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Sodium in PDB 7k96: Human Dna Polymerase Beta Ternary Complex with Templating Cytosine and Incoming Deoxyguanosine Diphosphate

Enzymatic activity of Human Dna Polymerase Beta Ternary Complex with Templating Cytosine and Incoming Deoxyguanosine Diphosphate

All present enzymatic activity of Human Dna Polymerase Beta Ternary Complex with Templating Cytosine and Incoming Deoxyguanosine Diphosphate:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta Ternary Complex with Templating Cytosine and Incoming Deoxyguanosine Diphosphate, PDB code: 7k96 was solved by F.A.Varela, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.8, 80.4, 55.5, 90, 107.9, 90
R / Rfree (%) 18.3 / 24.6

Other elements in 7k96:

The structure of Human Dna Polymerase Beta Ternary Complex with Templating Cytosine and Incoming Deoxyguanosine Diphosphate also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms
Calcium (Ca) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Dna Polymerase Beta Ternary Complex with Templating Cytosine and Incoming Deoxyguanosine Diphosphate (pdb code 7k96). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Human Dna Polymerase Beta Ternary Complex with Templating Cytosine and Incoming Deoxyguanosine Diphosphate, PDB code: 7k96:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7k96

Go back to Sodium Binding Sites List in 7k96
Sodium binding site 1 out of 4 in the Human Dna Polymerase Beta Ternary Complex with Templating Cytosine and Incoming Deoxyguanosine Diphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Dna Polymerase Beta Ternary Complex with Templating Cytosine and Incoming Deoxyguanosine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na101

b:40.0
occ:1.00
 O T:HOH217 2.4 35.2 1.0
O6 P:DG7 2.8 30.9 1.0
O6 T:DG9 2.9 25.8 1.0
O P:HOH203 2.9 43.0 1.0
O P:HOH204 3.2 41.7 1.0
N4 P:DC8 3.2 31.6 1.0
C6 P:DG7 3.9 29.4 1.0
C6 T:DG9 4.0 27.5 1.0
N4 T:DC8 4.3 25.9 1.0
C4 T:DC8 4.4 30.5 1.0
N4 T:DC10 4.4 25.2 1.0
C5 T:DC8 4.4 27.1 1.0
C4 P:DC8 4.4 30.2 1.0
N7 P:DG7 4.4 30.9 1.0
O4 P:DT6 4.5 33.5 1.0
C5 P:DG7 4.5 32.8 1.0
C5 T:DG9 4.8 25.4 1.0
N7 T:DG9 4.8 26.6 1.0
N3 P:DC8 4.9 30.3 1.0
C7 P:DT6 5.0 28.2 1.0

Sodium binding site 2 out of 4 in 7k96

Go back to Sodium Binding Sites List in 7k96
Sodium binding site 2 out of 4 in the Human Dna Polymerase Beta Ternary Complex with Templating Cytosine and Incoming Deoxyguanosine Diphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Dna Polymerase Beta Ternary Complex with Templating Cytosine and Incoming Deoxyguanosine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:27.9
occ:1.00
 OP1 P:DG9 2.2 24.9 1.0
O A:HOH691 2.3 26.6 1.0
O A:THR101 2.4 24.0 1.0
O A:VAL103 2.5 30.1 1.0
O A:ILE106 2.7 27.7 1.0
P P:DG9 3.2 26.8 1.0
OP2 P:DG9 3.2 26.7 1.0
C A:THR101 3.5 23.8 1.0
C A:VAL103 3.6 26.7 1.0
C A:ILE106 3.7 21.2 1.0
N A:ILE106 3.9 18.7 1.0
N A:GLY105 3.9 24.1 1.0
CA A:SER104 4.2 24.3 1.0
CA A:THR101 4.2 21.0 1.0
N A:VAL103 4.3 25.8 1.0
N A:SER104 4.3 24.6 1.0
O5' P:DG9 4.3 35.2 1.0
O3' P:DC8 4.3 28.0 1.0
CA A:ILE106 4.4 19.2 1.0
C A:ARG102 4.4 28.1 1.0
C A:SER104 4.4 24.7 1.0
N A:ARG102 4.5 23.6 1.0
CA A:VAL103 4.6 25.2 1.0
N A:GLY107 4.6 21.7 1.0
CA A:ARG102 4.7 28.5 1.0
C A:GLY105 4.7 23.9 1.0
CB A:THR101 4.7 19.6 1.0
O A:ARG102 4.8 36.5 1.0
CA A:GLY105 4.8 24.0 1.0
CA A:GLY107 4.9 19.5 1.0
CB A:ILE106 4.9 23.7 1.0

Sodium binding site 3 out of 4 in 7k96

Go back to Sodium Binding Sites List in 7k96
Sodium binding site 3 out of 4 in the Human Dna Polymerase Beta Ternary Complex with Templating Cytosine and Incoming Deoxyguanosine Diphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Dna Polymerase Beta Ternary Complex with Templating Cytosine and Incoming Deoxyguanosine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:31.4
occ:1.00
 O A:LYS60 2.3 27.0 1.0
O D:HOH106 2.4 38.7 1.0
O A:HOH709 2.4 37.9 1.0
O A:VAL65 2.4 29.8 1.0
O A:LEU62 2.6 27.0 1.0
OP1 D:DC3 2.8 28.7 1.0
C A:LYS60 3.4 30.0 1.0
C A:VAL65 3.6 25.1 1.0
C A:LEU62 3.6 28.5 1.0
P D:DC3 3.8 30.9 1.0
OP2 D:DC3 3.9 26.3 1.0
N A:VAL65 4.0 21.2 1.0
C A:LYS61 4.1 33.1 1.0
N A:LEU62 4.2 25.1 1.0
CA A:LYS60 4.2 28.4 1.0
CA A:VAL65 4.2 21.4 1.0
CG A:LYS60 4.2 31.0 1.0
CA A:PRO63 4.3 26.2 1.0
O A:LYS61 4.3 31.4 1.0
N A:PRO63 4.3 27.4 1.0
N A:GLY64 4.4 25.8 1.0
N A:LYS61 4.4 33.9 1.0
CB A:VAL65 4.4 27.5 1.0
CA A:LYS61 4.5 30.9 1.0
CA A:LEU62 4.5 30.8 1.0
N A:GLY66 4.6 25.4 1.0
C A:PRO63 4.7 29.1 1.0
O3' D:DT2 4.8 27.2 1.0
CB A:LYS60 4.9 28.6 1.0
CA A:GLY66 4.9 24.8 1.0
O A:ALA59 5.0 29.9 1.0
O5' D:DC3 5.0 30.4 1.0

Sodium binding site 4 out of 4 in 7k96

Go back to Sodium Binding Sites List in 7k96
Sodium binding site 4 out of 4 in the Human Dna Polymerase Beta Ternary Complex with Templating Cytosine and Incoming Deoxyguanosine Diphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Dna Polymerase Beta Ternary Complex with Templating Cytosine and Incoming Deoxyguanosine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na507

b:57.9
occ:1.00
 OD1 A:ASP92 2.6 56.7 1.0
O A:GLN90 2.6 36.1 1.0
O A:HOH714 2.6 58.3 1.0
O A:HOH708 2.6 44.5 1.0
CG A:ASP92 3.1 48.7 1.0
O A:HOH677 3.2 47.3 1.0
C A:GLN90 3.2 36.4 1.0
N A:ASP92 3.4 38.9 1.0
OD2 A:ASP92 3.7 54.6 1.0
CA A:ASP92 3.7 38.3 1.0
CA A:GLN90 3.9 36.4 1.0
C A:ASP91 3.9 38.1 1.0
CB A:ASP92 3.9 39.5 1.0
N A:ASP91 4.0 32.6 1.0
O A:HOH720 4.1 31.9 1.0
CA A:ASP91 4.3 31.4 1.0
O A:ASP91 4.5 31.2 1.0
O A:ARG89 4.6 36.8 1.0
CB A:GLN90 4.8 34.6 1.0

Reference:

F.A.Varela, B.D.Freudenthal. Mechanism of Deoxyguanosine Diphosphate Insertion By Human Dna Polymerase Beta. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 33475337
DOI: 10.1021/ACS.BIOCHEM.0C00847
Page generated: Mon Aug 18 10:20:52 2025

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