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Sodium in PDB 7s9q: Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog, PDB code: 7s9q was solved by B.D.Freudenthal, B.J.Ryan, M.R.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.15 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.624, 78.583, 54.916, 90, 112.44, 90
R / Rfree (%) 19.3 / 24.7

Other elements in 7s9q:

The structure of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog also contains other interesting chemical elements:

Manganese (Mn) 3 atoms
Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog (pdb code 7s9q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog, PDB code: 7s9q:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7s9q

Go back to Sodium Binding Sites List in 7s9q
Sodium binding site 1 out of 3 in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:20.9
occ:1.00
 OP1 P:DG9 2.4 14.1 1.0
O A:THR101 2.4 13.3 1.0
O A:ILE106 2.4 12.3 1.0
O A:VAL103 2.5 11.9 1.0
O A:HOH708 2.6 23.9 1.0
O P:HOH119 2.6 15.5 1.0
C A:ILE106 3.3 14.4 1.0
C A:THR101 3.3 15.7 1.0
C A:VAL103 3.4 14.8 1.0
P P:DG9 3.4 15.8 1.0
OP2 P:DG9 3.7 11.1 1.0
O A:HOH585 3.7 27.6 1.0
CA A:THR101 3.7 14.7 1.0
N A:ILE106 3.7 9.3 1.0
CA A:SER104 4.0 14.5 1.0
N A:GLY105 4.0 11.0 1.0
CA A:ILE106 4.1 10.1 1.0
N A:SER104 4.1 14.3 1.0
N A:GLY107 4.2 15.4 1.0
N A:VAL103 4.2 15.2 1.0
CB A:THR101 4.3 17.9 1.0
C A:SER104 4.4 16.8 1.0
CA A:GLY107 4.4 15.6 1.0
N A:ARG102 4.5 17.0 1.0
CA A:VAL103 4.5 16.9 1.0
O A:HOH809 4.5 28.2 1.0
O3' P:DC8 4.5 21.6 1.0
C A:ARG102 4.5 16.7 1.0
CB A:ILE106 4.5 12.4 1.0
O5' P:DG9 4.5 17.4 1.0
C A:GLY105 4.7 12.0 1.0
O A:LEU100 4.8 15.4 1.0
CA A:ARG102 4.8 19.1 1.0
CA A:GLY105 4.9 15.3 1.0
O A:HOH512 5.0 25.7 1.0

Sodium binding site 2 out of 3 in 7s9q

Go back to Sodium Binding Sites List in 7s9q
Sodium binding site 2 out of 3 in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:30.2
occ:1.00
 O D:HOH117 2.5 31.0 1.0
O A:HOH786 2.9 30.0 1.0
N A:HIS34 3.0 12.7 1.0
C A:ALA32 3.3 19.6 1.0
CA A:ALA32 3.3 16.0 1.0
CB A:HIS34 3.3 17.3 1.0
CB A:ALA32 3.4 18.0 1.0
N A:ILE33 3.5 14.6 1.0
CD2 A:HIS34 3.6 16.4 1.0
N A:LYS35 3.6 18.1 1.0
CA A:HIS34 3.6 15.1 1.0
CG A:HIS34 3.7 20.5 1.0
O A:ALA32 3.8 13.9 1.0
C A:HIS34 4.0 15.1 1.0
C A:ILE33 4.1 15.9 1.0
CA A:ILE33 4.4 18.2 1.0
CG A:LYS35 4.5 17.4 1.0
O A:HOH648 4.6 30.8 1.0
N A:ALA32 4.8 20.1 1.0
CB A:LYS35 4.8 10.8 1.0
CA A:LYS35 4.8 13.8 1.0
CG2 A:ILE33 4.8 19.7 1.0
NE2 A:HIS34 4.8 25.4 1.0
O6 D:DG1 4.9 21.4 1.0

Sodium binding site 3 out of 3 in 7s9q

Go back to Sodium Binding Sites List in 7s9q
Sodium binding site 3 out of 3 in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:20.3
occ:1.00
 O A:HOH701 2.3 22.2 1.0
O A:VAL65 2.4 20.3 1.0
O A:LYS60 2.4 18.1 1.0
OP1 D:DC3 2.4 16.2 1.0
O A:LEU62 2.5 16.9 1.0
O A:HOH505 2.7 20.3 1.0
O D:HOH120 3.0 43.6 1.0
C A:VAL65 3.5 21.6 1.0
C A:LEU62 3.5 20.5 1.0
C A:LYS60 3.5 19.8 1.0
P D:DC3 3.5 18.3 1.0
O A:HOH733 3.6 33.9 1.0
OP2 D:DC3 3.8 16.2 1.0
N A:VAL65 3.9 16.3 1.0
O D:HOH118 4.0 29.2 1.0
N A:LEU62 4.0 18.3 1.0
CA A:VAL65 4.1 13.6 1.0
C A:LYS61 4.2 23.4 1.0
CA A:PRO63 4.2 22.1 1.0
N A:PRO63 4.2 18.8 1.0
N A:GLY64 4.2 18.9 1.0
CA A:LYS60 4.3 15.6 1.0
CA A:LEU62 4.4 18.5 1.0
O A:LYS61 4.5 23.1 1.0
CB A:VAL65 4.5 22.0 1.0
CG A:LYS60 4.5 27.7 1.0
N A:GLY66 4.5 21.0 1.0
N A:LYS61 4.5 19.6 1.0
O5' D:DC3 4.6 17.0 1.0
C A:PRO63 4.6 20.6 1.0
O3' D:DT2 4.6 18.8 1.0
CA A:LYS61 4.6 14.9 1.0
NZ A:LYS60 4.7 26.2 1.0
CA A:GLY66 4.7 18.4 1.0
C A:GLY64 4.8 16.3 1.0
CD A:LYS60 4.9 31.2 1.0
O A:ALA59 4.9 16.9 1.0
CB A:LYS60 5.0 21.3 1.0

Reference:

B.J.Ryan, H.Yang, J.H.T.Bacurio, M.R.Smith, A.K.Basu, M.M.Greenberg, B.D.Freudenthal. Structural Dynamics of A Common Mutagenic Oxidative Dna Lesion in Duplex Dna and During Dna Replication. J.Am.Chem.Soc. V. 144 8054 2022.
ISSN: ESSN 1520-5126
PubMed: 35499923
DOI: 10.1021/JACS.2C00193
Page generated: Mon Aug 18 11:55:31 2025

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