Magnesium in PDB 5v1i: Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp

All present enzymatic activity of Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp:
2.7.7.7;

The structure of Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp, PDB code: 5v1i was solved by B.D.Freudenthal, M.R.Smith, A.M.Whitaker, M.A.Schaich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.60 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.564, 79.798, 55.539, 90.00, 107.62, 90.00
R / Rfree (%)	18.4 / 23.7

The structure of Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Sodium	(Na)	3 atoms

The binding sites of Magnesium atom in the Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp (pdb code 5v1i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp, PDB code: 5v1i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:32.3 occ:1.00 O P:HOH205 2.0 30.1 1.0 O A:HOH628 2.1 30.8 1.0 O A:HOH577 2.1 24.1 1.0 OP2 P:DC11 2.1 21.9 1.0 O A:HOH568 2.1 29.8 1.0 O32 A:PPV408 2.3 21.2 0.5 O32 A:PPV408 2.3 21.1 0.5 P P:DC11 3.2 21.1 1.0 O11 A:PPV408 3.6 23.8 0.5 P2 A:PPV408 3.6 20.9 0.5 P2 A:PPV408 3.7 21.3 0.5 OP1 P:DC11 3.7 18.3 1.0 O21 A:PPV408 3.7 29.6 0.5 O21 A:PPV408 3.8 30.8 0.5 OPP A:PPV408 3.8 25.4 0.5 O5' P:DC11 3.8 20.5 1.0 P1 A:PPV408 3.9 24.2 0.5 O A:HOH517 4.1 24.8 0.9 OPP A:PPV408 4.1 25.6 0.5 O A:HOH542 4.2 19.4 1.0 O A:HOH594 4.3 34.2 1.0 O12 A:PPV408 4.5 17.3 0.5 O22 A:PPV408 4.5 18.8 0.5 O A:HOH682 4.5 32.7 1.0 P1 A:PPV408 4.6 24.3 0.5 O12 A:PPV408 4.6 17.3 0.5 O22 A:PPV408 4.6 18.8 0.5 O3' P:8OG10 4.6 23.9 0.9 MG A:MG407 4.7 13.2 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase Beta Ternary Product Complex with 8-Oxog:C and Inserted Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:13.2 occ:1.00 O A:HOH517 1.8 24.8 0.9 OP1 P:DC11 2.0 18.3 1.0 O12 A:PPV408 2.0 17.3 0.5 O12 A:PPV408 2.1 17.3 0.5 OD2 A:ASP192 2.1 14.2 1.0 O A:HOH564 2.2 15.3 1.0 OD1 A:ASP190 2.2 17.3 1.0 O11 A:PPV408 2.5 23.8 0.5 CG A:ASP192 3.1 16.6 1.0 P2 A:PPV408 3.1 20.9 0.5 P2 A:PPV408 3.1 21.3 0.5 O32 A:PPV408 3.2 21.2 0.5 CG A:ASP190 3.4 17.7 1.0 O32 A:PPV408 3.4 21.1 0.5 P P:DC11 3.4 21.1 1.0 O31 A:PPV408 3.5 22.3 0.5 OD1 A:ASP192 3.5 19.7 1.0 NA A:NA409 3.6 25.0 1.0 P1 A:PPV408 3.6 24.2 0.5 OPP A:PPV408 3.7 25.4 0.5 OD2 A:ASP190 3.8 31.1 1.0 C5' P:DC11 3.9 17.0 1.0 O5' P:DC11 3.9 20.5 1.0 OPP A:PPV408 3.9 25.6 0.5 O A:HOH568 4.1 29.8 1.0 P1 A:PPV408 4.1 24.3 0.5 O A:ASP190 4.2 15.9 1.0 O31 A:PPV408 4.2 18.4 0.5 O21 A:PPV408 4.3 29.6 0.5 OP2 P:DC11 4.3 21.9 1.0 O A:HOH603 4.3 13.7 1.0 CA A:GLY179 4.4 15.8 1.0 O22 A:PPV408 4.4 18.8 0.5 O3' P:8OG10 4.4 23.9 0.9 O22 A:PPV408 4.4 18.8 0.5 CB A:ASP192 4.5 16.8 1.0 C A:ASP190 4.5 21.4 1.0 N A:ASP190 4.5 16.6 1.0 N A:SER180 4.6 17.7 1.0 CB A:ASP190 4.6 13.7 1.0 MG P:MG101 4.7 32.3 1.0 CA A:ASP190 4.8 16.1 1.0 O21 A:PPV408 4.9 30.8 0.5 N A:ASP192 4.9 13.9 1.0

A.M.Whitaker, M.R.Smith, M.A.Schaich, B.D.Freudenthal. Capturing A Mammalian Dna Polymerase Extending From An Oxidized Nucleotide. Nucleic Acids Res. V. 45 6934 2017.
ISSN: ESSN 1362-4962
PubMed: 28449123
DOI: 10.1093/NAR/GKX293