Sodium 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:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 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 Fapydg Base-Paired with A Da


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 Fapydg Base-Paired with A Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:18.9 occ:1.00 OP1 P:DG9 2.3 17.0 1.0 O A:THR101 2.4 17.1 1.0 O A:ILE106 2.4 15.1 1.0 O A:VAL103 2.4 17.4 1.0 O P:HOH112 2.5 20.0 1.0 O A:HOH778 2.7 24.5 1.0 C A:THR101 3.4 18.0 1.0 C A:VAL103 3.4 16.6 1.0 C A:ILE106 3.4 16.2 1.0 P P:DG9 3.5 18.3 1.0 OP2 P:DG9 3.7 18.4 1.0 N A:ILE106 3.7 17.6 1.0 CA A:THR101 3.9 15.9 1.0 CA A:SER104 4.0 15.8 1.0 N A:GLY105 4.0 12.9 1.0 N A:SER104 4.1 14.9 1.0 CA A:ILE106 4.1 15.1 1.0 N A:VAL103 4.1 16.3 1.0 O A:HOH784 4.2 40.0 1.0 C A:ARG102 4.3 18.8 1.0 C A:SER104 4.3 14.5 1.0 CA A:VAL103 4.4 19.1 1.0 CB A:THR101 4.4 19.3 1.0 N A:GLY107 4.4 16.3 1.0 N A:ARG102 4.4 15.7 1.0 CB A:ILE106 4.5 16.9 1.0 O3' P:DC8 4.5 17.3 1.0 O5' P:DG9 4.6 18.6 1.0 C A:GLY105 4.6 16.5 1.0 CA A:ARG102 4.6 20.9 1.0 CA A:GLY107 4.7 17.9 1.0 O A:ARG102 4.8 17.2 1.0 O A:LEU100 4.8 16.0 1.0 CA A:GLY105 4.9 18.0 1.0 O A:HOH771 5.0 33.1 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na404 b:25.1 occ:1.00 O A:LEU62 2.3 26.7 1.0 O A:VAL65 2.3 23.8 1.0 O A:HOH730 2.5 32.0 1.0 O A:LYS60 2.5 28.6 1.0 OP1 D:DC3 2.5 29.1 1.0 O D:HOH102 2.8 39.0 1.0 C A:LEU62 3.3 27.2 1.0 C A:VAL65 3.5 26.2 1.0 C A:LYS60 3.6 27.9 1.0 P D:DC3 3.6 26.5 1.0 O D:HOH109 3.8 39.5 1.0 N A:VAL65 3.8 22.9 1.0 OP2 D:DC3 3.9 22.9 1.0 CA A:PRO63 3.9 27.6 1.0 N A:PRO63 4.0 28.2 1.0 N A:LEU62 4.0 26.4 1.0 N A:GLY64 4.1 25.2 1.0 CA A:VAL65 4.1 24.1 1.0 C A:LYS61 4.1 30.9 1.0 CA A:LYS60 4.3 27.6 1.0 CA A:LEU62 4.3 26.8 1.0 O A:LYS61 4.3 30.4 1.0 C A:PRO63 4.4 27.9 1.0 CB A:VAL65 4.4 22.2 1.0 CG A:LYS60 4.5 27.8 1.0 N A:GLY66 4.5 23.2 1.0 N A:LYS61 4.5 29.1 1.0 O3' D:DT2 4.6 27.8 1.0 CA A:LYS61 4.7 28.5 1.0 C A:GLY64 4.8 26.3 1.0 O5' D:DC3 4.8 37.2 1.0 CA A:GLY66 4.8 28.4 1.0 O A:ALA59 4.9 23.1 1.0 CA A:GLY64 5.0 24.4 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