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

Protein crystallography data

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

Calcium Binding Sites:

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 7jk1

Go back to Calcium Binding Sites List in 7jk1
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 7jk1

Go back to Calcium Binding Sites List in 7jk1
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

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: Fri Jul 19 00:59:35 2024

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