0 occ:1.00 O2B A:DCP401 2.0 50.5 1.0 OE2 A:GLU116 2.3 56.7 1.0 O A:HOH508 2.3 46.7 1.0 O1A A:DCP401 2.4 38.4 1.0 OD1 A:ASP114 2.4 51.1 1.0 OD2 A:ASP114 2.4 51.1 1.0 O2G A:DCP401 2.6 56.5 1.0 CG A:ASP114 2.7 49.7 1.0 HB3 A:GLU116 3.3 63.3 1.0 CD A:GLU116 3.3 53.4 1.0 HE2 A:HIS169 3.3 59.5 1.0 HZ1 A:LYS165 3.5 69.4 1.0 PB A:DCP401 3.5 51.1 1.0 PA A:DCP401 3.7 43.0 1.0 HG2 A:GLU116 3.7 59.0 1.0 HE2 A:LYS165 3.8 67.2 1.0 CG A:GLU116 3.9 49.1 1.0 PG A:DCP401 4.0 52.0 1.0 CB A:GLU116 4.0 52.7 1.0 OG A:SER167 4.0 54.4 1.0 HG A:SER167 4.0 65.4 1.0 HZ3 A:LYS165 4.1 69.4 1.0 NZ A:LYS165 4.1 57.7 1.0 H5'2 A:DCP401 4.1 48.5 1.0 NE2 A:HIS169 4.1 49.5 1.0 O3A A:DCP401 4.1 51.8 1.0 OE1 A:GLU116 4.2 57.9 1.0 CB A:ASP114 4.2 47.0 1.0 O3B A:DCP401 4.3 60.3 1.0 HD2 A:HIS169 4.3 53.9 1.0 CE A:LYS165 4.4 56.0 1.0 HB2 A:GLU116 4.4 63.3 1.0 O A:LEU115 4.6 48.1 1.0 O1B A:DCP401 4.6 41.4 1.0 CD2 A:HIS169 4.6 44.8 1.0 O2A A:DCP401 4.6 48.8 1.0 HB3 A:ASP114 4.7 56.5 1.0 HB2 A:ASP114 4.7 56.5 1.0 HE3 A:LYS165 4.7 67.2 1.0 HA A:ASP114 4.7 58.8 1.0 O3G A:DCP401 4.8 47.7 1.0 OD2 A:ASP280 4.8 51.7 1.0 HG3 A:GLU116 4.8 59.0 1.0 O5' A:DCP401 4.8 48.2 1.0 C A:ASP114 4.8 46.9 1.0 C5' A:DCP401 4.9 40.4 1.0 CA A:ASP114 4.9 48.9 1.0 HZ2 A:LYS165 4.9 69.4 1.0 H A:LEU115 4.9 57.9 1.0 N A:LEU115 4.9 48.2 1.0 C A:LEU115 4.9 49.6 1.0 HA A:SER167 5.0 65.4 1.0

Calcium binding site 2 out of 2 in the Human Primpol Inserting Correct Dctp Opposite the 8-Oxoguanine Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Primpol Inserting Correct Dctp Opposite the 8-Oxoguanine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:54.4 occ:1.00 O1B B:DCP401 1.8 67.2 1.0 O2A B:DCP401 2.1 51.0 1.0 OE2 B:GLU116 2.4 68.6 1.0 OD1 B:ASP114 2.4 68.0 1.0 O B:HOH502 2.5 47.7 1.0 OD2 B:ASP114 2.5 65.2 1.0 O2G B:DCP401 2.5 74.1 1.0 CG B:ASP114 2.8 64.8 1.0 CD B:GLU116 3.2 62.0 1.0 PB B:DCP401 3.2 70.0 1.0 HG2 B:GLU116 3.3 67.7 1.0 PA B:DCP401 3.4 62.3 1.0 HB3 B:GLU116 3.4 73.7 1.0 HZ1 B:LYS165 3.6 79.1 1.0 CG B:GLU116 3.7 56.4 1.0 O3A B:DCP401 3.8 74.0 1.0 PG B:DCP401 3.9 61.9 1.0 HE2 B:LYS165 4.0 76.4 1.0 H5'2 B:DCP401 4.0 69.9 1.0 CB B:GLU116 4.0 61.3 1.0 O3B B:DCP401 4.1 71.3 1.0 OE1 B:GLU116 4.1 73.9 1.0 O1A B:DCP401 4.2 73.5 1.0 HZ3 B:LYS165 4.2 79.1 1.0 NZ B:LYS165 4.2 65.8 1.0 HG B:SER167 4.3 73.5 1.0 OG B:SER167 4.3 61.2 1.0 CB B:ASP114 4.3 60.0 1.0 O2B B:DCP401 4.3 54.2 1.0 NE2 B:HIS169 4.4 58.6 1.0 HB2 B:GLU116 4.5 73.7 1.0 O B:LEU115 4.5 65.0 1.0 CE B:LYS165 4.6 63.6 1.0 O5' B:DCP401 4.6 61.1 1.0 HG3 B:GLU116 4.6 67.7 1.0 HB3 B:ASP114 4.6 72.1 1.0 HD2 B:HIS169 4.7 65.0 1.0 O3G B:DCP401 4.7 65.4 1.0 C5' B:DCP401 4.7 58.1 1.0 OD2 B:ASP280 4.7 66.8 1.0 HB2 B:ASP114 4.8 72.1 1.0 HE3 B:LYS165 4.9 76.4 1.0 O1G B:DCP401 4.9 72.2 1.0 HA B:ASP114 4.9 71.2 1.0 C B:ASP114 4.9 58.1 1.0 CD2 B:HIS169 4.9 54.1 1.0 C B:LEU115 5.0 63.6 1.0 HO3' F:DG14 5.0 86.2 1.0 H5'1 B:DCP401 5.0 69.9 1.0 HB2 B:ASP280 5.0 64.9 1.0

O.Rechkoblit, R.E.Johnson, Y.K.Gupta, L.Prakash, S.Prakash, A.K.Aggarwal. Structural Basis of Dna Synthesis Opposite 8-Oxoguanine By Human Primpol Primase-Polymerase Nat Commun 2021.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-021-24317-Z