Calcium in PDB 7jkp: Human Primpol Misinserting Datp Opposite the 8-Oxoguanine Lesion

The structure of Human Primpol Misinserting Datp Opposite the 8-Oxoguanine Lesion, PDB code: 7jkp 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)	69.17 / 2.59
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	52.225, 65.656, 74.482, 69.3, 82.87, 88.06
R / Rfree (%)	24.8 / 30.7

The binding sites of Calcium atom in the Human Primpol Misinserting Datp Opposite the 8-Oxoguanine Lesion (pdb code 7jkp). 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 Misinserting Datp Opposite the 8-Oxoguanine Lesion, PDB code: 7jkp:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human Primpol Misinserting Datp 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 Misinserting Datp Opposite the 8-Oxoguanine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:67.2 occ:1.00 O2G A:DTP401 2.1 75.0 1.0 O2A A:DTP401 2.1 58.9 1.0 O A:HOH503 2.3 55.8 1.0 OE2 A:GLU116 2.3 77.5 1.0 O2B A:DTP401 2.3 60.1 1.0 OD1 A:ASP114 2.4 80.3 1.0 OD2 A:ASP114 2.5 71.1 1.0 CG A:ASP114 2.8 70.8 1.0 CD A:GLU116 3.1 79.8 1.0 HG2 A:GLU116 3.5 90.9 1.0 HB3 A:GLU116 3.5 84.2 1.0 PA A:DTP401 3.5 56.0 1.0 HE2 A:HIS169 3.5 72.3 1.0 PG A:DTP401 3.5 79.0 1.0 PB A:DTP401 3.6 65.2 1.0 HZ1 A:LYS165 3.7 88.5 1.0 CG A:GLU116 3.7 75.8 1.0 H5'2 A:DTP401 3.8 67.0 1.0 OE1 A:GLU116 4.0 84.1 1.0 O3A A:DTP401 4.0 66.3 1.0 O3B A:DTP401 4.0 76.1 1.0 CB A:GLU116 4.1 70.2 1.0 HE2 A:LYS165 4.1 85.9 1.0 O3G A:DTP401 4.2 53.4 1.0 CB A:ASP114 4.3 62.0 1.0 O5' A:DTP401 4.3 61.8 1.0 HG A:SER167 4.3 87.4 1.0 HZ3 A:LYS165 4.3 88.5 1.0 NE2 A:HIS169 4.3 60.3 1.0 NZ A:LYS165 4.4 73.7 1.0 C5' A:DTP401 4.4 55.9 1.0 OG A:SER167 4.4 72.8 1.0 H5'1 A:DTP401 4.4 67.0 1.0 HB2 A:GLU116 4.5 84.2 1.0 O1G A:DTP401 4.6 71.7 1.0 O1A A:DTP401 4.6 75.5 1.0 OD2 A:ASP280 4.6 74.5 1.0 HB2 A:ASP114 4.6 74.4 1.0 HG3 A:GLU116 4.6 90.9 1.0 HO3' D:DG14 4.7 87.3 1.0 HB3 A:ASP114 4.7 74.4 1.0 HD2 A:HIS169 4.7 68.1 1.0 CE A:LYS165 4.7 71.6 1.0 O1B A:DTP401 4.8 72.9 1.0 O A:LEU115 4.9 67.4 1.0 HA A:ASP114 4.9 78.4 1.0 CD2 A:HIS169 5.0 56.7 1.0

Calcium binding site 2 out of 3 in the Human Primpol Misinserting Datp 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 Misinserting Datp Opposite the 8-Oxoguanine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:67.7 occ:1.00 O2B B:DTP401 1.9 70.0 1.0 O2A B:DTP401 2.1 60.4 1.0 O2G B:DTP401 2.3 85.2 1.0 OE2 B:GLU116 2.3 78.4 1.0 OD2 B:ASP114 2.4 78.7 1.0 OD1 B:ASP114 2.4 78.8 1.0 O B:HOH501 2.5 57.6 1.0 CG B:ASP114 2.8 77.4 1.0 CA B:CA403 2.8 88.8 1.0 PB B:DTP401 2.9 72.9 1.0 PA B:DTP401 3.1 66.8 1.0 HE2 B:HIS169 3.2 89.7 1.0 O3A B:DTP401 3.3 74.3 1.0 CD B:GLU116 3.4 78.5 1.0 PG B:DTP401 3.4 69.7 1.0 O3B B:DTP401 3.4 78.2 1.0 H5'1 B:DTP401 3.5 89.6 1.0 O5' B:DTP401 3.6 76.7 1.0 OE1 B:GLU116 3.8 75.9 1.0 C5' B:DTP401 4.0 74.7 1.0 NE2 B:HIS169 4.1 74.8 1.0 H5'2 B:DTP401 4.1 89.6 1.0 O1B B:DTP401 4.3 73.5 1.0 O3G B:DTP401 4.3 72.2 1.0 CB B:ASP114 4.3 72.4 1.0 O1A B:DTP401 4.4 79.6 1.0 HB3 B:GLU116 4.4 99.2 1.0 HG B:SER167 4.5 92.3 1.0 O1G B:DTP401 4.5 83.6 1.0 OG B:SER167 4.6 76.9 1.0 HZ1 B:LYS297 4.7 78.3 1.0 CG B:GLU116 4.7 70.0 1.0 HB2 B:ASP114 4.7 86.9 1.0 HB3 B:ASP114 4.7 86.9 1.0 HD2 B:HIS169 4.8 79.1 1.0 O B:LEU115 4.8 74.2 1.0 HG2 B:GLU116 4.9 84.0 1.0 HZ3 B:LYS297 4.9 78.3 1.0 CD2 B:HIS169 4.9 65.9 1.0 HA B:ASP114 4.9 91.5 1.0 OD2 B:ASP280 4.9 83.5 1.0

Calcium binding site 3 out of 3 in the Human Primpol Misinserting Datp 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 Misinserting Datp Opposite the 8-Oxoguanine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:88.8 occ:1.00 OD2 B:ASP114 2.4 78.7 1.0 OE1 B:GLU116 2.4 75.9 1.0 OD2 B:ASP280 2.5 83.5 1.0 O2A B:DTP401 2.6 60.4 1.0 OE2 B:GLU116 2.8 78.4 1.0 CA B:CA402 2.8 67.7 1.0 CD B:GLU116 2.9 78.5 1.0 O5' B:DTP401 3.4 76.7 1.0 CG B:ASP114 3.4 77.4 1.0 CG B:ASP280 3.6 72.9 1.0 PA B:DTP401 3.6 66.8 1.0 HB2 B:ASP280 3.8 73.0 1.0 O3' H:DG14 3.9 94.8 1.0 C3' H:DG14 4.0 109.1 1.0 OD1 B:ASP114 4.0 78.8 1.0 CB B:ASP280 4.1 60.8 1.0 HB3 B:ASP280 4.1 73.0 1.0 H5'2 B:DTP401 4.2 89.6 1.0 CG B:GLU116 4.2 70.0 1.0 C5' B:DTP401 4.3 74.7 1.0 HB3 B:ASP114 4.3 86.9 1.0 HG2 B:GLU116 4.4 84.0 1.0 O1A B:DTP401 4.5 79.6 1.0 HG11 B:VAL283 4.5 98.2 1.0 O2G B:DTP401 4.5 85.2 1.0 H5'1 B:DTP401 4.5 89.6 1.0 CB B:ASP114 4.5 72.4 1.0 HG13 B:VAL283 4.5 98.2 1.0 HG3 B:GLU116 4.6 84.0 1.0 O2B B:DTP401 4.6 70.0 1.0 OD1 B:ASP280 4.6 71.0 1.0 O B:HOH501 4.7 57.6 1.0 C2' H:DG14 4.8 109.9 1.0 CG1 B:VAL283 4.8 81.8 1.0 HG12 B:VAL283 4.8 98.2 1.0 O3A B:DTP401 4.9 74.3 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