Sodium in PDB 4ppx: 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;

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

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 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 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

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