Sodium in PDB 8vf8: Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Dc Base-Paired with Fapydg

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

The structure of Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Dc Base-Paired with Fapydg, PDB code: 8vf8 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)	24.79 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.133, 79.436, 55.023, 90, 105.37, 90
R / Rfree (%)	19.2 / 22.2

The binding sites of Sodium atom in the Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Dc Base-Paired with Fapydg (pdb code 8vf8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Dc Base-Paired with Fapydg, PDB code: 8vf8:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Binary 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 Binary 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:Na401 b:17.9 occ:1.00 O A:ILE106 2.3 14.5 1.0 OP1 P:DG9 2.3 16.5 1.0 O A:THR101 2.3 18.9 1.0 O A:VAL103 2.4 16.9 1.0 O P:HOH127 2.5 20.2 1.0 O A:HOH669 2.8 23.1 1.0 C A:ILE106 3.3 13.9 1.0 C A:THR101 3.3 17.0 1.0 C A:VAL103 3.4 19.7 1.0 P P:DG9 3.4 14.2 1.0 O A:HOH538 3.5 21.5 1.0 OP2 P:DG9 3.7 17.4 1.0 N A:ILE106 3.7 12.9 1.0 CA A:THR101 3.8 15.3 1.0 CA A:SER104 3.9 14.1 1.0 CA A:ILE106 4.0 11.3 1.0 N A:GLY105 4.0 16.0 1.0 N A:SER104 4.0 20.1 1.0 N A:GLY107 4.2 15.2 1.0 CB A:THR101 4.2 16.5 1.0 N A:VAL103 4.3 18.8 1.0 C A:SER104 4.3 15.4 1.0 C A:ARG102 4.4 18.3 1.0 N A:ARG102 4.4 17.8 1.0 CA A:VAL103 4.5 18.2 1.0 CA A:GLY107 4.5 14.1 1.0 CB A:ILE106 4.5 17.9 1.0 O3' P:DC8 4.5 13.8 1.0 O5' P:DG9 4.6 16.2 1.0 C A:GLY105 4.6 13.3 1.0 CA A:ARG102 4.7 18.9 1.0 O A:ARG102 4.8 15.9 1.0 O A:LEU100 4.8 16.8 1.0 CA A:GLY105 4.9 15.8 1.0

Sodium binding site 2 out of 3 in the Binary 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 Binary 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:31.0 occ:1.00 O D:HOH107 2.3 22.8 1.0 O A:VAL65 2.4 28.2 1.0 O A:LYS60 2.4 32.2 1.0 O A:HOH645 2.5 29.5 1.0 O A:LEU62 2.6 31.6 1.0 OP1 D:DC3 2.8 23.6 1.0 C A:VAL65 3.5 21.5 1.0 C A:LYS60 3.5 30.7 1.0 P D:DC3 3.7 25.4 1.0 OP2 D:DC3 3.7 20.6 1.0 C A:LEU62 3.7 30.3 1.0 N A:VAL65 4.0 26.2 1.0 CG A:LYS60 4.1 30.1 1.0 CA A:LYS60 4.2 24.4 1.0 CA A:VAL65 4.2 20.6 1.0 N A:LEU62 4.2 28.8 1.0 C A:LYS61 4.3 31.4 1.0 N A:GLY64 4.5 26.8 1.0 CA A:PRO63 4.5 27.0 1.0 CB A:VAL65 4.5 20.6 1.0 N A:PRO63 4.5 28.6 1.0 O A:LYS61 4.6 33.7 1.0 N A:GLY66 4.6 22.4 1.0 N A:LYS61 4.6 29.4 1.0 CA A:LEU62 4.6 26.5 1.0 O3' D:DT2 4.7 23.4 1.0 CA A:LYS61 4.7 28.7 1.0 CB A:LYS60 4.8 25.5 1.0 CA A:GLY66 4.8 22.4 1.0 NZ A:LYS60 4.8 29.9 1.0 C A:PRO63 4.9 25.1 1.0 O5' D:DC3 4.9 24.8 1.0 C A:GLY64 5.0 27.2 1.0

Sodium binding site 3 out of 3 in the Binary 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 3 of Binary 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:37.0 occ:1.00 O A:HOH656 2.5 37.0 1.0 OG A:SER171 2.5 29.3 1.0 O A:HOH536 2.6 35.2 1.0 CB A:SER171 3.6 25.9 1.0 N A:SER171 4.2 27.1 1.0 CA A:SER171 4.5 27.0 1.0 OD1 A:ASP170 4.8 25.4 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