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

Enzymatic activity of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Da Base-Paired with Fapydg

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

Protein crystallography data

The structure of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Da Base-Paired with Fapydg, PDB code: 8vfb 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) 25.48 / 2.64
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.854, 79.307, 54.702, 90, 108.88, 90
R / Rfree (%) 19.6 / 22.8

Other elements in 8vfb:

The structure of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Da Base-Paired with Fapydg also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Da Base-Paired with Fapydg (pdb code 8vfb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Da Base-Paired with Fapydg, PDB code: 8vfb:

Sodium binding site 1 out of 1 in 8vfb

Go back to Sodium Binding Sites List in 8vfb
Sodium binding site 1 out of 1 in the Ternary 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 Ternary 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:29.8
occ:1.00
 OP1 P:DG9 2.0 28.2 1.0
O A:THR101 2.2 25.8 1.0
O A:ILE106 2.5 17.4 1.0
O A:HOH501 2.8 27.1 1.0
O A:VAL103 2.8 31.8 1.0
P P:DG9 3.3 25.4 1.0
C A:VAL103 3.4 17.4 1.0
C A:THR101 3.4 20.1 1.0
C A:ILE106 3.5 10.8 1.0
OP2 P:DG9 3.6 18.5 1.0
O P:HOH101 3.6 32.6 1.0
CA A:SER104 3.7 14.6 1.0
N A:SER104 3.8 18.8 1.0
N A:ILE106 3.8 14.4 1.0
N A:GLY105 4.0 22.4 1.0
CG2 A:THR101 4.1 20.8 1.0
CA A:ILE106 4.1 12.2 1.0
N A:VAL103 4.1 20.2 1.0
CA A:THR101 4.2 16.7 1.0
O5' P:DG9 4.2 13.4 1.0
C A:SER104 4.2 16.1 1.0
N A:GLY107 4.3 11.4 1.0
C A:ARG102 4.4 19.6 1.0
O3' P:DC8 4.4 18.8 1.0
CA A:VAL103 4.4 17.5 1.0
N A:ARG102 4.4 17.2 1.0
CB A:ILE106 4.6 13.0 1.0
CA A:GLY107 4.7 12.9 1.0
CA A:ARG102 4.7 12.8 1.0
C A:GLY105 4.8 13.3 1.0
CB A:THR101 4.8 19.3 1.0
O A:LEU100 4.9 23.7 1.0
CB A:SER104 4.9 10.9 1.0
O A:ARG102 5.0 29.3 1.0
CA A:GLY105 5.0 13.8 1.0

Reference:

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
Page generated: Mon Aug 18 16:02:03 2025

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