Magnesium in PDB 7rbl: Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mg Exchange

All present enzymatic activity of Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mg Exchange:
2.7.7.7;

The structure of Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mg Exchange, PDB code: 7rbl was solved by A.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.73 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.306, 81.394, 55.534, 90, 108.01, 90
R / Rfree (%)	18.8 / 23.6

The binding sites of Magnesium atom in the Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mg Exchange (pdb code 7rbl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mg Exchange, PDB code: 7rbl:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mg Exchange


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mg Exchange within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:23.5 occ:1.00 OD2 A:ASP190 1.9 36.3 1.0 OD2 A:ASP256 2.1 29.7 1.0 OD1 A:ASP192 2.1 23.4 1.0 O A:HOH531 2.2 28.8 1.0 OP1 P:DC11 2.2 30.3 1.0 O3' P:DC10 2.6 33.3 1.0 CG A:ASP190 2.7 27.5 1.0 OD1 A:ASP190 2.8 31.2 1.0 P P:DC11 2.9 35.2 1.0 CG A:ASP192 3.1 23.2 1.0 CG A:ASP256 3.2 28.3 1.0 OD2 A:ASP192 3.5 25.0 1.0 MG A:MG404 3.6 19.8 1.0 CB A:ASP256 3.9 27.6 1.0 C3' P:DC10 3.9 30.4 1.0 OP2 P:DC11 3.9 32.3 1.0 CB A:ASP190 4.1 29.1 1.0 C4' P:DC10 4.2 30.9 1.0 C5' P:DC10 4.2 28.5 1.0 OD1 A:ASP256 4.2 29.0 1.0 O5' P:DC11 4.2 28.4 1.0 O A:HOH552 4.3 41.2 1.0 C5' P:DC11 4.5 23.3 1.0 CB A:ASP192 4.5 23.9 1.0 NH2 A:ARG254 4.7 28.6 1.0 OP1 P:DC10 4.7 33.6 1.0 O A:MET191 4.7 25.5 1.0 N A:ASP256 4.8 23.8 1.0 CA A:ASP192 4.9 21.5 1.0 C A:MET191 4.9 21.9 1.0 O5' P:DC10 5.0 30.4 1.0 N A:ASP192 5.0 24.3 1.0 CA A:ASP256 5.0 25.6 1.0

Magnesium binding site 2 out of 3 in the Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mg Exchange


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mg Exchange within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:19.8 occ:1.00 OD1 A:ASP190 2.1 31.2 1.0 O A:HOH533 2.1 31.3 1.0 OD2 A:ASP192 2.2 25.0 1.0 OP1 P:DC11 2.2 30.3 1.0 O11 A:PPV402 2.2 25.1 1.0 O32 A:PPV402 2.3 31.5 1.0 O21 A:PPV402 3.1 30.1 1.0 P1 A:PPV402 3.1 27.8 1.0 CG A:ASP192 3.2 23.2 1.0 CG A:ASP190 3.3 27.5 1.0 OD1 A:ASP192 3.6 23.4 1.0 O A:HOH552 3.6 41.2 1.0 P2 A:PPV402 3.6 36.1 1.0 MG A:MG403 3.6 23.5 1.0 P P:DC11 3.6 35.2 1.0 OPP A:PPV402 3.7 31.9 1.0 OD2 A:ASP190 4.0 36.3 1.0 O A:ASP190 4.1 28.8 1.0 O5' P:DC11 4.1 28.4 1.0 N A:ASP190 4.2 26.3 1.0 O22 A:PPV402 4.3 28.2 1.0 C5' P:DC11 4.3 23.3 1.0 C A:ASP190 4.3 25.9 1.0 O A:HOH531 4.4 28.8 1.0 MG P:MG101 4.4 46.6 1.0 CB A:ASP190 4.4 29.1 1.0 OP2 P:DC11 4.4 32.3 1.0 O A:HOH566 4.4 29.3 1.0 CB A:ASP192 4.5 23.9 1.0 CA A:ASP190 4.5 26.3 1.0 O31 A:PPV402 4.5 27.5 1.0 CA A:GLY179 4.6 28.7 1.0 N A:SER180 4.7 31.5 1.0 O3' P:DC10 4.7 33.3 1.0 O12 A:PPV402 4.8 36.3 1.0 OG A:SER180 4.8 29.1 1.0 O A:HOH511 5.0 53.5 1.0

Magnesium binding site 3 out of 3 in the Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mg Exchange


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dna Polymerase Beta Crosslinked Complex, 60 S Ca to Mg Exchange within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:46.6 occ:1.00 OP2 P:DC11 2.0 32.3 1.0 O A:HOH511 2.1 53.5 1.0 O21 A:PPV402 2.1 30.1 1.0 O A:HOH598 2.2 30.8 1.0 O P:HOH205 2.2 42.9 1.0 O A:HOH552 2.6 41.2 1.0 P P:DC11 3.0 35.2 1.0 O5' P:DC11 3.5 28.4 1.0 OP1 P:DC11 3.5 30.3 1.0 P1 A:PPV402 3.6 27.8 1.0 O32 A:PPV402 3.9 31.5 1.0 OPP A:PPV402 4.1 31.9 1.0 O12 A:PPV402 4.2 36.3 1.0 O A:HOH519 4.3 34.6 1.0 O A:HOH531 4.3 28.8 1.0 P2 A:PPV402 4.4 36.1 1.0 O31 A:PPV402 4.4 27.5 1.0 MG A:MG404 4.4 19.8 1.0 O3' P:DC10 4.4 33.3 1.0 O11 A:PPV402 4.5 25.1 1.0 C5' P:DC11 4.8 23.3 1.0 C6 P:DC11 4.9 26.1 1.0 C3' P:DC10 5.0 30.4 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