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

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

The structure of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Da, PDB code: 8vfi 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 / 1.77
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 (%)	18.1 / 22.9

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

Chlorine	(Cl)	3 atoms
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Da (pdb code 8vfi). 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 Da, PDB code: 8vfi:
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 Da


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 Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:14.3 occ:1.00 OD1 A:ASP190 2.0 16.0 1.0 OD2 A:ASP192 2.1 13.8 1.0 O2A A:DCP408 2.2 15.1 1.0 O2B A:DCP408 2.2 11.7 1.0 O1G A:DCP408 2.2 15.9 1.0 O A:HOH585 2.3 14.6 1.0 CG A:ASP190 3.0 12.4 1.0 CG A:ASP192 3.1 12.4 1.0 PB A:DCP408 3.1 14.4 1.0 PA A:DCP408 3.2 17.9 1.0 PG A:DCP408 3.4 16.7 1.0 OD1 A:ASP192 3.4 11.8 1.0 O3A A:DCP408 3.4 15.6 1.0 OD2 A:ASP190 3.4 17.1 1.0 MG A:MG402 3.6 13.0 1.0 O3B A:DCP408 3.7 16.4 1.0 O5' A:DCP408 4.0 19.7 1.0 O A:ASP190 4.1 14.0 1.0 O2G A:DCP408 4.1 15.5 1.0 C5' A:DCP408 4.1 21.2 1.0 O A:HOH701 4.1 22.2 1.0 N A:ASP190 4.3 14.2 1.0 CB A:ASP190 4.3 13.3 1.0 C A:ASP190 4.3 13.8 1.0 O1A A:DCP408 4.3 16.0 1.0 O A:HOH679 4.3 15.6 1.0 OG A:SER180 4.4 16.6 1.0 CB A:ASP192 4.4 14.2 1.0 O1B A:DCP408 4.5 14.0 1.0 N A:SER180 4.5 15.1 1.0 O3G A:DCP408 4.5 20.1 1.0 CA A:ASP190 4.5 11.9 1.0 CA A:GLY179 4.5 12.3 1.0 O P:HOH111 4.7 16.9 1.0 N A:ASP192 4.8 12.9 1.0 O A:HOH601 4.9 18.5 1.0 N A:MET191 5.0 12.6 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 Da


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 Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:13.0 occ:1.00 OD1 A:ASP192 2.0 11.8 1.0 OD2 A:ASP190 2.1 17.1 1.0 O A:HOH601 2.1 18.5 1.0 OD2 A:ASP256 2.1 15.6 1.0 O P:HOH111 2.2 16.9 1.0 O2A A:DCP408 2.3 15.1 1.0 CG A:ASP190 3.0 12.4 1.0 CG A:ASP192 3.1 12.4 1.0 CG A:ASP256 3.3 19.8 1.0 OD1 A:ASP190 3.4 16.0 1.0 PA A:DCP408 3.4 17.9 1.0 OD2 A:ASP192 3.5 13.8 1.0 O5' A:DCP408 3.5 19.7 1.0 C4' P:8NI10 3.6 27.1 0.2 MG A:MG401 3.6 14.3 1.0 O1A A:DCP408 3.8 16.0 1.0 CB A:ASP256 4.0 19.4 1.0 O P:HOH109 4.1 24.1 1.0 C5' A:DCP408 4.2 21.2 1.0 O3' P:8NI10 4.2 27.9 0.4 C5' P:8NI10 4.3 29.3 0.4 OD1 A:ASP256 4.3 15.5 1.0 O4' P:8NI10 4.3 32.6 0.5 C3' P:8NI10 4.4 27.3 0.6 CB A:ASP192 4.4 14.2 1.0 CB A:ASP190 4.4 13.3 1.0 O A:HOH701 4.5 22.2 1.0 C2' P:8NI10 4.6 29.1 0.9 O5' P:8NI10 4.6 28.9 0.7 O P:HOH114 4.7 28.6 1.0 O3A A:DCP408 4.9 15.6 1.0 O1G A:DCP408 4.9 15.9 1.0 O A:MET191 4.9 15.3 1.0 CA A:ASP192 5.0 13.7 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