Manganese in PDB 8vfa: Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Dc Base-Paired with Fapydg

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

The structure of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Dc Base-Paired with Fapydg, PDB code: 8vfa 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)	24.94 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.437, 79.531, 54.889, 90, 108.26, 90
R / Rfree (%)	22.6 / 26.7

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

Sodium

(Na)

2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Dc Base-Paired with Fapydg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn404 b:33.4 occ:1.00 OD2 A:ASP192 2.1 25.4 1.0 OD1 A:ASP190 2.2 19.9 1.0 O1B A:G2P401 2.2 42.1 1.0 O1A A:G2P401 2.3 26.1 1.0 O A:HOH532 2.4 25.1 1.0 O2G A:G2P401 2.5 34.9 1.0 CG A:ASP192 3.0 24.0 1.0 PB A:G2P401 3.2 38.3 1.0 OD1 A:ASP192 3.2 23.6 1.0 CG A:ASP190 3.3 19.0 1.0 PA A:G2P401 3.4 36.0 1.0 MN A:MN405 3.5 28.1 1.0 PG A:G2P401 3.6 38.6 1.0 C3A A:G2P401 3.6 33.9 1.0 O3B A:G2P401 3.7 26.3 1.0 C5' A:G2P401 3.7 35.0 1.0 OD2 A:ASP190 3.7 31.8 1.0 O5' A:G2P401 4.0 25.6 1.0 O A:ASP190 4.2 17.1 1.0 O3G A:G2P401 4.2 40.7 1.0 O A:HOH504 4.3 24.4 1.0 CB A:ASP192 4.4 25.2 1.0 C A:ASP190 4.4 24.9 1.0 CA A:GLY179 4.4 29.1 1.0 O2B A:G2P401 4.5 38.9 1.0 CB A:ASP190 4.5 18.2 1.0 N A:ASP190 4.5 22.4 1.0 N A:SER180 4.6 30.0 1.0 O2A A:G2P401 4.6 32.2 1.0 N A:ASP192 4.7 20.1 1.0 CA A:ASP190 4.7 17.0 1.0 O A:HOH544 4.8 33.7 1.0 O1G A:G2P401 4.9 35.7 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Dc Base-Paired with Fapydg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn405 b:28.1 occ:1.00 OD2 A:ASP256 2.2 32.0 1.0 OD1 A:ASP192 2.2 23.6 1.0 OD2 A:ASP190 2.2 31.8 1.0 O A:HOH544 2.3 33.7 1.0 O1A A:G2P401 2.3 26.1 1.0 O P:HOH101 2.6 32.1 1.0 CG A:ASP190 3.0 19.0 1.0 OD1 A:ASP190 3.1 19.9 1.0 CG A:ASP192 3.3 24.0 1.0 CG A:ASP256 3.4 20.6 1.0 MN A:MN404 3.5 33.4 1.0 PA A:G2P401 3.6 36.0 1.0 OD2 A:ASP192 3.8 25.4 1.0 O2A A:G2P401 3.9 32.2 1.0 O5' A:G2P401 4.1 25.6 1.0 C5' A:G2P401 4.1 35.0 1.0 CB A:ASP256 4.2 18.3 1.0 OD1 A:ASP256 4.3 26.9 1.0 CB A:ASP190 4.4 18.2 1.0 C5' P:DC10 4.5 44.5 1.0 CB A:ASP192 4.6 25.2 1.0 OP1 P:DC10 4.7 30.0 1.0 O5' P:DC10 4.7 51.7 1.0 NH2 A:ARG254 4.8 23.9 1.0 O A:MET191 4.9 21.1 1.0 O2G A:G2P401 4.9 34.9 1.0 CA A:ASP192 5.0 18.6 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