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Sodium in PDB 4ub3: Dna Polymerase Beta Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 S

Enzymatic activity of Dna Polymerase Beta Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 S

All present enzymatic activity of Dna Polymerase Beta Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 S:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 S, PDB code: 4ub3 was solved by B.D.Freudenthal, 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) 21.34 / 2.06
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.698, 80.094, 55.358, 90.00, 107.80, 90.00
R / Rfree (%) 21.4 / 27.4

Other elements in 4ub3:

The structure of Dna Polymerase Beta Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 S also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Beta Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 S (pdb code 4ub3). 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 Dna Polymerase Beta Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 S, PDB code: 4ub3:

Sodium binding site 1 out of 1 in 4ub3

Go back to Sodium Binding Sites List in 4ub3
Sodium binding site 1 out of 1 in the Dna Polymerase Beta Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 S


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 Closed Product Complex with A Templating Cytosine and 8-Oxodgmp, 60 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:26.5
occ:1.00
 OD2 A:ASP190 2.1 35.3 1.0
OD2 A:ASP256 2.2 25.3 1.0
OP2 P:8OG11 2.2 23.5 1.0
OD1 A:ASP192 2.3 31.5 1.0
O3' P:DC10 2.6 34.1 1.0
P P:8OG11 2.9 34.5 1.0
CG A:ASP190 3.0 27.3 1.0
OD1 A:ASP190 3.2 26.4 1.0
CG A:ASP256 3.2 25.6 1.0
CG A:ASP192 3.3 23.7 1.0
OD2 A:ASP192 3.6 18.3 1.0
MG A:MG401 3.7 16.2 1.0
OP1 P:8OG11 3.7 27.7 1.0
CB A:ASP256 3.8 24.1 1.0
C3' P:DC10 3.8 30.4 1.0
C4' P:DC10 4.0 34.5 1.0
C5' P:DC10 4.0 24.6 1.0
O5' P:8OG11 4.2 27.6 1.0
OD1 A:ASP256 4.2 23.0 1.0
O A:MET191 4.4 26.6 1.0
CB A:ASP190 4.4 22.9 1.0
C5' P:8OG11 4.4 24.6 1.0
NH2 A:ARG254 4.5 18.9 1.0
O P:HOH215 4.5 30.5 1.0
OP1 P:DC10 4.6 32.6 1.0
CB A:ASP192 4.6 22.2 1.0
O5' P:DC10 4.8 28.8 1.0
N A:ASP256 4.9 16.9 1.0
C2' P:DC10 4.9 25.9 1.0
C A:MET191 4.9 18.6 1.0
O12 A:PPV402 5.0 29.2 0.6
CA A:ASP256 5.0 20.3 1.0

Reference:

B.D.Freudenthal, W.A.Beard, L.Perera, D.D.Shock, T.Kim, T.Schlick, S.H.Wilson. Uncovering the Polymerase-Induced Cytotoxicty of An Oxidized Nucleotide Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE13886
Page generated: Mon Oct 7 18:36:43 2024

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