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Sodium in PDB 6dic: D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog

Enzymatic activity of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog

All present enzymatic activity of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog:
2.7.7.7;

Protein crystallography data

The structure of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog, PDB code: 6dic 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) 20.66 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.800, 80.400, 55.500, 90.00, 107.90, 90.00
R / Rfree (%) 17.5 / 23.2

Other elements in 6dic:

The structure of D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog also contains other interesting chemical elements:

Calcium (Ca) 3 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog (pdb code 6dic). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the D276G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog, PDB code: 6dic:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6dic

Go back to Sodium Binding Sites List in 6dic
Sodium binding site 1 out of 4 in the D276G 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 D276G 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:Na401

b:23.9
occ:1.00
 O A:THR101 2.3 18.8 1.0
O P:HOH508 2.3 29.2 1.0
O A:HOH733 2.4 26.0 1.0
O A:ILE106 2.4 17.4 1.0
O A:VAL103 2.5 16.1 1.0
OP1 P:DG9 2.5 21.9 1.0
C A:THR101 3.3 16.3 1.0
C A:ILE106 3.5 16.5 1.0
C A:VAL103 3.5 19.0 1.0
P P:DG9 3.5 23.2 1.0
OP2 P:DG9 3.5 21.9 1.0
O A:HOH676 3.8 36.9 1.0
N A:ILE106 3.8 15.8 1.0
CA A:THR101 3.9 15.4 1.0
CA A:SER104 4.1 12.5 1.0
N A:GLY105 4.1 18.1 1.0
CA A:ILE106 4.1 18.7 1.0
N A:SER104 4.2 15.0 1.0
N A:VAL103 4.2 14.0 1.0
C A:ARG102 4.3 21.0 1.0
N A:ARG102 4.4 15.6 1.0
C A:SER104 4.4 16.2 1.0
N A:GLY107 4.4 15.2 1.0
CA A:VAL103 4.5 17.4 1.0
CB A:THR101 4.5 20.0 1.0
O3' P:DC8 4.5 21.3 1.0
CB A:ILE106 4.6 22.1 1.0
CA A:ARG102 4.6 12.8 1.0
O5' P:DG9 4.7 23.5 1.0
C A:GLY105 4.7 24.9 1.0
CA A:GLY107 4.7 20.0 1.0
O A:ARG102 4.8 16.4 1.0
O A:LEU100 4.8 17.2 1.0
CA A:GLY105 4.9 22.8 1.0

Sodium binding site 2 out of 4 in 6dic

Go back to Sodium Binding Sites List in 6dic
Sodium binding site 2 out of 4 in the D276G 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 D276G 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:Na404

b:34.2
occ:1.00
 O A:LEU62 2.2 36.5 1.0
O A:VAL65 2.4 26.8 1.0
OP1 D:DC3 2.4 30.2 1.0
O A:HOH681 2.4 40.0 1.0
O A:LYS60 2.5 31.1 1.0
O D:HOH202 2.8 31.1 1.0
C A:LEU62 3.3 34.7 1.0
C A:VAL65 3.5 27.7 1.0
C A:LYS60 3.6 36.7 1.0
P D:DC3 3.6 31.4 1.0
N A:VAL65 3.8 28.9 1.0
N A:LEU62 4.0 30.4 1.0
CA A:PRO63 4.0 34.1 1.0
OP2 D:DC3 4.1 29.1 1.0
N A:PRO63 4.1 36.6 1.0
N A:GLY64 4.1 30.0 1.0
CA A:VAL65 4.1 25.4 1.0
C A:LYS61 4.1 37.8 1.0
CA A:LEU62 4.3 28.7 1.0
CA A:LYS60 4.4 28.3 1.0
O A:LYS61 4.4 39.8 1.0
C A:PRO63 4.4 37.0 1.0
CB A:VAL65 4.5 28.4 1.0
CG A:LYS60 4.5 31.7 1.0
N A:GLY66 4.5 30.9 1.0
O3' D:DT2 4.6 34.6 1.0
N A:LYS61 4.6 30.9 1.0
CA A:LYS61 4.7 36.0 1.0
C A:GLY64 4.7 35.2 1.0
CA A:GLY66 4.7 24.8 1.0
O5' D:DC3 4.8 32.8 1.0
CA A:GLY64 5.0 36.6 1.0

Sodium binding site 3 out of 4 in 6dic

Go back to Sodium Binding Sites List in 6dic
Sodium binding site 3 out of 4 in the D276G 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 3 of D276G 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:Na408

b:26.1
occ:1.00
 O A:ARG126 2.5 35.0 1.0
O A:HOH750 2.7 41.4 1.0
O A:HOH689 3.6 30.0 1.0
C A:ARG126 3.7 30.5 1.0
O A:HOH755 3.8 29.6 1.0
N A:LYS127 4.5 28.4 1.0
CA A:LYS127 4.6 34.3 1.0
CA A:ARG126 4.6 22.3 1.0
CB A:ARG126 4.6 27.5 1.0

Sodium binding site 4 out of 4 in 6dic

Go back to Sodium Binding Sites List in 6dic
Sodium binding site 4 out of 4 in the D276G 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 4 of D276G 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:Na409

b:26.0
occ:1.00
 O A:HOH726 2.3 33.3 1.0
O A:HOH737 2.3 39.1 1.0
O A:HOH748 2.4 40.8 1.0
OE2 A:GLU249 2.5 32.0 1.0
OE1 A:GLU249 2.5 26.2 1.0
O A:HOH702 2.6 38.0 1.0
CD A:GLU249 2.8 28.7 1.0
O A:HOH507 4.0 31.7 1.0
CG A:GLU249 4.4 24.7 1.0
OE1 A:GLN240 4.5 21.1 1.0
O A:HOH540 4.8 30.1 1.0
NE2 A:GLN240 4.8 17.8 1.0

Reference:

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
Page generated: Tue Oct 8 07:42:52 2024

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