Calcium in PDB 7rbh: Human Dna Polymerase Beta Crosslinked Ternary Complex 2

All present enzymatic activity of Human Dna Polymerase Beta Crosslinked Ternary Complex 2:
2.7.7.7;

The structure of Human Dna Polymerase Beta Crosslinked Ternary Complex 2, PDB code: 7rbh was solved by A.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.27 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.67, 80.732, 55.705, 90, 107.69, 90
R / Rfree (%)	17.9 / 22.5

The binding sites of Calcium atom in the Human Dna Polymerase Beta Crosslinked Ternary Complex 2 (pdb code 7rbh). 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 2, PDB code: 7rbh:
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 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:23.7 occ:1.00 OD2 A:ASP192 2.2 21.3 1.0 O2G A:DCP402 2.3 25.4 1.0 O2B A:DCP402 2.3 19.6 1.0 OD1 A:ASP190 2.3 21.2 1.0 O A:HOH514 2.4 26.6 1.0 O2A A:DCP402 2.4 22.5 1.0 O A:ASP190 3.0 25.4 1.0 CG A:ASP192 3.2 19.9 1.0 PB A:DCP402 3.3 22.2 1.0 CG A:ASP190 3.5 23.0 1.0 PG A:DCP402 3.5 24.9 1.0 PA A:DCP402 3.6 24.5 1.0 OD1 A:ASP192 3.6 21.4 1.0 O3A A:DCP402 3.6 25.4 1.0 CA A:CA404 3.7 24.1 1.0 C A:ASP190 3.8 21.5 1.0 O3B A:DCP402 3.8 23.3 1.0 N A:ASP190 3.9 20.4 1.0 CA A:ASP190 4.2 20.3 1.0 O A:HOH650 4.2 23.5 1.0 O1G A:DCP402 4.2 22.8 1.0 O A:HOH703 4.3 37.5 1.0 OD2 A:ASP190 4.3 26.4 1.0 CB A:ASP190 4.3 20.5 1.0 C5' A:DCP402 4.4 20.4 1.0 OG A:SER180 4.5 23.7 1.0 O5' A:DCP402 4.5 22.5 1.0 CB A:ASP192 4.5 19.8 1.0 N A:MET191 4.5 20.3 1.0 N A:SER180 4.6 22.7 1.0 O3G A:DCP402 4.6 25.8 1.0 CA A:GLY179 4.6 20.9 1.0 N A:ASP192 4.7 20.6 1.0 O1A A:DCP402 4.7 25.7 1.0 O1B A:DCP402 4.7 23.0 1.0 C A:MET191 4.8 20.6 1.0 O P:HOH103 4.9 28.3 1.0 CA A:MET191 4.9 22.5 1.0 C A:GLY189 5.0 22.1 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:24.1 occ:1.00 OD2 A:ASP256 2.2 21.8 1.0 OD1 A:ASP192 2.2 21.4 1.0 OD2 A:ASP190 2.3 26.4 1.0 O3' P:DC10 2.4 25.0 1.0 O P:HOH103 2.4 28.3 1.0 O2A A:DCP402 2.5 22.5 1.0 OD1 A:ASP190 2.6 21.2 1.0 CG A:ASP190 2.8 23.0 1.0 CG A:ASP192 3.3 19.9 1.0 CG A:ASP256 3.4 21.8 1.0 PA A:DCP402 3.6 24.5 1.0 C3' P:DC10 3.6 24.6 1.0 OD2 A:ASP192 3.7 21.3 1.0 CA A:CA403 3.7 23.7 1.0 O5' A:DCP402 4.1 22.5 1.0 CB A:ASP256 4.1 21.2 1.0 C5' P:DC10 4.2 24.7 1.0 O1A A:DCP402 4.2 25.7 1.0 C4' P:DC10 4.2 24.5 1.0 C5' A:DCP402 4.2 20.4 1.0 CB A:ASP190 4.3 20.5 1.0 OD1 A:ASP256 4.4 22.7 1.0 O A:HOH703 4.5 37.5 1.0 OP1 P:DC10 4.5 25.9 1.0 CB A:ASP192 4.6 19.8 1.0 O A:MET191 4.6 21.7 1.0 NH2 A:ARG254 4.7 22.6 1.0 O5' P:DC10 4.7 24.8 1.0 C2' P:DC10 4.9 24.4 1.0 O3A A:DCP402 5.0 25.4 1.0 C A:MET191 5.0 20.6 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:49.0 occ:1.00 OE1 A:GLU295 2.6 28.1 1.0 NH1 A:ARG283 2.8 24.7 1.0 N3 T:DG7 2.8 24.6 1.0 N2 T:DG7 3.4 24.9 1.0 O4' T:DC8 3.4 26.5 1.0 CD A:GLU295 3.4 28.0 1.0 NH2 A:ARG283 3.5 24.5 1.0 C2 T:DG7 3.5 25.1 1.0 CZ A:ARG283 3.6 24.1 1.0 O A:HOH554 3.7 26.7 1.0 C1' T:DG7 3.8 25.8 1.0 OE2 A:GLU295 3.8 29.0 1.0 C4' T:DC8 3.9 26.3 1.0 C5' T:DC8 3.9 26.8 1.0 C4 T:DG7 3.9 24.8 1.0 N A:GLU295 4.0 22.7 1.0 O4' T:DG7 4.2 26.1 1.0 N9 T:DG7 4.3 25.4 1.0 CB A:ASN294 4.3 22.4 1.0 CA A:ASN294 4.4 22.4 1.0 C4' T:DG7 4.5 26.6 1.0 N2 T:DG6 4.5 25.1 1.0 CD1 A:TYR271 4.5 21.9 1.0 CE1 A:TYR271 4.6 22.1 1.0 CB A:GLU295 4.6 24.6 1.0 CG A:GLU295 4.6 25.6 1.0 C A:ASN294 4.6 22.4 1.0 C1' T:DC8 4.6 26.9 1.0 O3' T:DG7 4.8 28.2 1.0 O5' T:DC8 4.8 28.4 1.0 NE A:ARG283 4.9 23.2 1.0 CA A:GLU295 4.9 23.5 1.0 N1 T:DG7 4.9 23.9 1.0 C2' T:DG7 4.9 26.1 1.0 N1 T:DC8 5.0 26.9 1.0 C3' T:DG7 5.0 27.0 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