Sodium in PDB 6dia: Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog:
2.7.7.7;

The structure of Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog, PDB code: 6dia was solved by B.D.Freudenthal, M.R.Smith, S.H.Wilson, W.A.Beard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.57 / 1.97
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.947, 80.584, 55.314, 90.00, 109.94, 90.00
R / Rfree (%)	19.6 / 24.6

The structure of Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog (pdb code 6dia). 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 Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog, PDB code: 6dia:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog


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 Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:19.6 occ:1.00 O A:THR101 2.3 17.7 1.0 OP1 P:DG9 2.3 15.2 1.0 O A:ILE106 2.4 17.3 1.0 O P:HOH209 2.5 19.7 1.0 O A:VAL103 2.5 16.1 1.0 O A:HOH689 2.6 21.6 1.0 C A:THR101 3.3 14.4 1.0 C A:ILE106 3.4 16.9 1.0 P P:DG9 3.4 17.3 1.0 C A:VAL103 3.5 17.6 1.0 OP2 P:DG9 3.7 16.8 1.0 N A:ILE106 3.7 15.5 1.0 CA A:THR101 3.8 15.6 1.0 O A:HOH641 4.0 30.1 1.0 N A:GLY105 4.0 16.5 1.0 CA A:SER104 4.0 19.6 1.0 CA A:ILE106 4.1 15.1 1.0 N A:SER104 4.2 16.3 1.0 N A:VAL103 4.2 16.8 1.0 CB A:THR101 4.3 20.7 1.0 C A:ARG102 4.4 19.5 1.0 N A:GLY107 4.4 14.9 1.0 N A:ARG102 4.4 18.8 1.0 C A:SER104 4.4 19.7 1.0 O3' P:DC8 4.5 16.1 1.0 CA A:VAL103 4.5 18.5 1.0 CB A:ILE106 4.5 19.9 1.0 O5' P:DG9 4.5 19.1 1.0 C A:GLY105 4.6 14.2 1.0 CA A:GLY107 4.6 15.9 1.0 CA A:ARG102 4.7 19.2 1.0 O P:HOH236 4.8 38.2 1.0 O A:ARG102 4.8 18.6 1.0 CA A:GLY105 4.9 14.8 1.0 O A:LEU100 4.9 17.0 1.0 O A:HOH556 5.0 27.3 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog


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 Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog within 5.0Å range: probe atom residue distance (Å) B Occ P:Na101 b:46.3 occ:1.00 O P:HOH233 2.2 42.9 1.0 O A:HOH520 2.4 39.2 1.0 O A:HOH519 2.6 48.5 1.0 O A:HOH722 2.8 41.8 1.0 O A:HOH512 3.2 29.0 1.0 O3' P:DC10 3.5 32.2 1.0 OD2 A:ASP190 3.6 38.1 1.0 O3G A:GKS401 3.7 38.2 1.0 O2A A:GKS401 4.0 43.9 1.0 C3' P:DC10 4.0 32.6 1.0 O5' P:DC10 4.1 23.1 1.0 O P:HOH205 4.1 26.0 1.0 O A:HOH706 4.2 34.8 1.0 CG A:ASP190 4.3 30.7 1.0 O P:HOH224 4.3 37.7 1.0 O A:HOH661 4.3 48.0 1.0 C5' P:DC10 4.5 24.0 1.0 OD1 A:ASP190 4.5 27.1 1.0 CA A:CA403 4.6 34.9 1.0 OP2 P:DC10 4.6 21.3 1.0 O1G A:GKS401 4.7 41.0 1.0 P P:DC10 4.7 21.6 1.0 PG A:GKS401 4.8 41.9 1.0 PA A:GKS401 4.8 40.6 1.0 C4' P:DC10 4.8 31.2 1.0 OP1 P:DC10 4.8 20.1 1.0 O1A A:GKS401 4.9 32.1 1.0

M.R.Smith, D.D.Shock, W.A.Beard, M.M.Greenberg, B.D.Freudenthal, S.H.Wilson. A Guardian Residue Hinders Insertion of A Fapy•Dgtp Analog By Modulating the Open-Closed Dna Polymerase Transition. Nucleic Acids Res. V. 47 3197 2019.
ISSN: ESSN 1362-4962
PubMed: 30649431
DOI: 10.1093/NAR/GKZ002