Calcium in PDB 7jl8: Human Primpol Extending From the Correct Primer Base C Opposite the 8- Oxoguanine Lesion

The structure of Human Primpol Extending From the Correct Primer Base C Opposite the 8- Oxoguanine Lesion, PDB code: 7jl8 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)	28.16 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.689, 65.33, 72.001, 68.47, 85.67, 86.92
R / Rfree (%)	18.7 / 21.3

The binding sites of Calcium atom in the Human Primpol Extending From the Correct Primer Base C Opposite the 8- Oxoguanine Lesion (pdb code 7jl8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Human Primpol Extending From the Correct Primer Base C Opposite the 8- Oxoguanine Lesion, PDB code: 7jl8:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human Primpol Extending From the Correct Primer Base C 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 Extending From the Correct Primer Base C Opposite the 8- Oxoguanine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:47.1 occ:1.00 OE2 A:GLU116 2.1 64.8 1.0 O2A A:DTP401 2.2 36.6 1.0 O2B A:DTP401 2.4 43.6 1.0 O2G A:DTP401 2.4 51.5 1.0 O A:HOH514 2.4 46.4 1.0 OD1 A:ASP114 2.4 45.9 1.0 OD2 A:ASP114 2.5 48.9 1.0 CD A:GLU116 2.6 60.4 1.0 CG A:ASP114 2.8 43.8 1.0 HG3 A:GLU116 3.0 69.5 1.0 HG2 A:GLU116 3.0 69.5 1.0 CG A:GLU116 3.1 58.0 1.0 HE2 A:HIS169 3.5 50.8 1.0 OE1 A:GLU116 3.5 67.8 1.0 PB A:DTP401 3.5 47.8 1.0 PA A:DTP401 3.5 45.4 1.0 HZ3 A:LYS165 3.6 70.8 1.0 H5'1 A:DTP401 3.6 50.0 1.0 PG A:DTP401 3.7 52.8 1.0 O3A A:DTP401 3.9 48.8 1.0 O3B A:DTP401 4.0 54.2 1.0 HE2 A:LYS165 4.1 82.1 1.0 NE2 A:HIS169 4.2 42.4 1.0 OG A:SER167 4.3 52.6 1.0 HG A:SER167 4.3 63.0 1.0 CB A:ASP114 4.3 41.5 1.0 NZ A:LYS165 4.4 59.0 1.0 HD2 A:HIS169 4.4 54.3 1.0 C5' A:DTP401 4.4 41.8 1.0 O3G A:DTP401 4.5 54.0 1.0 O5' A:DTP401 4.5 44.9 1.0 CB A:GLU116 4.6 49.9 1.0 H5'2 A:DTP401 4.6 50.0 1.0 OD2 A:ASP280 4.6 50.9 1.0 O A:LEU115 4.6 44.7 1.0 O1A A:DTP401 4.6 52.1 1.0 HZ2 A:LYS165 4.7 70.8 1.0 CD2 A:HIS169 4.7 45.3 1.0 HB3 A:ASP114 4.7 49.8 1.0 CE A:LYS165 4.8 68.5 1.0 HB2 A:ASP114 4.8 49.8 1.0 H A:LEU115 4.8 50.2 1.0 O1G A:DTP401 4.8 59.5 1.0 HA A:ASP114 4.9 48.4 1.0 HB2 A:GLU116 4.9 59.8 1.0 O1B A:DTP401 4.9 41.1 1.0 HB3 A:GLU116 4.9 59.8 1.0 N A:LEU115 5.0 41.9 1.0

Calcium binding site 2 out of 3 in the Human Primpol Extending From the Correct Primer Base C 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 Extending From the Correct Primer Base C Opposite the 8- Oxoguanine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:33.8 occ:1.00 O B:HOH517 2.1 34.3 1.0 O1B B:DTP401 2.2 34.6 1.0 OE1 B:GLU116 2.2 49.4 1.0 O2A B:DTP401 2.3 30.7 1.0 O2G B:DTP401 2.4 36.7 1.0 OD1 B:ASP114 2.4 38.6 1.0 OD2 B:ASP114 2.5 43.1 1.0 CA B:CA403 2.8 75.6 1.0 CG B:ASP114 2.8 40.0 1.0 CD B:GLU116 3.4 50.0 1.0 PB B:DTP401 3.4 38.6 1.0 HZ3 B:LYS165 3.5 64.8 1.0 PA B:DTP401 3.5 39.5 1.0 H5'2 B:DTP401 3.5 44.9 1.0 HE2 B:HIS169 3.6 41.7 1.0 HB3 B:GLU116 3.6 45.4 1.0 PG B:DTP401 3.7 43.2 1.0 O3A B:DTP401 3.7 36.5 1.0 O3B B:DTP401 4.0 40.2 1.0 HE2 B:LYS165 4.1 62.4 1.0 OE2 B:GLU116 4.1 58.8 1.0 NZ B:LYS165 4.2 54.1 1.0 O B:HOH502 4.3 58.4 1.0 NE2 B:HIS169 4.3 34.8 1.0 CB B:ASP114 4.3 33.4 1.0 C5' B:DTP401 4.3 37.5 1.0 CG B:GLU116 4.4 48.8 1.0 CB B:GLU116 4.4 37.8 1.0 HZ2 B:LYS165 4.4 64.8 1.0 O5' B:DTP401 4.4 41.7 1.0 OG B:SER167 4.5 37.6 1.0 HD2 B:HIS169 4.5 49.8 1.0 O3G B:DTP401 4.5 34.8 1.0 HG B:SER167 4.5 45.1 1.0 H5'1 B:DTP401 4.5 44.9 1.0 HG2 B:GLU116 4.6 58.5 1.0 CE B:LYS165 4.7 52.0 1.0 O1A B:DTP401 4.7 38.9 1.0 O1G B:DTP401 4.7 42.5 1.0 HB2 B:GLU116 4.7 45.4 1.0 HB2 B:ASP114 4.7 40.0 1.0 HB3 B:ASP114 4.7 40.0 1.0 O2B B:DTP401 4.8 39.4 1.0 O B:LEU115 4.8 33.6 1.0 OD2 B:ASP280 4.8 49.1 1.0 CD2 B:HIS169 4.8 41.5 1.0 HZ1 B:LYS165 4.9 64.8 1.0 HE3 B:LYS165 4.9 62.4 1.0 HA B:ASP114 4.9 38.0 1.0

Calcium binding site 3 out of 3 in the Human Primpol Extending From the Correct Primer Base C 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 3 of Human Primpol Extending From the Correct Primer Base C Opposite the 8- Oxoguanine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:75.6 occ:1.00 O2A B:DTP401 2.1 30.7 1.0 OD2 B:ASP114 2.3 43.1 1.0 OD2 B:ASP280 2.4 49.1 1.0 OE1 B:GLU116 2.5 49.4 1.0 OE2 B:GLU116 2.5 58.8 1.0 O B:HOH502 2.6 58.4 1.0 CD B:GLU116 2.7 50.0 1.0 CA B:CA402 2.8 33.8 1.0 O3' H:DC14 3.0 58.7 1.0 H3' H:DC14 3.2 67.4 1.0 HO3' H:DC14 3.2 70.3 1.0 CG B:ASP280 3.4 43.9 1.0 CG B:ASP114 3.5 40.0 1.0 PA B:DTP401 3.5 39.5 1.0 C3' H:DC14 3.6 56.2 1.0 HB2 B:ASP280 3.6 43.9 1.0 H5'1 B:DTP401 3.7 44.9 1.0 CB B:ASP280 3.9 36.6 1.0 H5'2 B:DTP401 3.9 44.9 1.0 HB3 B:ASP280 3.9 43.9 1.0 H5'' H:DC14 4.0 86.8 1.0 O5' B:DTP401 4.0 41.7 1.0 HZ3 B:LYS165 4.0 64.8 1.0 OD1 B:ASP114 4.0 38.6 1.0 CG B:GLU116 4.1 48.8 1.0 C5' B:DTP401 4.1 37.5 1.0 HG2 B:GLU116 4.2 58.5 1.0 O1A B:DTP401 4.3 38.9 1.0 O1B B:DTP401 4.4 34.6 1.0 O2G B:DTP401 4.4 36.7 1.0 OD1 B:ASP280 4.4 39.9 1.0 HB3 B:ASP114 4.5 40.0 1.0 HG13 B:VAL283 4.5 46.8 1.0 C4' H:DC14 4.5 66.2 1.0 C5' H:DC14 4.6 72.3 1.0 HG11 B:VAL283 4.6 46.8 1.0 HG3 B:GLU116 4.6 58.5 1.0 CB B:ASP114 4.6 33.4 1.0 HB3 B:GLU116 4.7 45.4 1.0 H4' H:DC14 4.7 79.4 1.0 O B:HOH517 4.7 34.3 1.0 O3A B:DTP401 4.7 36.5 1.0 C2' H:DC14 4.8 56.5 1.0 O5' H:DC14 4.8 80.5 1.0 H2'' H:DC14 4.9 67.7 1.0 CG1 B:VAL283 4.9 39.0 1.0 NZ B:LYS165 4.9 54.1 1.0 H2' H:DC14 5.0 67.7 1.0 CB B:GLU116 5.0 37.8 1.0 HG12 B:VAL283 5.0 46.8 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