Sodium in PDB 8vf9: Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Da Base-Paired with Fapydg

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

The structure of Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Da Base-Paired with Fapydg, PDB code: 8vf9 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)	24.92 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.441, 78.632, 54.52, 90, 105.89, 90
R / Rfree (%)	20.8 / 23.2

The binding sites of Sodium atom in the Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Da Base-Paired with Fapydg (pdb code 8vf9). 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 Da Base-Paired with Fapydg, PDB code: 8vf9:
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 Da 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 Da Base-Paired with Fapydg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:6.5 occ:1.00 O A:THR101 2.3 8.1 1.0 O A:VAL103 2.4 7.4 1.0 O A:ILE106 2.4 6.6 1.0 OP1 P:DG9 2.4 7.0 1.0 O P:HOH108 2.5 11.3 1.0 O A:HOH657 2.6 13.4 1.0 C A:THR101 3.2 9.3 1.0 NA A:NA403 3.2 17.0 1.0 C A:VAL103 3.3 10.0 1.0 C A:ILE106 3.4 6.8 1.0 P P:DG9 3.6 9.3 1.0 CA A:THR101 3.8 10.9 1.0 N A:ILE106 3.8 5.8 1.0 OP2 P:DG9 3.8 13.5 1.0 CA A:SER104 3.9 8.6 1.0 N A:GLY105 4.0 9.0 1.0 N A:SER104 4.0 8.4 1.0 N A:VAL103 4.1 7.2 1.0 CA A:ILE106 4.1 7.0 1.0 C A:ARG102 4.2 8.8 1.0 CB A:THR101 4.3 11.3 1.0 N A:ARG102 4.3 8.8 1.0 CA A:VAL103 4.3 7.1 1.0 N A:GLY107 4.3 7.6 1.0 C A:SER104 4.4 9.9 1.0 CB A:ILE106 4.5 6.4 1.0 CA A:GLY107 4.5 11.6 1.0 CA A:ARG102 4.6 8.5 1.0 C A:GLY105 4.7 9.1 1.0 O A:ARG102 4.7 9.1 1.0 O3' P:DC8 4.7 10.0 1.0 O5' P:DG9 4.7 11.0 1.0 O A:LEU100 4.7 7.9 1.0 O A:HOH671 4.7 32.5 1.0 CA A:GLY105 4.9 8.4 1.0 O A:HOH527 5.0 23.7 1.0

Sodium binding site 2 out of 3 in the Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Da 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 Da Base-Paired with Fapydg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:20.8 occ:1.00 O A:VAL65 2.2 20.1 1.0 O A:LYS60 2.3 25.4 1.0 O A:LEU62 2.3 18.4 1.0 O D:HOH104 2.4 21.7 1.0 O A:HOH659 2.6 24.5 1.0 OP1 D:DC3 3.0 24.4 1.0 C A:VAL65 3.3 17.0 1.0 C A:LYS60 3.4 23.2 1.0 C A:LEU62 3.4 19.0 1.0 N A:VAL65 3.7 15.9 1.0 P D:DC3 3.9 19.2 1.0 OP2 D:DC3 3.9 18.1 1.0 CA A:VAL65 4.0 12.8 1.0 N A:LEU62 4.0 18.9 1.0 C A:LYS61 4.0 22.8 1.0 CA A:LYS60 4.1 20.0 1.0 O A:LYS61 4.2 25.5 1.0 CB A:VAL65 4.2 17.2 1.0 CA A:PRO63 4.2 19.0 1.0 N A:GLY64 4.2 15.7 1.0 N A:PRO63 4.2 20.1 1.0 CA A:LEU62 4.3 15.6 1.0 N A:LYS61 4.4 21.1 1.0 CG A:LYS60 4.4 32.5 1.0 N A:GLY66 4.4 15.4 1.0 CA A:LYS61 4.5 19.3 1.0 C A:PRO63 4.6 17.0 1.0 O A:ALA59 4.7 17.0 1.0 O3' D:DT2 4.8 19.1 1.0 CA A:GLY66 4.8 15.3 1.0 C A:GLY64 4.8 19.4 1.0 CB A:LYS60 4.9 24.9 1.0

Sodium binding site 3 out of 3 in the Binary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Da 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 Da Base-Paired with Fapydg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:17.0 occ:1.00 O A:HOH665 2.2 26.2 1.0 O A:THR101 2.5 8.1 1.0 O P:HOH108 2.5 11.3 1.0 O A:HOH671 2.5 32.5 1.0 O A:HOH657 2.5 13.4 1.0 O A:HOH617 2.6 18.6 1.0 NA A:NA401 3.2 6.5 1.0 C A:THR101 3.5 9.3 1.0 CA A:ARG102 4.0 8.5 1.0 N A:ARG102 4.1 8.8 1.0 CB A:THR101 4.3 11.3 1.0 NZ A:LYS27 4.3 39.1 1.0 O A:HOH527 4.4 23.7 1.0 OG1 A:THR101 4.5 14.3 1.0 CA A:THR101 4.5 10.9 1.0 C A:ARG102 4.5 8.8 1.0 O P:HOH107 4.7 25.5 1.0 OP1 P:DG9 4.7 7.0 1.0 O A:ARG102 4.8 9.1 1.0 O A:HOH544 4.8 20.4 1.0 OP2 P:DG9 4.9 13.5 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