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

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

The structure of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Da Base-Paired with Fapydg, PDB code: 8vfb 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)	25.48 / 2.64
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.854, 79.307, 54.702, 90, 108.88, 90
R / Rfree (%)	19.6 / 22.8

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

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Da Base-Paired with Fapydg (pdb code 8vfb). 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 Da Base-Paired with Fapydg, PDB code: 8vfb:
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 Da 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 Da Base-Paired with Fapydg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:44.1 occ:1.00 O1B A:G2P401 1.9 56.7 1.0 OD1 A:ASP190 2.2 14.2 1.0 OD1 A:ASP192 2.3 21.9 1.0 O1A A:G2P401 2.4 36.8 1.0 O3G A:G2P401 2.7 38.2 1.0 OD2 A:ASP192 2.7 25.4 1.0 CG A:ASP192 2.8 23.6 1.0 PB A:G2P401 2.9 45.0 1.0 CG A:ASP190 3.3 23.7 1.0 PG A:G2P401 3.3 37.2 1.0 O3B A:G2P401 3.4 42.6 1.0 PA A:G2P401 3.4 41.8 1.0 O2G A:G2P401 3.5 51.0 1.0 C5' A:G2P401 3.6 35.4 1.0 OD2 A:ASP190 3.7 20.5 1.0 C3A A:G2P401 3.7 55.5 1.0 OG A:SER180 3.7 38.7 1.0 O5' A:G2P401 4.0 29.6 1.0 N A:SER180 4.0 27.3 1.0 O2B A:G2P401 4.2 68.6 1.0 MN A:MN404 4.2 44.9 1.0 CB A:ASP192 4.2 17.0 1.0 CA A:GLY179 4.4 20.1 1.0 N A:ASP190 4.4 23.2 1.0 CB A:SER180 4.6 35.3 1.0 CB A:ASP190 4.6 20.9 1.0 O A:ASP190 4.6 23.9 1.0 C A:GLY179 4.7 29.2 1.0 O2A A:G2P401 4.8 32.3 1.0 O1G A:G2P401 4.8 39.8 1.0 C A:ASP190 4.8 22.7 1.0 N A:ASP192 4.8 21.9 1.0 CA A:ASP190 4.9 17.1 1.0 CA A:SER180 5.0 29.3 1.0 C4' A:G2P401 5.0 43.1 1.0

Manganese binding site 2 out of 2 in the Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Da 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 Da Base-Paired with Fapydg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn404 b:44.9 occ:1.00 OD2 A:ASP190 2.1 20.5 1.0 OD2 A:ASP192 2.5 25.4 1.0 OD2 A:ASP256 2.5 19.4 1.0 O1A A:G2P401 2.7 36.8 1.0 C3' P:DA10 2.9 46.3 1.0 O5' A:G2P401 3.0 29.6 1.0 C5' P:DA10 3.1 47.8 1.0 PA A:G2P401 3.2 41.8 1.0 CG A:ASP190 3.3 23.7 1.0 C4' P:DA10 3.4 48.0 1.0 O2A A:G2P401 3.5 32.3 1.0 O3' P:DA10 3.6 51.2 1.0 CG A:ASP256 3.7 20.0 1.0 CG A:ASP192 3.7 23.6 1.0 C5' A:G2P401 3.7 35.4 1.0 OD1 A:ASP190 3.8 14.2 1.0 C2' P:DA10 4.1 46.5 1.0 CE1 A:PHE272 4.1 33.2 1.0 MN A:MN403 4.2 44.1 1.0 CB A:ASP256 4.3 15.3 1.0 OP1 P:DA10 4.4 51.3 1.0 CB A:ASP190 4.5 20.9 1.0 CB A:ASP192 4.5 17.0 1.0 OD1 A:ASP192 4.5 21.9 1.0 O5' P:DA10 4.5 50.0 1.0 CZ A:PHE272 4.6 24.4 1.0 OD1 A:ASP256 4.7 16.0 1.0 O4' P:DA10 4.8 50.2 1.0 O4' A:G2P401 4.8 46.8 1.0 C4' A:G2P401 4.9 43.1 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