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

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

The structure of Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal T Base-Paired with Fapydg, PDB code: 8vfc 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)	24.74 / 2.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.064, 79.728, 55.683, 90, 105.67, 90
R / Rfree (%)	19.7 / 25.5

The binding sites of Sodium atom in the Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal T Base-Paired with Fapydg (pdb code 8vfc). 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 T Base-Paired with Fapydg, PDB code: 8vfc:
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 T 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 Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal T Base-Paired with Fapydg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:25.0 occ:1.00 O A:THR101 2.2 26.9 1.0 O A:VAL103 2.4 23.4 1.0 O A:ILE106 2.5 23.4 1.0 OP1 P:DG9 2.5 22.9 1.0 O P:HOH104 2.6 25.0 1.0 O A:HOH555 2.8 33.5 1.0 C A:VAL103 3.3 27.4 1.0 C A:THR101 3.3 26.8 1.0 C A:ILE106 3.5 23.4 1.0 P P:DG9 3.5 21.5 1.0 OP2 P:DG9 3.7 28.0 1.0 CA A:SER104 3.8 19.2 1.0 N A:ILE106 3.8 19.6 1.0 N A:SER104 3.8 27.6 1.0 CA A:THR101 3.9 24.8 1.0 O A:HOH554 3.9 35.4 1.0 N A:GLY105 3.9 19.7 1.0 CA A:ILE106 4.2 20.3 1.0 C A:SER104 4.2 21.1 1.0 N A:VAL103 4.2 24.2 1.0 C A:ARG102 4.3 27.2 1.0 N A:ARG102 4.4 27.1 1.0 CB A:THR101 4.4 25.8 1.0 CA A:VAL103 4.4 23.1 1.0 N A:GLY107 4.4 22.7 1.0 O A:HOH560 4.5 27.3 1.0 O5' P:DG9 4.5 31.0 1.0 CA A:ARG102 4.6 23.1 1.0 CB A:ILE106 4.6 23.1 1.0 O A:ARG102 4.6 24.6 1.0 C A:GLY105 4.7 22.4 1.0 O3' P:DC8 4.7 26.5 1.0 CA A:GLY107 4.7 25.1 1.0 CA A:GLY105 4.9 19.2 1.0 O A:HOH526 4.9 30.0 1.0

Sodium binding site 2 out of 2 in the Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal T 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 Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal T Base-Paired with Fapydg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:37.7 occ:1.00 O A:LYS60 2.3 43.7 1.0 O A:VAL65 2.4 41.5 1.0 O A:LEU62 2.5 36.4 1.0 O D:HOH105 2.5 39.9 1.0 OP1 D:DC3 2.9 37.2 1.0 O A:HOH516 3.0 38.9 1.0 C A:LYS60 3.4 41.6 1.0 C A:LEU62 3.4 37.2 1.0 C A:VAL65 3.5 33.9 1.0 P D:DC3 3.8 34.5 1.0 OP2 D:DC3 3.8 34.9 1.0 N A:VAL65 3.9 36.2 1.0 N A:LEU62 3.9 37.8 1.0 C A:LYS61 4.0 42.3 1.0 CA A:LYS60 4.1 37.2 1.0 CA A:VAL65 4.1 33.2 1.0 O A:LYS61 4.2 45.8 1.0 N A:PRO63 4.3 36.8 1.0 CA A:PRO63 4.3 41.4 1.0 CG A:LYS60 4.3 38.8 1.0 CA A:LEU62 4.3 35.2 1.0 N A:GLY64 4.4 33.5 1.0 N A:LYS61 4.4 42.8 1.0 CB A:VAL65 4.4 32.0 1.0 O3' D:DT2 4.5 29.1 1.0 CA A:LYS61 4.6 42.0 1.0 N A:GLY66 4.6 34.0 1.0 C A:PRO63 4.7 41.1 1.0 O A:ALA59 4.8 31.1 1.0 CB A:LYS60 4.8 35.0 1.0 CA A:GLY66 4.8 30.3 1.0 C A:GLY64 4.9 41.1 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