Sodium 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:

Manganese

(Mn)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Dc Base-Paired with Fapydg, PDB code: 8vfa:
Jump to Sodium binding site number: 1; 2;

Sodium 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 Sodium with other atoms in the Na 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:Na402 b:14.0 occ:1.00 O A:THR101 2.2 14.7 1.0 O A:ILE106 2.3 10.7 1.0 OP1 P:DG9 2.4 16.8 1.0 O A:VAL103 2.4 12.5 1.0 O A:HOH555 2.5 17.4 1.0 O P:HOH103 2.7 19.3 1.0 C A:THR101 3.2 16.7 1.0 C A:ILE106 3.3 11.9 1.0 C A:VAL103 3.4 17.3 1.0 P P:DG9 3.6 21.0 1.0 O A:HOH547 3.7 23.8 1.0 OP2 P:DG9 3.7 18.4 1.0 N A:ILE106 3.7 13.9 1.0 CA A:THR101 3.8 12.8 1.0 CA A:SER104 4.0 15.4 1.0 CA A:ILE106 4.0 11.5 1.0 N A:SER104 4.1 14.2 1.0 N A:GLY105 4.1 14.0 1.0 N A:VAL103 4.1 11.0 1.0 C A:ARG102 4.3 18.8 1.0 N A:ARG102 4.3 14.8 1.0 CB A:THR101 4.3 14.9 1.0 N A:GLY107 4.3 10.0 1.0 C A:SER104 4.4 13.8 1.0 CA A:VAL103 4.4 16.2 1.0 CB A:ILE106 4.4 13.6 1.0 CA A:ARG102 4.6 15.0 1.0 O3' P:DC8 4.6 24.5 1.0 CA A:GLY107 4.6 12.3 1.0 C A:GLY105 4.7 13.5 1.0 O5' P:DG9 4.7 18.4 1.0 O A:ARG102 4.8 15.6 1.0 O A:HOH528 4.8 27.2 1.0 O A:LEU100 4.8 13.8 1.0 CA A:GLY105 5.0 15.9 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na403 b:36.4 occ:1.00 O A:HOH562 2.2 36.1 1.0 O A:VAL65 2.3 27.8 1.0 O A:LYS60 2.3 35.1 1.0 O D:HOH103 2.6 31.0 1.0 O A:LEU62 2.6 21.9 1.0 OP1 D:DC3 2.9 31.6 1.0 C A:LYS60 3.4 31.3 1.0 C A:VAL65 3.5 26.7 1.0 C A:LEU62 3.5 31.3 1.0 N A:LEU62 3.9 32.2 1.0 P D:DC3 3.9 25.4 1.0 N A:VAL65 3.9 26.0 1.0 OP2 D:DC3 3.9 18.2 1.0 C A:LYS61 4.0 34.6 1.0 CA A:LYS60 4.1 30.6 1.0 CA A:VAL65 4.1 15.7 1.0 O A:LYS61 4.3 33.6 1.0 CA A:LEU62 4.4 25.1 1.0 N A:PRO63 4.4 27.8 1.0 N A:GLY64 4.4 26.6 1.0 CB A:VAL65 4.4 19.1 1.0 N A:LYS61 4.5 29.9 1.0 CA A:PRO63 4.5 25.4 1.0 CA A:LYS61 4.5 23.1 1.0 N A:GLY66 4.6 20.6 1.0 CG A:LYS60 4.8 36.9 1.0 CB A:LYS60 4.8 35.8 1.0 O3' D:DT2 4.8 32.6 1.0 O A:ALA59 4.8 26.6 1.0 C A:PRO63 4.8 33.9 1.0 CA A:GLY66 4.9 23.4 1.0 C A:GLY64 5.0 24.1 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