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Sodium in PDB 6mr7: Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog

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

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

Protein crystallography data

The structure of Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog, PDB code: 6mr7 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) 24.71 / 2.14
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.032, 79.825, 55.518, 90.00, 110.60, 90.00
R / Rfree (%) 18.6 / 25.2

Other elements in 6mr7:

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

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog (pdb code 6mr7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog, PDB code: 6mr7:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6mr7

Go back to Sodium Binding Sites List in 6mr7
Sodium binding site 1 out of 4 in the 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 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:31.9
occ:1.00
 O D:HOH106 2.2 31.1 1.0
O A:VAL65 2.3 33.9 1.0
O A:LEU62 2.3 32.9 1.0
O A:LYS60 2.5 34.3 1.0
O A:HOH643 2.6 39.5 1.0
OP1 D:DC3 2.9 28.1 1.0
C A:VAL65 3.4 28.5 1.0
C A:LEU62 3.5 34.0 1.0
C A:LYS60 3.6 34.7 1.0
N A:VAL65 3.7 23.6 1.0
P D:DC3 3.8 33.1 1.0
OP2 D:DC3 3.8 26.4 1.0
CA A:VAL65 4.1 26.7 1.0
N A:LEU62 4.1 27.3 1.0
N A:GLY64 4.1 30.2 1.0
CA A:PRO63 4.2 32.6 1.0
CG A:LYS60 4.2 36.9 1.0
C A:LYS61 4.2 35.4 1.0
CA A:LYS60 4.2 29.6 1.0
N A:PRO63 4.3 30.0 1.0
CB A:VAL65 4.4 28.6 1.0
CA A:LEU62 4.4 30.4 1.0
N A:GLY66 4.5 27.7 1.0
O A:LYS61 4.5 35.6 1.0
C A:PRO63 4.5 35.0 1.0
O3' D:DT2 4.5 29.3 1.0
N A:LYS61 4.6 34.2 1.0
C A:GLY64 4.7 30.1 1.0
CA A:GLY66 4.7 22.1 1.0
CA A:LYS61 4.7 39.4 1.0
CB A:LYS60 4.9 34.2 1.0
O A:ALA59 5.0 28.4 1.0
CA A:GLY64 5.0 33.6 1.0

Sodium binding site 2 out of 4 in 6mr7

Go back to Sodium Binding Sites List in 6mr7
Sodium binding site 2 out of 4 in the 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 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:24.6
occ:1.00
 OP1 P:DG9 2.3 21.0 1.0
O A:THR101 2.3 20.4 1.0
O A:ILE106 2.4 22.2 1.0
O A:VAL103 2.4 23.7 1.0
O P:HOH103 2.5 28.5 1.0
O P:HOH121 2.6 28.9 1.0
C A:THR101 3.3 22.8 1.0
P P:DG9 3.4 22.7 1.0
C A:VAL103 3.4 22.0 1.0
C A:ILE106 3.4 20.2 1.0
OP2 P:DG9 3.6 24.8 1.0
N A:ILE106 3.8 21.9 1.0
CA A:THR101 3.9 24.0 1.0
CA A:SER104 3.9 22.3 1.0
N A:GLY105 4.0 20.2 1.0
O A:HOH628 4.0 42.6 1.0
N A:SER104 4.0 23.0 1.0
CA A:ILE106 4.2 19.8 1.0
N A:VAL103 4.2 27.3 1.0
C A:ARG102 4.3 27.4 1.0
C A:SER104 4.3 25.9 1.0
N A:GLY107 4.3 18.6 1.0
CB A:THR101 4.4 30.0 1.0
O5' P:DG9 4.4 24.3 1.0
CA A:VAL103 4.4 24.6 1.0
N A:ARG102 4.4 27.8 1.0
O3' P:DC8 4.4 21.7 1.0
CA A:GLY107 4.5 21.0 1.0
CB A:ILE106 4.6 24.3 1.0
C A:GLY105 4.7 19.4 1.0
O A:ARG102 4.7 26.7 1.0
CA A:ARG102 4.7 24.8 1.0
CA A:GLY105 4.9 19.7 1.0
O A:LEU100 4.9 25.3 1.0

Sodium binding site 3 out of 4 in 6mr7

Go back to Sodium Binding Sites List in 6mr7
Sodium binding site 3 out of 4 in the 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 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:Na406

b:52.4
occ:1.00
 O A:HOH501 2.6 47.6 1.0
O2G A:GKS401 2.7 42.8 0.7
O2G A:GKS401 2.8 42.8 0.3
OD2 A:ASP190 2.9 46.2 1.0
O A:HOH515 3.2 37.9 1.0
C1 A:EDO410 3.4 45.9 1.0
O A:HOH602 3.5 49.2 1.0
CG A:ASP190 3.7 36.6 1.0
PG A:GKS401 3.8 45.7 0.7
O3G A:GKS401 3.9 46.9 0.7
PG A:GKS401 3.9 45.6 0.3
CA A:CA402 4.0 33.1 1.0
O3G A:GKS401 4.0 46.8 0.3
OD1 A:ASP190 4.0 31.6 1.0
O A:HOH684 4.1 42.6 1.0
O P:HOH105 4.1 39.5 1.0
O2A A:GKS401 4.3 44.9 0.7
O1 A:EDO410 4.3 46.4 1.0
O2A A:GKS401 4.4 44.8 0.3
O3' P:DC10 4.5 47.6 1.0
O P:HOH102 4.6 44.0 1.0
O3A A:GKS401 4.6 43.9 0.7
C2 A:EDO410 4.6 48.7 1.0
O3A A:GKS401 4.7 43.8 0.3
CB A:ASP190 4.7 28.1 1.0
PA A:GKS401 4.8 42.5 0.7
O3B A:GKS401 4.9 44.0 0.7
O1G A:GKS401 4.9 41.5 0.7
CA A:GLY189 4.9 34.7 1.0
O A:HOH523 4.9 40.9 1.0
PA A:GKS401 4.9 43.0 0.3
O3B A:GKS401 5.0 43.9 0.3
O1G A:GKS401 5.0 41.4 0.3
C A:GLY189 5.0 34.6 1.0

Sodium binding site 4 out of 4 in 6mr7

Go back to Sodium Binding Sites List in 6mr7
Sodium binding site 4 out of 4 in the 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 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:32.3
occ:1.00
 O T:HOH227 2.3 47.2 1.0
O D:HOH110 2.4 35.7 1.0
O T:HOH220 2.6 33.1 1.0
O D:HOH111 2.7 40.3 1.0
O D:HOH118 4.2 42.4 1.0
O4 D:DT2 4.4 26.3 1.0
N6 T:DA4 4.4 25.0 1.0
O D:HOH107 4.6 28.1 1.0
N7 T:DG3 4.7 31.7 1.0
O6 T:DG3 4.7 29.0 1.0
O T:HOH222 5.0 45.6 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 12:01:19 2024

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