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: Sat Jul 10 11:29:24 2021

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy