Sodium 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:

Calcium	(Ca)	3 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Dna Polymerase Beta Crosslinked Ternary Complex 1, PDB code: 7rbg:
Jump to Sodium binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na406 b:29.5 occ:1.00 OD2 A:ASP190 2.1 19.1 1.0 OD1 A:ASP192 2.2 12.5 1.0 O1A A:DCP401 2.5 10.7 1.0 OD2 A:ASP256 2.6 25.6 1.0 CG A:ASP190 3.0 16.4 1.0 CG A:ASP192 3.2 12.4 1.0 C3' P:DC10 3.3 20.3 1.0 OD1 A:ASP190 3.3 17.0 1.0 PA A:DCP401 3.4 12.0 1.0 OD2 A:ASP192 3.5 13.0 1.0 CG A:ASP256 3.5 19.3 1.0 O3' P:DC10 3.6 23.1 1.0 O5' A:DCP401 3.6 11.1 1.0 CA A:CA403 3.7 27.7 1.0 C5' A:DCP401 3.8 11.3 1.0 C5' P:DC10 4.0 23.1 1.0 O2A A:DCP401 4.0 10.8 1.0 C4' P:DC10 4.1 20.4 1.0 CB A:ASP256 4.2 15.4 1.0 C2' P:DC10 4.3 18.3 1.0 OD1 A:ASP256 4.4 24.1 1.0 CB A:ASP190 4.4 15.9 1.0 O5' P:DC10 4.5 21.1 1.0 O A:HOH590 4.5 19.9 1.0 CB A:ASP192 4.5 12.2 1.0 OP1 P:DC10 4.8 21.1 1.0 O3A A:DCP401 4.8 12.2 1.0 O1G A:DCP401 4.9 13.9 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na407 b:20.5 occ:1.00 O D:HOH110 2.6 13.2 1.0 O A:GLY64 2.7 16.1 1.0 O A:ALA38 2.8 14.1 1.0 CA A:ALA38 3.4 14.6 1.0 C A:ALA38 3.4 14.3 1.0 C A:GLY64 3.5 16.4 1.0 CA A:GLY64 3.6 18.0 1.0 C4' D:DT2 3.6 14.9 1.0 CB A:ALA38 3.8 13.6 1.0 C5' D:DT2 3.8 14.1 1.0 CB A:LYS41 3.9 18.4 1.0 CD A:LYS41 3.9 21.1 1.0 O4' D:DT2 4.0 14.7 1.0 N A:ALA42 4.1 14.7 1.0 CG A:LYS41 4.1 20.7 1.0 O A:HOH515 4.2 20.9 1.0 CB A:ALA42 4.4 14.5 1.0 C A:LYS41 4.6 16.5 1.0 CA A:ALA42 4.7 15.0 1.0 N A:TYR39 4.7 15.1 1.0 CA A:LYS41 4.7 17.9 1.0 CE A:LYS41 4.7 24.7 1.0 N A:ALA38 4.8 14.7 1.0 N A:VAL65 4.8 15.3 1.0 CD1 A:ILE69 4.9 16.1 1.0 O D:HOH113 4.9 30.9 1.0 O A:ASN37 4.9 14.5 1.0 O3' D:DT2 4.9 17.4 1.0 C3' D:DT2 4.9 15.4 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