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Sodium in PDB 4uay: Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S

Enzymatic activity of Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S

All present enzymatic activity of Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S, PDB code: 4uay 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) 31.27 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.867, 80.445, 55.391, 90.00, 107.69, 90.00
R / Rfree (%) 18.4 / 24.7

Other elements in 4uay:

The structure of Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S (pdb code 4uay). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S, PDB code: 4uay:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4uay

Go back to Sodium Binding Sites List in 4uay
Sodium binding site 1 out of 3 in the Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 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 Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:23.1
occ:1.00
 OD1 A:ASP192 2.2 26.3 1.0
OD2 A:ASP190 2.2 32.1 1.0
OD2 A:ASP256 2.4 25.3 1.0
O3' P:DC10 2.5 29.4 1.0
OP2 P:8OG11 2.5 17.2 0.9
CG A:ASP190 2.9 24.4 1.0
OD1 A:ASP190 3.0 20.9 1.0
P P:8OG11 3.1 26.7 0.9
CG A:ASP192 3.2 16.7 1.0
CG A:ASP256 3.4 21.0 1.0
OD2 A:ASP192 3.5 15.1 1.0
MG A:MG402 3.6 15.3 1.0
C3' P:DC10 3.7 20.1 1.0
C4' P:DC10 3.9 28.5 1.0
CB A:ASP256 4.0 18.0 1.0
OP1 P:8OG11 4.1 25.1 0.9
O5' P:8OG11 4.2 18.4 0.9
C5' P:DC10 4.2 22.1 1.0
C5' P:8OG11 4.3 16.4 0.9
CB A:ASP190 4.3 13.8 1.0
OD1 A:ASP256 4.4 18.1 1.0
CB A:ASP192 4.5 16.4 1.0
O A:MET191 4.6 14.0 1.0
O A:HOH715 4.7 17.9 1.0
C2' P:DC10 4.7 25.9 1.0
NH2 A:ARG254 4.8 17.4 1.0
O P:HOH209 4.8 33.6 1.0
C A:MET191 4.9 16.6 1.0
CA A:ASP192 4.9 15.4 1.0
N A:ASP256 4.9 15.2 1.0
O5' P:DC10 5.0 22.7 1.0
OP1 P:DC10 5.0 21.1 1.0

Sodium binding site 2 out of 3 in 4uay

Go back to Sodium Binding Sites List in 4uay
Sodium binding site 2 out of 3 in the Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S


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 Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:30.0
occ:1.00
 O A:THR101 2.3 17.9 1.0
OP1 P:DG9 2.4 17.8 1.0
O P:HOH204 2.4 21.8 1.0
O A:ILE106 2.5 11.7 1.0
O A:HOH652 2.5 26.0 1.0
O A:VAL103 2.6 14.6 1.0
C A:THR101 3.3 18.9 1.0
P P:DG9 3.4 19.4 1.0
C A:ILE106 3.5 16.9 1.0
C A:VAL103 3.5 14.5 1.0
OP2 P:DG9 3.6 18.7 1.0
N A:ILE106 3.8 12.4 1.0
O A:HOH658 3.9 32.4 1.0
CA A:THR101 3.9 20.9 1.0
CA A:SER104 4.0 14.2 1.0
N A:GLY105 4.1 13.4 1.0
N A:SER104 4.1 14.6 1.0
CA A:ILE106 4.1 11.4 1.0
N A:VAL103 4.2 16.2 1.0
N A:ARG102 4.3 16.5 1.0
C A:ARG102 4.4 19.0 1.0
N A:GLY107 4.4 14.8 1.0
C A:SER104 4.4 14.5 1.0
O3' P:DC8 4.4 15.4 1.0
CB A:THR101 4.5 19.1 1.0
CA A:VAL103 4.5 12.3 1.0
CB A:ILE106 4.5 16.4 1.0
O5' P:DG9 4.6 18.7 1.0
CA A:ARG102 4.6 20.6 1.0
CA A:GLY107 4.7 18.1 1.0
C A:GLY105 4.7 16.5 1.0
O A:ARG102 4.8 18.7 1.0
O A:LEU100 4.9 18.4 1.0
CA A:GLY105 5.0 16.8 1.0

Sodium binding site 3 out of 3 in 4uay

Go back to Sodium Binding Sites List in 4uay
Sodium binding site 3 out of 3 in the Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dna Polymerase Beta Product Complex with A Templating Adenine and Inserted 8-Oxodgmp, 40 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:30.0
occ:1.00
 O A:LEU62 2.3 28.8 1.0
O A:LYS60 2.3 33.6 1.0
O A:VAL65 2.6 31.5 1.0
OP1 D:DC3 2.6 26.9 1.0
O D:HOH104 3.0 36.2 1.0
O A:HOH687 3.0 34.5 1.0
C A:LEU62 3.3 27.1 1.0
C A:LYS60 3.4 33.9 1.0
C A:VAL65 3.6 27.7 1.0
P D:DC3 3.8 31.8 1.0
N A:VAL65 4.0 26.1 1.0
OP2 D:DC3 4.0 29.6 1.0
CA A:PRO63 4.0 28.5 1.0
N A:PRO63 4.0 32.9 1.0
C A:LYS61 4.1 36.8 1.0
N A:LEU62 4.1 27.5 1.0
CA A:LYS60 4.1 32.7 1.0
CA A:VAL65 4.2 25.0 1.0
CG A:LYS60 4.2 30.1 1.0
O A:LYS61 4.2 30.0 1.0
N A:GLY64 4.3 24.7 1.0
CA A:LEU62 4.3 24.3 1.0
N A:LYS61 4.4 26.7 1.0
CB A:VAL65 4.4 22.1 1.0
C A:PRO63 4.5 30.1 1.0
CA A:LYS61 4.5 30.9 1.0
N A:GLY66 4.6 25.4 1.0
O3' D:DT2 4.6 33.8 1.0
CB A:LYS60 4.8 31.7 1.0
CA A:GLY66 4.9 29.4 1.0
O A:ALA59 4.9 24.4 1.0
C A:GLY64 5.0 29.8 1.0
O5' D:DC3 5.0 34.1 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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