Atomistry » Sodium » PDB 4u9u-4us7 » 4uay
Atomistry »
  Sodium »
    PDB 4u9u-4us7 »
      4uay »

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: Tue Dec 15 07:40:44 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy