Magnesium in PDB 8vfh: Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Dc

All present enzymatic activity of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Dc:
2.7.7.7;

The structure of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Dc, PDB code: 8vfh was solved by P.N.Oden, B.J.Ryan, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.65 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.8, 80.4, 55.5, 90, 107.9, 90
R / Rfree (%)	17.7 / 24.6

The structure of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Dc also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Dc (pdb code 8vfh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Dc, PDB code: 8vfh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Dc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:19.5 occ:1.00 OD1 A:ASP190 1.9 26.2 1.0 O2A A:DCP404 2.0 17.7 1.0 OD2 A:ASP192 2.1 15.9 1.0 O2B A:DCP404 2.1 21.2 1.0 O1G A:DCP404 2.1 25.8 1.0 O A:HOH579 2.4 17.1 1.0 CG A:ASP190 2.9 20.3 1.0 PB A:DCP404 3.1 22.6 1.0 CG A:ASP192 3.1 23.3 1.0 PA A:DCP404 3.2 31.2 1.0 O3A A:DCP404 3.2 22.9 1.0 OD2 A:ASP190 3.3 23.7 1.0 PG A:DCP404 3.3 29.5 1.0 O3B A:DCP404 3.4 28.4 1.0 OD1 A:ASP192 3.5 21.0 1.0 MG A:MG402 3.5 22.4 1.0 C5' A:DCP404 4.1 20.2 1.0 O3G A:DCP404 4.1 17.4 1.0 O5' A:DCP404 4.1 21.6 1.0 O A:ASP190 4.2 19.7 1.0 CB A:ASP190 4.2 16.6 1.0 O1A A:DCP404 4.3 22.2 1.0 O A:HOH703 4.3 35.5 1.0 N A:ASP190 4.4 18.5 1.0 O A:HOH595 4.4 21.1 1.0 C A:ASP190 4.4 20.7 1.0 O A:HOH511 4.4 35.1 1.0 O1B A:DCP404 4.5 23.2 1.0 CB A:ASP192 4.5 15.4 1.0 O2G A:DCP404 4.5 29.4 1.0 CA A:GLY179 4.5 13.8 1.0 CA A:ASP190 4.6 16.5 1.0 N A:SER180 4.6 24.0 1.0 O A:HOH610 4.7 34.1 1.0 OG A:SER180 4.9 28.1 1.0 N A:ASP192 4.9 18.6 1.0

Magnesium binding site 2 out of 2 in the Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Dc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:22.4 occ:1.00 OD2 A:ASP190 2.0 23.7 1.0 OD1 A:ASP192 2.0 21.0 1.0 O A:HOH610 2.2 34.1 1.0 OD2 A:ASP256 2.3 24.6 1.0 O2A A:DCP404 2.3 17.7 1.0 O A:HOH511 2.4 35.1 1.0 CG A:ASP190 3.0 20.3 1.0 CG A:ASP192 3.0 23.3 1.0 OD1 A:ASP190 3.3 26.2 1.0 OD2 A:ASP192 3.3 15.9 1.0 CG A:ASP256 3.4 23.0 1.0 PA A:DCP404 3.5 31.2 1.0 MG A:MG401 3.5 19.5 1.0 O1A A:DCP404 3.9 22.2 1.0 CB A:ASP256 3.9 21.2 1.0 O5' A:DCP404 4.0 21.6 1.0 O P:HOH105 4.0 33.8 1.0 C5' A:DCP404 4.1 20.2 1.0 C5' P:8NI10 4.2 53.0 1.0 CB A:ASP190 4.3 16.6 1.0 CB A:ASP192 4.4 15.4 1.0 OD1 A:ASP256 4.4 19.5 1.0 O5' P:8NI10 4.5 47.7 1.0 C3' P:8NI10 4.6 59.3 1.0 C4' P:8NI10 4.6 54.3 1.0 O A:HOH703 4.6 35.5 1.0 O1G A:DCP404 4.8 25.8 1.0 O A:MET191 4.8 22.2 1.0 O3A A:DCP404 4.9 22.9 1.0 CA A:ASP192 5.0 16.5 1.0

S.Gao, P.N.Oden, B.J.Ryan, H.Yang, B.D.Freudenthal, M.M.Greenberg. Biochemical and Structural Characterization of Fapy•Dg Replication By Human Dna Polymerase Beta. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 38634780
DOI: 10.1093/NAR/GKAE277