Calcium in PDB 7rbg: Human Dna Polymerase Beta Crosslinked Ternary Complex 1

All present enzymatic activity of Human Dna Polymerase Beta Crosslinked Ternary Complex 1:
2.7.7.7;

The structure of Human Dna Polymerase Beta Crosslinked Ternary Complex 1, PDB code: 7rbg was solved by A.J.Reed, A.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.07 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.51, 78.43, 57.19, 90, 113.22, 90
R / Rfree (%)	17.9 / 22.3

The structure of Human Dna Polymerase Beta Crosslinked Ternary Complex 1 also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the Human Dna Polymerase Beta Crosslinked Ternary Complex 1 (pdb code 7rbg). 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 Dna Polymerase Beta Crosslinked Ternary Complex 1, PDB code: 7rbg:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human Dna Polymerase Beta Crosslinked Ternary Complex 1


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 Beta Crosslinked Ternary Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:27.7 occ:1.00 O1B A:DCP401 2.0 13.1 1.0 O1A A:DCP401 2.1 10.7 1.0 OD1 A:ASP190 2.1 17.0 1.0 O1G A:DCP401 2.1 13.9 1.0 OD2 A:ASP192 2.1 13.0 1.0 O A:HOH610 2.2 14.0 1.0 PB A:DCP401 3.0 12.7 1.0 CG A:ASP190 3.1 16.4 1.0 CG A:ASP192 3.2 12.4 1.0 PA A:DCP401 3.2 12.0 1.0 PG A:DCP401 3.3 15.1 1.0 O3A A:DCP401 3.4 12.2 1.0 O3B A:DCP401 3.5 13.4 1.0 OD2 A:ASP190 3.6 19.1 1.0 OD1 A:ASP192 3.6 12.5 1.0 NA A:NA406 3.7 29.5 1.0 O A:ASP190 3.9 12.5 1.0 O A:HOH590 4.0 19.9 1.0 O3G A:DCP401 4.1 15.5 1.0 C5' A:DCP401 4.1 11.3 1.0 O5' A:DCP401 4.2 11.1 1.0 C A:ASP190 4.2 13.6 1.0 N A:ASP190 4.2 14.7 1.0 OG A:SER180 4.3 14.2 1.0 O A:HOH619 4.4 13.5 1.0 O2G A:DCP401 4.4 15.0 1.0 CA A:GLY179 4.4 13.7 1.0 CB A:ASP190 4.4 15.9 1.0 O2A A:DCP401 4.4 10.8 1.0 O2B A:DCP401 4.4 13.4 1.0 CB A:ASP192 4.5 12.2 1.0 N A:SER180 4.5 13.7 1.0 CA A:ASP190 4.5 14.8 1.0 N A:ASP192 4.8 12.1 1.0 N A:MET191 4.9 13.7 1.0 C A:GLY179 5.0 14.0 1.0

Calcium binding site 2 out of 3 in the Human Dna Polymerase Beta Crosslinked Ternary Complex 1


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 Beta Crosslinked Ternary Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:33.6 occ:1.00 O A:VAL65 2.3 18.1 1.0 O A:LYS60 2.4 22.1 1.0 O A:LEU62 2.5 17.7 1.0 O A:HOH638 2.5 21.8 1.0 O D:HOH102 2.5 18.7 1.0 OP1 D:DC3 2.7 18.5 1.0 C A:VAL65 3.5 15.8 1.0 C A:LYS60 3.5 22.5 1.0 C A:LEU62 3.5 19.9 1.0 P D:DC3 3.6 19.9 1.0 OP2 D:DC3 3.7 19.4 1.0 O D:HOH106 3.8 29.2 1.0 N A:VAL65 3.8 15.3 1.0 N A:LEU62 4.0 24.1 1.0 C A:LYS61 4.0 25.6 1.0 CA A:VAL65 4.1 15.9 1.0 CA A:LYS60 4.2 23.6 1.0 CA A:PRO63 4.2 21.3 1.0 N A:PRO63 4.2 20.5 1.0 N A:GLY64 4.2 19.2 1.0 O A:LYS61 4.2 25.9 1.0 CA A:LEU62 4.4 23.0 1.0 CB A:VAL65 4.4 16.1 1.0 N A:LYS61 4.4 22.6 1.0 O3' D:DT2 4.5 17.4 1.0 CG A:LYS60 4.5 28.0 1.0 N A:GLY66 4.5 15.1 1.0 CA A:LYS61 4.6 25.3 1.0 C A:PRO63 4.6 21.2 1.0 C A:GLY64 4.8 16.4 1.0 O5' D:DC3 4.9 18.8 1.0 CA A:GLY66 4.9 15.5 1.0 O A:ALA59 4.9 18.1 1.0 NZ A:LYS60 4.9 32.6 1.0 CB A:LYS60 4.9 26.2 1.0

Calcium binding site 3 out of 3 in the Human Dna Polymerase Beta Crosslinked Ternary Complex 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Dna Polymerase Beta Crosslinked Ternary Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:28.4 occ:1.00 O A:THR101 2.3 15.6 1.0 O A:ILE106 2.3 12.8 1.0 OP1 P:DG9 2.3 13.3 1.0 O A:VAL103 2.5 11.6 1.0 O A:HOH668 2.5 21.2 1.0 O P:HOH102 2.6 20.5 1.0 C A:THR101 3.3 15.6 1.0 C A:ILE106 3.4 12.3 1.0 P P:DG9 3.4 15.0 1.0 C A:VAL103 3.4 12.8 1.0 OP2 P:DG9 3.6 15.2 1.0 N A:ILE106 3.8 12.8 1.0 O A:HOH642 3.8 41.8 1.0 CA A:THR101 3.9 15.0 1.0 N A:SER104 4.0 12.6 1.0 N A:GLY105 4.0 13.5 1.0 CA A:SER104 4.1 12.9 1.0 CA A:ILE106 4.1 12.8 1.0 N A:VAL103 4.2 14.1 1.0 C A:ARG102 4.3 15.3 1.0 O3' P:DC8 4.3 14.2 1.0 N A:ARG102 4.4 16.3 1.0 N A:GLY107 4.4 12.5 1.0 C A:SER104 4.4 12.9 1.0 CB A:THR101 4.4 14.7 1.0 CA A:VAL103 4.4 13.7 1.0 CB A:ILE106 4.5 12.6 1.0 O5' P:DG9 4.6 14.3 1.0 CA A:ARG102 4.6 16.1 1.0 C A:GLY105 4.6 13.3 1.0 CA A:GLY107 4.7 13.5 1.0 O A:ARG102 4.8 18.1 1.0 O A:LEU100 4.9 13.7 1.0 CA A:GLY105 5.0 13.3 1.0

A.Kumar, A.J.Reed, W.J.Zahurancik, S.M.Daskalova, S.M.Hecht, Z.Suo. Interlocking Activities of Dna Polymerase Beta in the Base Excision Repair Pathway. Proc.Natl.Acad.Sci.Usa V. 119 40119 2022.
ISSN: ESSN 1091-6490
PubMed: 35238634
DOI: 10.1073/PNAS.2118940119