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

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

The structure of Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Da, PDB code: 8vff 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)	23.64 / 1.69
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.399, 79.277, 54.885, 90, 105.53, 90
R / Rfree (%)	21.5 / 23.2

The binding sites of Sodium atom in the Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Da (pdb code 8vff). 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 Da, PDB code: 8vff:
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 Da


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 Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:11.0 occ:1.00 O A:ILE106 2.3 10.3 1.0 OP1 P:DG9 2.3 9.2 1.0 O A:THR101 2.4 11.3 1.0 O P:HOH309 2.4 12.8 1.0 O A:VAL103 2.5 10.5 1.0 O A:HOH721 2.5 15.1 1.0 O A:HOH527 3.2 24.7 1.0 C A:ILE106 3.3 9.6 1.0 C A:THR101 3.4 11.2 1.0 P P:DG9 3.4 10.3 1.0 C A:VAL103 3.4 12.7 1.0 OP2 P:DG9 3.6 11.9 1.0 N A:ILE106 3.7 7.2 1.0 CA A:THR101 3.9 11.6 1.0 CA A:SER104 4.0 9.8 1.0 N A:GLY105 4.0 8.9 1.0 CA A:ILE106 4.0 7.3 1.0 N A:SER104 4.1 10.7 1.0 N A:GLY107 4.2 8.3 1.0 N A:VAL103 4.3 10.5 1.0 CB A:THR101 4.3 9.8 1.0 C A:SER104 4.4 8.7 1.0 C A:ARG102 4.4 11.2 1.0 O3' P:DC8 4.5 12.7 1.0 CA A:GLY107 4.5 9.8 1.0 N A:ARG102 4.5 10.0 1.0 CA A:VAL103 4.5 11.5 1.0 CB A:ILE106 4.5 7.9 1.0 O5' P:DG9 4.6 12.2 1.0 C A:GLY105 4.6 8.2 1.0 O A:HOH560 4.6 25.9 1.0 O P:HOH315 4.6 28.1 1.0 CA A:ARG102 4.7 12.5 1.0 O A:ARG102 4.8 12.2 1.0 CA A:GLY105 4.9 8.2 1.0 O A:LEU100 5.0 10.6 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 Da


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 Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:21.5 occ:1.00 O D:HOH109 2.1 19.6 1.0 O A:VAL65 2.3 19.1 1.0 O A:LYS60 2.3 19.4 1.0 O A:LEU62 2.4 20.9 1.0 O A:HOH725 2.5 26.7 1.0 OP1 D:DC3 2.9 18.4 1.0 C A:LYS60 3.4 22.7 1.0 C A:VAL65 3.4 17.0 1.0 C A:LEU62 3.5 20.4 1.0 P D:DC3 3.8 15.2 1.0 N A:VAL65 3.8 15.6 1.0 OP2 D:DC3 3.8 13.2 1.0 N A:LEU62 4.0 18.6 1.0 CA A:LYS60 4.1 16.5 1.0 CA A:VAL65 4.1 14.9 1.0 C A:LYS61 4.1 20.9 1.0 CG A:LYS60 4.2 22.8 1.0 CA A:PRO63 4.3 22.6 1.0 N A:GLY64 4.3 23.1 1.0 N A:PRO63 4.3 23.6 1.0 CB A:VAL65 4.3 15.9 1.0 CA A:LEU62 4.4 17.3 1.0 N A:LYS61 4.4 20.2 1.0 N A:GLY66 4.5 13.0 1.0 O A:LYS61 4.5 23.6 1.0 CA A:LYS61 4.6 20.4 1.0 O3' D:DT2 4.7 15.9 1.0 C A:PRO63 4.7 19.9 1.0 CA A:GLY66 4.7 10.3 1.0 CB A:LYS60 4.7 18.6 1.0 O A:ALA59 4.8 20.5 1.0 C A:GLY64 4.8 19.8 1.0 NZ A:LYS60 4.9 21.0 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