Sodium in PDB 8vfe: Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A T

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

The structure of Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A T, PDB code: 8vfe 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)	24.89 / 2.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.68, 79.287, 54.958, 90, 106.15, 90
R / Rfree (%)	20 / 23.5

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

Sodium binding site 1 out of 2 in the Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A T


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A T within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:19.8 occ:1.00 O A:THR101 2.2 16.9 1.0 O A:ILE106 2.2 16.3 1.0 OP1 P:DG9 2.4 16.1 1.0 O A:VAL103 2.4 16.4 1.0 O P:HOH110 2.5 19.7 1.0 O P:HOH118 2.9 22.2 1.0 C A:THR101 3.1 18.0 1.0 O A:HOH520 3.3 24.7 1.0 C A:ILE106 3.3 15.2 1.0 C A:VAL103 3.4 19.1 1.0 P P:DG9 3.6 17.7 1.0 CA A:THR101 3.6 14.5 1.0 OP2 P:DG9 3.8 21.7 1.0 N A:ILE106 3.8 15.2 1.0 N A:VAL103 4.0 17.2 1.0 CA A:ILE106 4.1 18.4 1.0 N A:SER104 4.1 17.7 1.0 CA A:SER104 4.1 16.6 1.0 N A:GLY105 4.1 14.6 1.0 N A:ARG102 4.2 16.9 1.0 C A:ARG102 4.2 17.4 1.0 CB A:THR101 4.2 17.8 1.0 N A:GLY107 4.3 15.9 1.0 CA A:VAL103 4.3 17.6 1.0 CB A:ILE106 4.4 16.8 1.0 C A:SER104 4.4 17.9 1.0 CA A:ARG102 4.4 18.4 1.0 CA A:GLY107 4.5 14.8 1.0 O A:LEU100 4.6 17.4 1.0 O3' P:DC8 4.6 19.4 1.0 O A:ARG102 4.7 16.8 1.0 O5' P:DG9 4.7 18.1 1.0 C A:GLY105 4.7 15.8 1.0 N A:THR101 4.9 14.2 1.0

Sodium binding site 2 out of 2 in the Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A T


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A T within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:28.2 occ:1.00 O A:VAL65 2.3 33.2 1.0 O A:HOH575 2.3 28.8 1.0 O A:LYS60 2.4 32.2 1.0 O A:LEU62 2.4 27.7 1.0 OP1 D:DC3 2.7 28.2 1.0 O A:HOH525 2.8 27.4 1.0 C A:VAL65 3.4 22.3 1.0 C A:LEU62 3.5 28.0 1.0 C A:LYS60 3.5 29.9 1.0 P D:DC3 3.7 29.2 1.0 N A:VAL65 3.8 25.1 1.0 OP2 D:DC3 3.8 21.6 1.0 CA A:VAL65 4.1 22.3 1.0 C A:LYS61 4.1 28.4 1.0 N A:LEU62 4.1 26.4 1.0 N A:GLY64 4.1 25.3 1.0 O A:LYS61 4.2 35.6 1.0 CA A:PRO63 4.2 32.6 1.0 CA A:LYS60 4.3 27.2 1.0 CG A:LYS60 4.3 31.1 1.0 N A:PRO63 4.3 27.8 1.0 CB A:VAL65 4.4 25.6 1.0 CA A:LEU62 4.5 23.8 1.0 N A:GLY66 4.5 23.0 1.0 O3' D:DT2 4.5 24.6 1.0 N A:LYS61 4.5 30.4 1.0 C A:PRO63 4.6 27.8 1.0 CA A:LYS61 4.6 30.2 1.0 NZ A:LYS60 4.7 31.7 1.0 C A:GLY64 4.8 29.5 1.0 CA A:GLY66 4.8 21.9 1.0 CB A:LYS60 4.9 27.4 1.0 O5' D:DC3 5.0 27.2 1.0 O A:ALA59 5.0 22.8 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