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Sodium in PDB 4ppx: Dna Polymerase Beta E295K with Spiroiminodihydantoin in Templating Position

Enzymatic activity of Dna Polymerase Beta E295K with Spiroiminodihydantoin in Templating Position

All present enzymatic activity of Dna Polymerase Beta E295K with Spiroiminodihydantoin in Templating Position:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta E295K with Spiroiminodihydantoin in Templating Position, PDB code: 4ppx was solved by B.E.Eckenroth, S.Doublie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 13.68 / 2.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.276, 79.102, 54.742, 90.00, 105.40, 90.00
R / Rfree (%) 17.7 / 21.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Beta E295K with Spiroiminodihydantoin in Templating Position (pdb code 4ppx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Beta E295K with Spiroiminodihydantoin in Templating Position, PDB code: 4ppx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4ppx

Go back to Sodium Binding Sites List in 4ppx
Sodium binding site 1 out of 2 in the Dna Polymerase Beta E295K with Spiroiminodihydantoin in Templating Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Beta E295K with Spiroiminodihydantoin in Templating Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:38.5
occ:1.00
O A:LYS60 2.4 36.3 1.0
O D:HOH102 2.5 31.7 1.0
O A:LEU62 2.5 36.5 1.0
O A:VAL65 2.5 29.9 1.0
O A:HOH566 2.6 46.0 1.0
OP1 D:DC3 2.7 26.6 1.0
C A:LEU62 3.5 33.1 1.0
C A:LYS60 3.6 34.9 1.0
C A:VAL65 3.6 25.5 1.0
P D:DC3 3.7 25.9 1.0
OP2 D:DC3 3.8 24.5 1.0
N A:VAL65 3.9 24.8 1.0
N A:LEU62 4.1 31.6 1.0
CA A:PRO63 4.1 32.3 1.0
N A:PRO63 4.2 32.7 1.0
C A:LYS61 4.2 37.2 1.0
N A:GLY64 4.2 27.0 1.0
CA A:VAL65 4.2 24.2 1.0
CA A:LYS60 4.4 30.7 1.0
CA A:LEU62 4.4 31.0 1.0
O A:LYS61 4.4 38.3 1.0
N A:LYS61 4.5 35.4 1.0
CB A:VAL65 4.5 26.1 1.0
O3' D:DT2 4.5 26.6 1.0
C A:PRO63 4.6 32.1 1.0
CA A:LYS61 4.6 37.2 1.0
N A:GLY66 4.6 25.2 1.0
CD A:LYS60 4.7 31.7 1.0
CG A:LYS60 4.8 36.2 1.0
CA A:GLY66 4.9 25.8 1.0
C A:GLY64 4.9 26.8 1.0
O5' D:DC3 4.9 22.4 1.0
O A:ALA59 4.9 30.7 1.0

Sodium binding site 2 out of 2 in 4ppx

Go back to Sodium Binding Sites List in 4ppx
Sodium binding site 2 out of 2 in the Dna Polymerase Beta E295K with Spiroiminodihydantoin in Templating Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Beta E295K with Spiroiminodihydantoin in Templating Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:17.4
occ:1.00
O A:THR101 2.3 17.7 1.0
OP1 P:DG9 2.3 20.4 1.0
O A:ILE106 2.5 22.0 1.0
O A:VAL103 2.5 16.4 1.0
O P:HOH101 2.5 16.4 1.0
O A:HOH521 2.6 21.0 1.0
C A:THR101 3.3 16.1 1.0
O A:HOH727 3.4 29.0 1.0
C A:VAL103 3.4 21.7 1.0
P P:DG9 3.4 18.7 1.0
C A:ILE106 3.4 18.4 1.0
OP2 P:DG9 3.6 17.4 1.0
N A:ILE106 3.7 13.4 1.0
CA A:THR101 3.9 16.1 1.0
CA A:SER104 3.9 20.7 1.0
N A:GLY105 3.9 18.3 1.0
N A:SER104 4.0 18.2 1.0
CA A:ILE106 4.1 16.1 1.0
N A:VAL103 4.2 20.2 1.0
C A:SER104 4.3 19.0 1.0
C A:ARG102 4.4 20.4 1.0
N A:ARG102 4.4 14.5 1.0
N A:GLY107 4.4 17.4 1.0
CB A:THR101 4.4 18.5 1.0
CA A:VAL103 4.4 19.8 1.0
O3' P:DC8 4.5 18.2 1.0
O5' P:DG9 4.5 17.2 1.0
CB A:ILE106 4.5 16.7 1.0
C A:GLY105 4.6 20.4 1.0
CA A:GLY107 4.7 17.5 1.0
CA A:ARG102 4.7 17.1 1.0
O A:HOH742 4.8 54.3 1.0
O A:ARG102 4.8 20.9 1.0
CA A:GLY105 4.9 18.8 1.0
O A:LEU100 4.9 19.1 1.0
O A:HOH730 5.0 37.6 1.0

Reference:

B.E.Eckenroth, A.M.Fleming, J.B.Sweasy, C.J.Burrows, S.Doublie. Crystal Structure of Dna Polymerase Beta with Dna Containing the Base Lesion Spiroiminodihydantoin in A Templating Position. Biochemistry V. 53 2075 2014.
ISSN: ISSN 0006-2960
PubMed: 24649945
DOI: 10.1021/BI500270E
Page generated: Sun Aug 17 21:15:10 2025

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