Sodium in PDB 8vfj: Polymerase Beta Host Guest Complex Containing Fapydg Base Paired with Tmp

All present enzymatic activity of Polymerase Beta Host Guest Complex Containing Fapydg Base Paired with Tmp:
2.7.7.7;

The structure of Polymerase Beta Host Guest Complex Containing Fapydg Base Paired with Tmp, PDB code: 8vfj 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)	24.75 / 2.14
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.378, 80.89, 58.302, 90, 110.15, 90
R / Rfree (%)	21.1 / 26.5

The binding sites of Sodium atom in the Polymerase Beta Host Guest Complex Containing Fapydg Base Paired with Tmp (pdb code 8vfj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Polymerase Beta Host Guest Complex Containing Fapydg Base Paired with Tmp, PDB code: 8vfj:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Polymerase Beta Host Guest Complex Containing Fapydg Base Paired with Tmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Polymerase Beta Host Guest Complex Containing Fapydg Base Paired with Tmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:24.1 occ:1.00 O A:THR101 2.0 20.0 1.0 O A:ILE106 2.2 16.7 1.0 OP1 P:DG9 2.4 16.3 1.0 O P:HOH108 2.6 20.3 1.0 O A:VAL103 2.6 18.3 1.0 O P:HOH114 2.9 20.3 1.0 C A:THR101 3.1 15.8 1.0 C A:ILE106 3.3 18.0 1.0 C A:VAL103 3.4 16.5 1.0 P P:DG9 3.5 16.3 1.0 NA A:NA403 3.5 34.1 1.0 OP2 P:DG9 3.7 17.7 1.0 N A:ILE106 3.7 18.9 1.0 CA A:THR101 3.7 20.0 1.0 CA A:ILE106 4.0 16.6 1.0 CA A:SER104 4.0 18.8 1.0 N A:SER104 4.0 20.9 1.0 N A:VAL103 4.0 17.5 1.0 N A:GLY105 4.1 17.2 1.0 CB A:THR101 4.2 21.0 1.0 N A:ARG102 4.2 17.8 1.0 N A:GLY107 4.3 22.1 1.0 C A:ARG102 4.3 19.0 1.0 CB A:ILE106 4.4 19.2 1.0 CA A:VAL103 4.4 19.4 1.0 C A:SER104 4.4 17.6 1.0 CA A:GLY107 4.5 21.1 1.0 CA A:ARG102 4.6 19.6 1.0 O3' P:DC8 4.6 19.8 1.0 O5' P:DG9 4.6 18.9 1.0 C A:GLY105 4.6 17.0 1.0 O A:HOH601 4.8 38.9 1.0 O A:LEU100 4.8 15.9 1.0 O A:ARG102 4.8 19.6 1.0 CA A:GLY105 4.9 15.2 1.0

Sodium binding site 2 out of 3 in the Polymerase Beta Host Guest Complex Containing Fapydg Base Paired with Tmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Polymerase Beta Host Guest Complex Containing Fapydg Base Paired with Tmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:43.2 occ:1.00 O D:HOH104 2.2 35.7 1.0 O A:HOH587 2.5 46.4 1.0 O A:VAL65 2.6 38.7 1.0 O A:LYS60 2.6 34.0 1.0 O A:LEU62 2.7 36.4 1.0 OP1 D:DC3 2.7 29.0 1.0 OP2 D:DC3 3.5 27.9 1.0 P D:DC3 3.5 37.3 1.0 C A:VAL65 3.8 27.4 1.0 C A:LYS60 3.8 35.2 1.0 C A:LEU62 3.9 34.0 1.0 C A:LYS61 4.4 38.0 1.0 N A:GLY64 4.4 33.0 1.0 CG A:LYS60 4.4 30.3 1.0 O A:LYS61 4.4 39.0 1.0 CA A:PRO63 4.4 39.2 1.0 N A:VAL65 4.5 32.3 1.0 O3' D:DT2 4.5 33.8 1.0 N A:LEU62 4.5 34.7 1.0 N A:PRO63 4.6 38.5 1.0 CA A:LYS60 4.6 32.6 1.0 NZ A:LYS60 4.6 31.5 1.0 CA A:VAL65 4.7 25.4 1.0 N A:GLY66 4.7 25.2 1.0 CA A:GLY66 4.7 22.5 1.0 N A:LYS61 4.8 36.2 1.0 O5' D:DC3 4.8 28.7 1.0 CA A:LEU62 4.8 33.4 1.0 CA A:LYS61 4.9 33.9 1.0 C A:PRO63 4.9 35.4 1.0

Sodium binding site 3 out of 3 in the Polymerase Beta Host Guest Complex Containing Fapydg Base Paired with Tmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Polymerase Beta Host Guest Complex Containing Fapydg Base Paired with Tmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:34.1 occ:1.00 O A:HOH601 2.2 38.9 1.0 O P:HOH108 2.7 20.3 1.0 O P:HOH114 2.9 20.3 1.0 O P:HOH115 3.0 44.6 1.0 O A:THR101 3.1 20.0 1.0 O A:HOH581 3.2 30.9 1.0 NA A:NA401 3.5 24.1 1.0 C A:THR101 3.9 15.8 1.0 NZ A:LYS27 4.1 34.1 1.0 CA A:ARG102 4.4 19.6 1.0 N A:ARG102 4.5 17.8 1.0 CB A:THR101 4.6 21.0 1.0 OG1 A:THR101 4.6 13.9 1.0 OP1 P:DG9 4.9 16.3 1.0 CA A:THR101 4.9 20.0 1.0 OP2 P:DG9 4.9 17.7 1.0 C A:ARG102 4.9 19.0 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