Magnesium in PDB 7rbj: Human Dna Polymerase Beta Crosslinked Complex, 30 S Ca to Mg Exchange

All present enzymatic activity of Human Dna Polymerase Beta Crosslinked Complex, 30 S Ca to Mg Exchange:
2.7.7.7;

The structure of Human Dna Polymerase Beta Crosslinked Complex, 30 S Ca to Mg Exchange, PDB code: 7rbj was solved by A.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.37 / 1.91
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.794, 80.841, 55.716, 90, 107.79, 90
R / Rfree (%)	18.8 / 22.9

The binding sites of Magnesium atom in the Human Dna Polymerase Beta Crosslinked Complex, 30 S Ca to Mg Exchange (pdb code 7rbj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Dna Polymerase Beta Crosslinked Complex, 30 S Ca to Mg Exchange, PDB code: 7rbj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human Dna Polymerase Beta Crosslinked Complex, 30 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, 30 S Ca to Mg Exchange within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:14.7 occ:1.00 O2G A:DCP403 1.8 33.5 0.5 O12 A:PPV402 2.2 11.8 0.5 OD1 A:ASP190 2.2 21.7 1.0 O A:HOH517 2.2 28.2 1.0 O3A A:DCP403 2.2 36.2 0.5 OP1 P:DC11 2.2 13.4 0.5 OD2 A:ASP192 2.2 19.4 1.0 O21 A:PPV402 2.6 19.4 0.5 O2A A:DCP403 2.6 34.0 0.5 O2B A:DCP403 3.0 37.0 0.5 PA A:DCP403 3.0 32.8 0.5 PB A:DCP403 3.1 35.4 0.5 P2 A:PPV402 3.2 13.0 0.5 CG A:ASP192 3.2 19.5 1.0 PG A:DCP403 3.2 39.5 0.5 O32 A:PPV402 3.2 13.3 0.5 CG A:ASP190 3.4 24.5 1.0 OD1 A:ASP192 3.5 20.8 1.0 O3B A:DCP403 3.6 35.5 0.5 MG A:MG405 3.6 19.2 1.0 P P:DC11 3.7 13.9 0.5 O A:HOH582 3.7 40.7 1.0 P1 A:PPV402 3.8 16.8 0.5 OPP A:PPV402 3.8 14.5 0.5 O A:ASP190 3.9 23.6 1.0 O1G A:DCP403 4.0 30.7 0.5 O5' A:DCP403 4.0 27.9 0.5 OD2 A:ASP190 4.1 35.6 1.0 C5' A:DCP403 4.1 25.9 0.5 O1A A:DCP403 4.1 27.4 0.5 N A:ASP190 4.1 17.4 1.0 C A:ASP190 4.2 19.1 1.0 O5' P:DC11 4.2 13.6 0.5 O3G A:DCP403 4.3 30.7 0.5 C5' P:DC11 4.3 12.7 0.5 O A:HOH528 4.4 25.9 1.0 O A:HOH587 4.4 21.9 1.0 CB A:ASP190 4.4 22.1 1.0 CA A:ASP190 4.5 19.1 1.0 O31 A:PPV402 4.5 15.0 0.5 O1B A:DCP403 4.5 35.2 0.5 O22 A:PPV402 4.5 12.2 0.5 OP2 P:DC11 4.5 12.2 0.5 CB A:ASP192 4.5 20.5 1.0 CA A:GLY179 4.7 20.3 1.0 O3' P:DC10 4.7 15.7 0.5 OG A:SER180 4.8 21.2 1.0 N A:SER180 4.8 21.6 1.0 O A:HOH501 4.9 46.7 1.0 O11 A:PPV402 4.9 16.4 0.5 O3' P:DC10 4.9 28.5 0.5 N A:ASP192 5.0 19.9 1.0 N A:MET191 5.0 19.4 1.0

Magnesium binding site 2 out of 4 in the Human Dna Polymerase Beta Crosslinked Complex, 30 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, 30 S Ca to Mg Exchange within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:19.2 occ:1.00 OD2 A:ASP256 2.0 23.0 1.0 OD2 A:ASP190 2.0 35.6 1.0 OD1 A:ASP192 2.2 20.8 1.0 O A:HOH528 2.2 25.9 1.0 O2A A:DCP403 2.3 34.0 0.5 OP1 P:DC11 2.3 13.4 0.5 O3' P:DC10 2.6 28.5 0.5 O3' P:DC10 2.6 15.7 0.5 CG A:ASP190 2.7 24.5 1.0 OD1 A:ASP190 2.8 21.7 1.0 P P:DC11 3.0 13.9 0.5 CG A:ASP256 3.2 21.5 1.0 CG A:ASP192 3.3 19.5 1.0 MG A:MG404 3.6 14.7 1.0 OD2 A:ASP192 3.7 19.4 1.0 PA A:DCP403 3.8 32.8 0.5 C3' P:DC10 3.8 24.7 0.5 C3' P:DC10 3.9 16.8 0.5 CB A:ASP256 3.9 20.5 1.0 OP2 P:DC11 3.9 12.2 0.5 C4' P:DC10 4.1 19.0 0.5 C5' P:DC10 4.1 25.2 0.5 C5' P:DC10 4.1 20.3 0.5 CB A:ASP190 4.2 22.1 1.0 C4' P:DC10 4.2 26.0 0.5 OD1 A:ASP256 4.2 23.7 1.0 O5' P:DC11 4.2 13.6 0.5 O A:HOH582 4.3 40.7 1.0 C5' A:DCP403 4.4 25.9 0.5 O5' A:DCP403 4.4 27.9 0.5 C5' P:DC11 4.5 12.7 0.5 OP1 P:DC10 4.5 25.2 0.5 O3A A:DCP403 4.5 36.2 0.5 CB A:ASP192 4.6 20.5 1.0 O2G A:DCP403 4.7 33.5 0.5 O A:MET191 4.7 21.3 1.0 OP1 P:DC10 4.7 27.2 0.5 NH2 A:ARG254 4.7 24.1 1.0 O1A A:DCP403 4.8 27.4 0.5 O5' P:DC10 4.8 22.4 0.5 O5' P:DC10 4.9 25.5 0.5 N A:ASP256 4.9 18.7 1.0 C A:MET191 5.0 18.4 1.0 CA A:ASP192 5.0 18.0 1.0 C2' P:DC10 5.0 17.8 0.5

Magnesium binding site 3 out of 4 in the Human Dna Polymerase Beta Crosslinked Complex, 30 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, 30 S Ca to Mg Exchange within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:42.0 occ:1.00 O A:HOH614 1.8 41.1 1.0 O A:THR101 2.2 22.3 1.0 O A:HOH520 2.2 31.2 1.0 O A:HOH526 2.2 24.9 1.0 C A:THR101 3.3 22.5 1.0 O A:HOH530 3.7 36.7 1.0 O A:ILE106 4.1 25.1 1.0 CB A:THR101 4.1 23.2 1.0 CA A:THR101 4.1 22.9 1.0 OP2 P:DG9 4.2 25.7 1.0 N A:ARG102 4.2 21.3 1.0 OP1 P:DG9 4.3 28.9 1.0 CA A:ARG102 4.4 22.7 1.0 C A:ARG102 4.7 22.3 1.0 P P:DG9 4.8 27.1 1.0 O A:VAL103 4.8 21.2 1.0 OG1 A:THR101 4.8 27.2 1.0

Magnesium binding site 4 out of 4 in the Human Dna Polymerase Beta Crosslinked Complex, 30 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 4 of Human Dna Polymerase Beta Crosslinked Complex, 30 S Ca to Mg Exchange within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:64.0 occ:1.00 OE1 A:GLU316 2.5 38.4 1.0 O A:HOH605 2.7 31.6 1.0 CD A:GLU316 3.4 36.3 1.0 CG A:GLU316 3.6 33.9 1.0 NH2 A:ARG182 3.6 35.1 1.0 CE1 A:TYR266 3.9 38.1 1.0 CD1 A:TYR266 3.9 32.5 1.0 CB A:GLU316 4.2 30.1 1.0 CG1 A:VAL269 4.3 20.7 1.0 CE2 A:TYR265 4.5 27.9 1.0 OE2 A:GLU316 4.6 40.0 1.0 OH A:TYR265 4.7 27.7 1.0 N A:GLU316 4.7 25.3 1.0 CZ A:ARG182 4.7 31.4 1.0 O A:HOH600 4.9 31.9 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