Calcium in PDB 7jkl: Human Primpol Misinserting Datp Opposite the 8-Oxoguanine Lesion (3'- End Base of the Primer Strand Is 2',3'-Dideoxy-Terminated).

The structure of Human Primpol Misinserting Datp Opposite the 8-Oxoguanine Lesion (3'- End Base of the Primer Strand Is 2',3'-Dideoxy-Terminated)., PDB code: 7jkl 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 / 2.38
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.525, 65.641, 74.307, 69.44, 83.43, 87.74
R / Rfree (%)	22 / 27.7

The binding sites of Calcium atom in the Human Primpol Misinserting Datp Opposite the 8-Oxoguanine Lesion (3'- End Base of the Primer Strand Is 2',3'-Dideoxy-Terminated). (pdb code 7jkl). 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 (3'- End Base of the Primer Strand Is 2',3'-Dideoxy-Terminated)., PDB code: 7jkl:
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 (3'- End Base of the Primer Strand Is 2',3'-Dideoxy-Terminated).


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 (3'- End Base of the Primer Strand Is 2',3'-Dideoxy-Terminated). within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:71.8 occ:1.00 O2B A:DTP401 2.2 45.5 1.0 O A:HOH508 2.3 62.2 1.0 O2A A:DTP401 2.3 48.2 1.0 OE2 A:GLU116 2.4 74.7 1.0 OD1 A:ASP114 2.4 64.7 1.0 OD2 A:ASP114 2.4 61.9 1.0 O2G A:DTP401 2.5 67.5 1.0 CG A:ASP114 2.8 62.1 1.0 CD A:GLU116 3.1 69.9 1.0 HE2 A:HIS169 3.4 63.4 1.0 PB A:DTP401 3.5 57.5 1.0 OE1 A:GLU116 3.6 67.5 1.0 HB3 A:GLU116 3.6 74.5 1.0 PA A:DTP401 3.7 50.9 1.0 HZ1 A:LYS165 3.7 80.6 1.0 PG A:DTP401 3.8 62.8 1.0 H5'2 A:DTP401 3.8 65.0 1.0 CG A:GLU116 4.1 60.7 1.0 O3A A:DTP401 4.1 58.6 1.0 HG2 A:GLU116 4.1 72.9 1.0 O3B A:DTP401 4.1 75.9 1.0 HG A:SER167 4.2 83.2 1.0 NE2 A:HIS169 4.2 52.8 1.0 HE2 A:LYS165 4.2 82.5 1.0 OG A:SER167 4.2 69.3 1.0 HZ3 A:LYS165 4.2 80.6 1.0 CB A:ASP114 4.3 55.1 1.0 CB A:GLU116 4.3 62.0 1.0 NZ A:LYS165 4.3 67.2 1.0 H5'1 A:DTP401 4.3 65.0 1.0 C5' A:DTP401 4.4 54.2 1.0 O5' A:DTP401 4.4 66.7 1.0 HD2 A:HIS169 4.5 65.0 1.0 O1B A:DTP401 4.6 61.2 1.0 HB2 A:GLU116 4.7 74.5 1.0 O3G A:DTP401 4.7 66.7 1.0 HB3 A:ASP114 4.7 66.1 1.0 O A:LEU115 4.7 54.0 1.0 HB2 A:ASP114 4.7 66.1 1.0 CD2 A:HIS169 4.8 54.1 1.0 CE A:LYS165 4.8 68.8 1.0 O1G A:DTP401 4.8 79.7 1.0 O1A A:DTP401 4.8 75.4 1.0 HA A:ASP114 4.8 68.8 1.0 OD2 A:ASP280 4.8 66.7 1.0 HG3 A:GLU116 4.9 72.9 1.0 CA A:ASP114 4.9 57.4 1.0 C A:ASP114 4.9 64.5 1.0

Calcium binding site 2 out of 3 in the Human Primpol Misinserting Datp Opposite the 8-Oxoguanine Lesion (3'- End Base of the Primer Strand Is 2',3'-Dideoxy-Terminated).


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 (3'- End Base of the Primer Strand Is 2',3'-Dideoxy-Terminated). within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:53.2 occ:1.00 O2A B:DTP403 2.1 41.0 1.0 O B:HOH509 2.3 51.6 1.0 O2B B:DTP403 2.3 46.7 1.0 OE2 B:GLU116 2.4 63.0 1.0 O2G B:DTP403 2.4 53.4 1.0 OD1 B:ASP114 2.4 53.8 1.0 OD2 B:ASP114 2.5 58.7 1.0 CG B:ASP114 2.8 50.9 1.0 CA B:CA402 3.1 65.0 0.6 HE2 B:HIS169 3.2 60.4 1.0 CD B:GLU116 3.3 60.3 1.0 PB B:DTP403 3.5 54.3 1.0 PA B:DTP403 3.5 44.6 1.0 HB3 B:GLU116 3.6 64.3 1.0 PG B:DTP403 3.7 56.4 1.0 H5'2 B:DTP403 3.8 64.1 1.0 O3A B:DTP403 3.9 50.0 1.0 O3B B:DTP403 3.9 64.5 1.0 OE1 B:GLU116 4.0 69.8 1.0 NE2 B:HIS169 4.1 50.4 1.0 CG B:GLU116 4.2 56.9 1.0 HG2 B:GLU116 4.2 68.3 1.0 CB B:ASP114 4.3 46.5 1.0 HG B:SER167 4.3 73.4 1.0 OG B:SER167 4.3 61.1 1.0 H5'1 B:DTP403 4.4 64.1 1.0 CB B:GLU116 4.4 53.6 1.0 C5' B:DTP403 4.4 53.4 1.0 HD2 B:HIS169 4.5 59.7 1.0 O3G B:DTP403 4.5 61.0 1.0 O5' B:DTP403 4.5 52.9 1.0 O1A B:DTP403 4.5 69.6 1.0 CD2 B:HIS169 4.7 49.8 1.0 HB3 B:ASP114 4.7 55.9 1.0 O B:LEU115 4.7 49.5 1.0 O1G B:DTP403 4.7 55.8 1.0 O1B B:DTP403 4.7 58.3 1.0 HB2 B:ASP114 4.7 55.9 1.0 HB2 B:GLU116 4.8 64.3 1.0 HA B:ASP114 4.8 60.7 1.0 CA B:ASP114 5.0 50.6 1.0 H B:LEU115 5.0 61.5 1.0

Calcium binding site 3 out of 3 in the Human Primpol Misinserting Datp Opposite the 8-Oxoguanine Lesion (3'- End Base of the Primer Strand Is 2',3'-Dideoxy-Terminated).


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 (3'- End Base of the Primer Strand Is 2',3'-Dideoxy-Terminated). within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:65.0 occ:0.58 OE1 B:GLU116 2.3 69.8 1.0 OD2 B:ASP114 2.4 58.7 1.0 OD2 B:ASP280 2.4 63.0 1.0 O2A B:DTP403 2.5 41.0 1.0 CD B:GLU116 2.8 60.3 1.0 OE2 B:GLU116 2.9 63.0 1.0 H3'1 H:DDG14 3.0 108.1 1.0 CA B:CA401 3.1 53.2 1.0 CG B:ASP280 3.4 56.5 1.0 H3'2 H:DDG14 3.5 108.1 1.0 CG B:ASP114 3.6 50.9 1.0 PA B:DTP403 3.6 44.6 1.0 C3' H:DDG14 3.6 90.1 1.0 H5'1 B:DTP403 3.7 64.1 1.0 HB2 B:ASP280 3.7 57.2 1.0 O5' B:DTP403 3.9 52.9 1.0 CB B:ASP280 4.0 47.7 1.0 HB3 B:ASP280 4.0 57.2 1.0 O1A B:DTP403 4.0 69.6 1.0 CG B:GLU116 4.1 56.9 1.0 C5' B:DTP403 4.1 53.4 1.0 HG2 B:GLU116 4.2 68.3 1.0 H5'2 B:DTP403 4.2 64.1 1.0 OD1 B:ASP114 4.2 53.8 1.0 HG11 B:VAL283 4.3 63.2 1.0 H2' H:DDG14 4.3 102.8 1.0 HG13 B:VAL283 4.4 63.2 1.0 HB3 B:ASP114 4.4 55.9 1.0 OD1 B:ASP280 4.5 52.4 1.0 H5' H:DDG14 4.5 127.5 1.0 C2' H:DDG14 4.5 85.7 1.0 HG12 B:VAL283 4.6 63.2 1.0 HG3 B:GLU116 4.6 68.3 1.0 CG1 B:VAL283 4.6 52.7 1.0 O2G B:DTP403 4.6 53.4 1.0 CB B:ASP114 4.6 46.5 1.0 C4' H:DDG14 4.7 93.2 1.0 O2B B:DTP403 4.7 46.7 1.0 H4' H:DDG14 4.8 111.8 1.0 O B:HOH535 4.9 54.9 1.0 H2'' H:DDG14 4.9 102.8 1.0 HB3 B:GLU116 5.0 64.3 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