Calcium in PDB 7jlg: Human Primpol Extending From the Erroneous Primer Base A Opposite the 8-Oxoguanine Lesion

Protein crystallography data

The structure of Human Primpol Extending From the Erroneous Primer Base A Opposite the 8-Oxoguanine Lesion, PDB code: 7jlg 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) 26.81 / 2.07
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 51.031, 65.21, 73.115, 71.36, 84.31, 88.63
R / Rfree (%) 20.1 / 21.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Primpol Extending From the Erroneous Primer Base A Opposite the 8-Oxoguanine Lesion (pdb code 7jlg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Human Primpol Extending From the Erroneous Primer Base A Opposite the 8-Oxoguanine Lesion, PDB code: 7jlg:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7jlg

Go back to Calcium Binding Sites List in 7jlg
Calcium binding site 1 out of 4 in the Human Primpol Extending From the Erroneous Primer Base A 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 Erroneous Primer Base A Opposite the 8-Oxoguanine Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:101.8
occ:1.00
OD1 A:ASP114 2.1 55.4 1.0
O2B A:DTP401 2.2 56.3 1.0
OE2 A:GLU116 2.2 81.4 1.0
O2A A:DTP401 2.4 55.5 1.0
O A:HOH504 2.4 59.4 1.0
O2G A:DTP401 2.4 68.2 1.0
OD2 A:ASP114 2.5 61.3 1.0
CG A:ASP114 2.6 60.5 1.0
HG2 A:GLU116 2.7 81.0 1.0
CD A:GLU116 2.9 68.6 1.0
HG3 A:GLU116 3.0 81.0 1.0
CG A:GLU116 3.0 67.3 1.0
HE2 A:HIS169 3.1 64.3 1.0
CA A:CA403 3.5 87.0 1.0
PB A:DTP401 3.5 52.3 1.0
H5'1 A:DTP401 3.6 71.7 1.0
PA A:DTP401 3.7 53.1 1.0
PG A:DTP401 3.8 61.5 1.0
NE2 A:HIS169 3.8 53.4 1.0
HD2 A:HIS169 4.0 65.5 1.0
O3A A:DTP401 4.0 60.9 1.0
O3B A:DTP401 4.0 59.5 1.0
OG A:SER167 4.0 61.7 1.0
HG A:SER167 4.1 74.3 1.0
OE1 A:GLU116 4.1 73.1 1.0
CB A:ASP114 4.1 60.0 1.0
HZ1 A:LYS165 4.1 78.2 1.0
CD2 A:HIS169 4.3 54.4 1.0
O A:LEU115 4.4 51.3 1.0
HE2 A:LYS165 4.4 83.1 1.0
C5' A:DTP401 4.4 59.5 1.0
H A:LEU115 4.5 60.7 1.0
HZ3 A:LYS165 4.5 78.2 1.0
HA A:ASP114 4.5 65.8 1.0
H5'2 A:DTP401 4.5 71.7 1.0
CB A:GLU116 4.5 57.0 1.0
HB2 A:ASP114 4.6 72.2 1.0
HB3 A:ASP114 4.6 72.2 1.0
O3G A:DTP401 4.6 59.4 1.0
O5' A:DTP401 4.6 57.8 1.0
N A:LEU115 4.7 50.4 1.0
NZ A:LYS165 4.7 64.9 1.0
CA A:ASP114 4.7 54.6 1.0
C A:ASP114 4.8 60.9 1.0
O1B A:DTP401 4.8 59.7 1.0
O1A A:DTP401 4.8 75.2 1.0
C A:LEU115 4.8 61.8 1.0
HB3 A:GLU116 4.8 68.6 1.0
O1G A:DTP401 4.8 64.5 1.0
HB2 A:GLU116 5.0 68.6 1.0

Calcium binding site 2 out of 4 in 7jlg

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Calcium binding site 2 out of 4 in the Human Primpol Extending From the Erroneous Primer Base A 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 Erroneous Primer Base A Opposite the 8-Oxoguanine Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:87.0
occ:1.00
OE2 A:GLU116 2.3 81.4 1.0
OD2 A:ASP280 2.4 70.5 1.0
OE1 A:GLU116 2.4 73.1 1.0
CD A:GLU116 2.4 68.6 1.0
OD2 A:ASP114 2.5 61.3 1.0
O2A A:DTP401 2.7 55.5 1.0
HO3' D:DA14 2.8 137.4 1.0
H3' D:DA14 3.1 137.9 1.0
HB2 A:ASP280 3.1 65.4 1.0
CG A:ASP280 3.2 60.1 1.0
HB3 A:ASP280 3.5 65.4 1.0
CB A:ASP280 3.5 54.3 1.0
CA A:CA402 3.5 101.8 1.0
O3' D:DA14 3.5 115.5 1.0
HG3 A:GLU116 3.6 81.0 1.0
CG A:GLU116 3.6 67.3 1.0
CG A:ASP114 3.7 60.5 1.0
C3' D:DA14 3.8 116.0 1.0
PA A:DTP401 3.8 53.1 1.0
H5'2 A:DTP401 4.0 71.7 1.0
HZ1 A:LYS165 4.2 78.2 1.0
HG2 A:GLU116 4.2 81.0 1.0
OD1 A:ASP280 4.2 56.5 1.0
O1A A:DTP401 4.2 75.2 1.0
O5' A:DTP401 4.4 57.8 1.0
HB3 A:ASP114 4.4 72.2 1.0
OD1 A:ASP114 4.4 55.4 1.0
HB2 A:GLU116 4.4 68.6 1.0
HG13 A:VAL283 4.5 68.0 1.0
HG11 A:VAL283 4.5 68.0 1.0
C5' A:DTP401 4.5 59.5 1.0
H5'1 A:DTP401 4.5 71.7 1.0
H5'' D:DA14 4.6 141.2 1.0
CB A:GLU116 4.7 57.0 1.0
CB A:ASP114 4.7 60.0 1.0
H4' D:DA14 4.7 137.6 1.0
C4' D:DA14 4.7 115.7 1.0
O2G A:DTP401 4.8 68.2 1.0
HG12 A:VAL283 4.8 68.0 1.0
CG1 A:VAL283 4.8 56.5 1.0
O2B A:DTP401 4.8 56.3 1.0
C2' D:DA14 5.0 117.3 1.0
CA A:ASP280 5.0 48.9 1.0

Calcium binding site 3 out of 4 in 7jlg

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Calcium binding site 3 out of 4 in the Human Primpol Extending From the Erroneous Primer Base A 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 Erroneous Primer Base A Opposite the 8-Oxoguanine Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:42.1
occ:1.00
O2A B:DTP401 2.2 36.4 1.0
O2G B:DTP401 2.2 43.6 1.0
O2B B:DTP401 2.3 38.9 1.0
OE1 B:GLU116 2.3 49.0 1.0
O B:HOH521 2.4 46.0 1.0
OD1 B:ASP114 2.4 41.9 1.0
OD2 B:ASP114 2.5 47.9 1.0
CG B:ASP114 2.8 43.5 1.0
CA B:CA403 3.1 62.5 1.0
CD B:GLU116 3.3 50.0 1.0
HE2 B:HIS169 3.4 49.2 1.0
HB3 B:GLU116 3.5 54.6 1.0
PB B:DTP401 3.5 33.3 1.0
PA B:DTP401 3.6 75.7 1.0
PG B:DTP401 3.7 47.9 1.0
H5'2 B:DTP401 3.7 56.4 1.0
HZ1 B:LYS165 3.8 65.8 1.0
OE2 B:GLU116 3.9 49.1 1.0
O3A B:DTP401 4.0 48.2 1.0
O3B B:DTP401 4.0 45.9 1.0
HE2 B:LYS165 4.1 65.9 1.0
NE2 B:HIS169 4.1 40.8 1.0
CB B:ASP114 4.3 40.5 1.0
CB B:GLU116 4.3 45.3 1.0
CG B:GLU116 4.3 49.0 1.0
OG B:SER167 4.4 45.0 1.0
O B:HOH557 4.4 55.6 1.0
HD2 B:HIS169 4.4 49.2 1.0
C5' B:DTP401 4.4 46.8 1.0
HG B:SER167 4.4 54.3 1.0
O3G B:DTP401 4.4 42.5 1.0
H5'1 B:DTP401 4.5 56.4 1.0
NZ B:LYS165 4.5 54.6 1.0
O5' B:DTP401 4.5 55.1 1.0
HZ3 B:LYS165 4.5 65.8 1.0
O B:LEU115 4.6 40.0 1.0
HG2 B:GLU116 4.7 59.0 1.0
HB2 B:GLU116 4.7 54.6 1.0
CD2 B:HIS169 4.7 40.8 1.0
O1A B:DTP401 4.7 51.2 1.0
HB3 B:ASP114 4.7 48.8 1.0
O1G B:DTP401 4.7 47.9 1.0
HB2 B:ASP114 4.7 48.8 1.0
CE B:LYS165 4.8 54.7 1.0
HA B:ASP114 4.8 45.1 1.0
O1B B:DTP401 4.8 47.0 1.0
OD2 B:ASP280 4.9 56.6 1.0
CA B:ASP114 5.0 37.4 1.0
C B:ASP114 5.0 43.5 1.0

Calcium binding site 4 out of 4 in 7jlg

Go back to Calcium Binding Sites List in 7jlg
Calcium binding site 4 out of 4 in the Human Primpol Extending From the Erroneous Primer Base A 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 4 of Human Primpol Extending From the Erroneous Primer Base A Opposite the 8-Oxoguanine Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:62.5
occ:1.00
OD2 B:ASP280 2.3 56.6 1.0
OD2 B:ASP114 2.4 47.9 1.0
OE2 B:GLU116 2.4 49.1 1.0
O2A B:DTP401 2.4 36.4 1.0
O B:HOH557 2.4 55.6 1.0
O H:HOH101 2.5 49.0 1.0
OE1 B:GLU116 2.9 49.0 1.0
CD B:GLU116 3.0 50.0 1.0
CA B:CA402 3.1 42.1 1.0
CG B:ASP280 3.4 52.6 1.0
H5'1 B:DTP401 3.5 56.4 1.0
PA B:DTP401 3.6 75.7 1.0
CG B:ASP114 3.6 43.5 1.0
O3' H:DA14 3.8 77.8 1.0
HB2 B:ASP280 3.8 56.2 1.0
O5' B:DTP401 3.9 55.1 1.0
CB B:ASP280 4.0 46.7 1.0
C5' B:DTP401 4.0 46.8 1.0
HB3 B:ASP280 4.1 56.2 1.0
H5'2 B:DTP401 4.1 56.4 1.0
O1A B:DTP401 4.1 51.2 1.0
HO3' H:DA14 4.2 92.2 1.0
HG11 B:VAL283 4.2 53.1 1.0
HG13 B:VAL283 4.3 53.1 1.0
OD1 B:ASP114 4.3 41.9 1.0
HG12 B:VAL283 4.4 53.1 1.0
OD1 B:ASP280 4.4 44.0 1.0
CG B:GLU116 4.4 49.0 1.0
HZ1 B:LYS165 4.4 65.8 1.0
CG1 B:VAL283 4.5 44.1 1.0
HB3 B:ASP114 4.5 48.8 1.0
O2B B:DTP401 4.5 38.9 1.0
O2G B:DTP401 4.5 43.6 1.0
HG2 B:GLU116 4.6 59.0 1.0
CB B:ASP114 4.7 40.5 1.0
H4' H:DA14 4.8 96.3 1.0
H3' H:DA14 4.8 96.6 1.0
C3' H:DA14 4.8 81.0 1.0
HG3 B:GLU116 4.9 59.0 1.0
O3A B:DTP401 4.9 48.2 1.0

Reference:

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
Page generated: Sat Jul 10 11:29:16 2021

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