Calcium in PDB 8evf: Human Dna Polymerase Eta Extension Complex with An Incoming Dctp

All present enzymatic activity of Human Dna Polymerase Eta Extension Complex with An Incoming Dctp:
2.7.7.7;

The structure of Human Dna Polymerase Eta Extension Complex with An Incoming Dctp, PDB code: 8evf was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.53 / 2.87
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.671, 98.671, 81.736, 90, 90, 120
R / Rfree (%)	20.4 / 25.1

The binding sites of Calcium atom in the Human Dna Polymerase Eta Extension Complex with An Incoming Dctp (pdb code 8evf). 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 Dna Polymerase Eta Extension Complex with An Incoming Dctp, PDB code: 8evf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human Dna Polymerase Eta Extension Complex with An Incoming Dctp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Dna Polymerase Eta Extension Complex with An Incoming Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:37.0 occ:1.00 O A:MET14 2.2 43.0 1.0 OD2 A:ASP115 2.3 44.0 1.0 OD2 A:ASP13 2.4 43.4 1.0 O2G A:DCP501 2.5 45.8 1.0 O2B A:DCP501 2.5 42.9 1.0 O2A A:DCP501 2.7 40.4 1.0 CG A:ASP13 3.1 46.4 1.0 OD1 A:ASP13 3.1 52.1 1.0 O3A A:DCP501 3.1 38.0 1.0 PB A:DCP501 3.1 40.5 1.0 O3B A:DCP501 3.2 45.3 1.0 CG A:ASP115 3.4 44.7 1.0 C A:MET14 3.4 42.3 1.0 PG A:DCP501 3.4 37.5 1.0 CA A:CA503 3.5 63.1 1.0 PA A:DCP501 3.5 37.7 1.0 OD1 A:ASP115 3.9 43.6 1.0 N A:MET14 4.0 38.7 1.0 C5' A:DCP501 4.2 42.5 1.0 O3G A:DCP501 4.2 38.5 1.0 CA A:MET14 4.2 40.2 1.0 O5' A:DCP501 4.3 47.1 1.0 N A:ASP15 4.4 40.7 1.0 N A:CYS16 4.5 43.4 1.0 CB A:ASP13 4.5 41.6 1.0 C A:ASP13 4.5 38.0 1.0 CA A:ASP15 4.6 44.3 1.0 O1B A:DCP501 4.6 37.2 1.0 O1G A:DCP501 4.6 33.4 1.0 CB A:ASP115 4.7 36.9 1.0 O1A A:DCP501 4.8 47.2 1.0 C A:ASP15 4.8 42.9 1.0 CB A:MET14 4.8 37.6 1.0 N A:PHE17 4.8 40.4 1.0 CB A:PHE17 4.9 35.5 1.0 NZ A:LYS231 5.0 50.9 1.0

Calcium binding site 2 out of 2 in the Human Dna Polymerase Eta Extension Complex with An Incoming Dctp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Dna Polymerase Eta Extension Complex with An Incoming Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:63.1 occ:1.00 OD2 A:ASP13 2.2 43.4 1.0 OE1 A:GLU116 2.3 48.6 1.0 O2A A:DCP501 2.3 40.4 1.0 C3' P:DG8 2.6 50.4 0.3 O3' P:DG8 2.8 47.0 1.0 OD1 A:ASP115 3.1 43.6 1.0 CG A:ASP13 3.3 46.4 1.0 CD A:GLU116 3.5 42.9 1.0 CA A:CA502 3.5 37.0 1.0 C2' P:DG8 3.6 52.0 0.6 C4' P:DG8 3.7 51.9 0.4 OD2 A:ASP115 3.7 44.0 1.0 PA A:DCP501 3.7 37.7 1.0 CG A:ASP115 3.8 44.7 1.0 CB A:ASP13 4.0 41.6 1.0 C5' P:DG8 4.1 56.8 0.0 OD1 A:ASP13 4.2 52.1 1.0 NZ A:LYS224 4.2 56.3 1.0 O1A A:DCP501 4.3 47.2 1.0 OE2 A:GLU116 4.3 47.6 1.0 CB A:GLU116 4.3 41.0 1.0 OG A:SER113 4.3 43.0 1.0 O5' P:DG8 4.3 69.1 1.0 CG A:GLU116 4.5 37.7 1.0 O2G A:DCP501 4.6 45.8 1.0 O3A A:DCP501 4.6 38.0 1.0 C5' A:DCP501 4.6 42.5 1.0 O5' A:DCP501 4.7 47.1 1.0 C1' P:DG8 4.8 49.7 1.0 O4' P:DG8 4.9 51.5 0.6

R.Richie-Jannetta, P.Pallan, P.J.Kingsley, N.Kamdar, M.Egli, L.J.Marnett. The Peroxidation-Derived Dna Adduct, 6-Oxo-M 1 Dg, Is A Strong Block to Replication By Human Dna Polymerase Eta. J.Biol.Chem. 05067 2023.
ISSN: ESSN 1083-351X
PubMed: 37468099
DOI: 10.1016/J.JBC.2023.105067