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Sodium in PDB 6mr8: D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog

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

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

Protein crystallography data

The structure of D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog, PDB code: 6mr8 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) 24.80 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.015, 80.282, 55.564, 90.00, 110.46, 90.00
R / Rfree (%) 19.6 / 23.9

Other elements in 6mr8:

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

Calcium (Ca) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog (pdb code 6mr8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog, PDB code: 6mr8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6mr8

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Sodium binding site 1 out of 5 in the D276G Dna Polymerase Beta Substrate Complex with Templating Adenine 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 Adenine and Incoming Fapy-Dgtp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:48.4
occ:1.00
 O P:HOH208 2.3 31.9 1.0
O A:HOH734 2.4 46.3 1.0
O A:HOH607 2.5 28.0 1.0
O P:HOH212 2.8 31.7 1.0
O A:HOH743 3.0 27.2 1.0
O A:HOH689 3.8 45.8 1.0
O P:HOH235 3.8 37.3 0.5
O A:HOH567 3.9 35.8 1.0
O A:GLY189 4.1 25.2 1.0
O A:PHE146 4.3 23.6 1.0
OD2 A:ASP190 4.4 34.8 1.0
O A:HOH726 4.4 30.8 1.0
OP1 P:DC10 4.5 20.1 1.0
OP2 P:DC10 4.7 28.7 1.0
C A:GLY189 4.7 25.9 1.0
O P:HOH221 4.8 23.5 1.0
O P:HOH235 4.8 42.7 0.5
CB A:ASP190 4.8 20.5 1.0
CG A:ARG254 5.0 19.6 1.0

Sodium binding site 2 out of 5 in 6mr8

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Sodium binding site 2 out of 5 in the D276G Dna Polymerase Beta Substrate Complex with Templating Adenine 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 Adenine and Incoming Fapy-Dgtp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:31.0
occ:1.00
 O A:HOH566 2.1 34.1 1.0
O A:HOH660 2.4 34.2 1.0
CD A:GLU288 2.9 45.3 1.0
O A:HOH649 2.9 42.3 1.0
OE2 A:GLU288 3.1 47.8 1.0
OE1 A:GLU288 3.1 53.5 1.0
CG A:GLU288 3.3 49.6 1.0
CB A:GLU288 4.7 42.9 1.0

Sodium binding site 3 out of 5 in 6mr8

Go back to Sodium Binding Sites List in 6mr8
Sodium binding site 3 out of 5 in the D276G Dna Polymerase Beta Substrate Complex with Templating Adenine 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 Adenine and Incoming Fapy-Dgtp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:18.9
occ:1.00
 OP1 P:DG9 2.3 18.4 1.0
O A:THR101 2.3 17.7 1.0
O A:HOH694 2.4 21.3 1.0
O A:ILE106 2.4 17.1 1.0
O A:VAL103 2.5 15.4 1.0
O P:HOH204 2.6 22.7 1.0
C A:THR101 3.3 18.3 1.0
P P:DG9 3.4 18.6 1.0
C A:VAL103 3.4 16.1 1.0
C A:ILE106 3.4 15.0 1.0
OP2 P:DG9 3.7 18.5 1.0
N A:ILE106 3.8 15.6 1.0
CA A:THR101 3.9 18.6 1.0
O A:HOH622 3.9 36.6 1.0
CA A:SER104 3.9 21.5 1.0
N A:GLY105 4.0 15.0 1.0
N A:SER104 4.0 15.6 1.0
CA A:ILE106 4.1 14.1 1.0
N A:VAL103 4.2 19.6 1.0
C A:ARG102 4.3 19.9 1.0
CB A:THR101 4.3 21.8 1.0
C A:SER104 4.3 18.7 1.0
N A:GLY107 4.3 13.8 1.0
N A:ARG102 4.4 20.0 1.0
O3' P:DC8 4.4 15.7 1.0
CA A:VAL103 4.4 19.6 1.0
O5' P:DG9 4.5 19.9 1.0
CB A:ILE106 4.5 18.3 1.0
CA A:GLY107 4.6 15.8 1.0
C A:GLY105 4.6 16.7 1.0
CA A:ARG102 4.7 21.4 1.0
O A:ARG102 4.7 19.9 1.0
CA A:GLY105 4.8 18.2 1.0
O A:LEU100 4.9 20.0 1.0

Sodium binding site 4 out of 5 in 6mr8

Go back to Sodium Binding Sites List in 6mr8
Sodium binding site 4 out of 5 in the D276G Dna Polymerase Beta Substrate Complex with Templating Adenine 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 Adenine and Incoming Fapy-Dgtp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:27.1
occ:1.00
 O A:HOH706 2.1 39.1 1.0
O A:HOH713 2.6 41.9 1.0
OE2 A:GLU172 2.7 46.4 1.0
O A:HOH699 3.0 42.2 1.0
OE1 A:GLU172 3.1 46.9 1.0
CD A:GLU172 3.3 41.3 1.0
O A:HOH509 4.6 38.5 1.0
CG A:GLU172 4.8 42.0 1.0
OG A:SER171 4.9 37.5 1.0

Sodium binding site 5 out of 5 in 6mr8

Go back to Sodium Binding Sites List in 6mr8
Sodium binding site 5 out of 5 in the D276G Dna Polymerase Beta Substrate Complex with Templating Adenine 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 5 of D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Na101

b:40.1
occ:1.00
 O T:HOH252 2.1 44.1 1.0
O T:HOH209 2.3 36.6 1.0
O D:HOH102 2.6 43.8 1.0
O T:HOH230 2.6 36.0 1.0
O D:HOH118 2.7 30.0 1.0
O T:HOH251 3.7 41.4 1.0
O4' D:DG5 4.2 44.4 1.0
O4' T:DA4 4.4 33.4 1.0
C4' T:DA4 4.5 28.3 1.0
N2 T:DG3 4.5 23.8 1.0
C4' D:DG5 4.6 46.3 1.0
O D:HOH119 4.7 43.7 1.0
C5' T:DA4 4.7 31.7 1.0
N3 T:DG3 4.8 21.4 1.0
N2 D:DG4 4.9 29.0 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 12:01:29 2024

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