Sodium in PDB 8vfh: Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Dc

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

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

Protein crystallography data

The structure of Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Dc, PDB code: 8vfh 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) 24.65 / 2.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.8, 80.4, 55.5, 90, 107.9, 90
R / Rfree (%) 17.7 / 24.6

Other elements in 8vfh:

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

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Dc (pdb code 8vfh). 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 Fapydg Base-Paired with A Dc, PDB code: 8vfh:

Sodium binding site 1 out of 1 in 8vfh

Go back to Sodium Binding Sites List in 8vfh
Sodium binding site 1 out of 1 in the Ternary Dna Polymerase Beta Bound to Dna Containing Primer Terminal Fapydg Base-Paired with A Dc


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 Fapydg Base-Paired with A Dc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:21.6
occ:1.00
 OP1 P:DG9 2.3 24.4 1.0
O A:THR101 2.3 22.1 1.0
O P:HOH104 2.4 26.4 1.0
O A:ILE106 2.4 17.8 1.0
O A:VAL103 2.5 21.9 1.0
O A:HOH709 2.6 28.2 1.0
C A:THR101 3.3 24.1 1.0
C A:ILE106 3.4 21.8 1.0
C A:VAL103 3.4 28.1 1.0
P P:DG9 3.4 23.5 1.0
OP2 P:DG9 3.7 22.7 1.0
N A:ILE106 3.7 21.8 1.0
CA A:THR101 3.9 20.5 1.0
CA A:SER104 4.0 23.7 1.0
N A:VAL103 4.0 24.4 1.0
N A:GLY105 4.0 24.4 1.0
CA A:ILE106 4.1 20.1 1.0
N A:SER104 4.1 16.0 1.0
C A:ARG102 4.2 24.0 1.0
N A:ARG102 4.3 22.4 1.0
O A:HOH718 4.3 44.1 1.0
C A:SER104 4.4 22.4 1.0
CA A:VAL103 4.4 23.4 1.0
N A:GLY107 4.4 27.4 1.0
CB A:THR101 4.4 22.5 1.0
O3' P:DC8 4.5 24.4 1.0
CB A:ILE106 4.5 22.7 1.0
O5' P:DG9 4.6 27.4 1.0
CA A:ARG102 4.6 26.0 1.0
C A:GLY105 4.6 27.8 1.0
O A:ARG102 4.6 25.6 1.0
CA A:GLY107 4.7 27.3 1.0
O A:LEU100 4.8 18.6 1.0
CA A:GLY105 4.9 26.3 1.0
O A:HOH713 4.9 36.7 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: Wed Oct 9 14:00:28 2024

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