Sodium in PDB 7s9p: Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp Analog

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

The structure of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp Analog, PDB code: 7s9p 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)	24.50 / 1.86
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.673, 79.621, 55.347, 90, 108.02, 90
R / Rfree (%)	17.6 / 22.8

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

Chlorine	(Cl)	2 atoms
Manganese	(Mn)	3 atoms

The binding sites of Sodium atom in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp Analog (pdb code 7s9p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp Analog, PDB code: 7s9p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp 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 Dctp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:24.2 occ:1.00 O A:LYS60 2.4 26.9 1.0 O A:HOH763 2.4 36.3 1.0 O A:VAL65 2.4 22.8 1.0 O A:LEU62 2.5 26.6 1.0 O D:HOH106 2.6 27.5 1.0 OP1 D:DC3 2.7 23.5 1.0 C A:LYS60 3.4 26.0 1.0 C A:LEU62 3.4 24.7 1.0 C A:VAL65 3.6 20.2 1.0 P D:DC3 3.7 27.0 1.0 OP2 D:DC3 3.8 24.3 1.0 N A:LEU62 4.0 24.4 1.0 C A:LYS61 4.0 30.1 1.0 N A:VAL65 4.0 24.0 1.0 CA A:PRO63 4.2 30.7 1.0 N A:PRO63 4.2 30.5 1.0 CA A:LYS60 4.2 22.5 1.0 N A:GLY64 4.3 24.8 1.0 CA A:VAL65 4.3 21.2 1.0 N A:LYS61 4.3 26.4 1.0 CG A:LYS60 4.3 27.8 1.0 O A:LYS61 4.3 30.2 1.0 CA A:LEU62 4.3 23.2 1.0 CA A:LYS61 4.4 27.8 1.0 CB A:VAL65 4.5 17.5 1.0 N A:GLY66 4.6 20.6 1.0 C A:PRO63 4.6 28.4 1.0 O3' D:DT2 4.8 28.6 1.0 CA A:GLY66 4.8 22.3 1.0 O5' D:DC3 4.9 35.5 1.0 CB A:LYS60 4.9 23.4 1.0 O A:ALA59 4.9 18.9 1.0 C A:GLY64 4.9 26.6 1.0

Sodium binding site 2 out of 2 in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp 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 Dctp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:16.5 occ:1.00 O A:THR101 2.3 14.6 1.0 O A:ILE106 2.4 12.2 1.0 OP1 P:DG9 2.4 13.9 1.0 O A:VAL103 2.4 11.2 1.0 O P:HOH105 2.6 21.3 1.0 O A:HOH760 2.7 17.4 1.0 C A:THR101 3.3 14.7 1.0 C A:VAL103 3.4 13.4 1.0 P P:DG9 3.4 18.3 1.0 C A:ILE106 3.4 13.7 1.0 OP2 P:DG9 3.6 14.3 1.0 N A:ILE106 3.8 15.1 1.0 CA A:THR101 3.9 17.3 1.0 N A:GLY105 4.0 15.0 1.0 CA A:SER104 4.0 15.6 1.0 O A:HOH743 4.0 29.4 1.0 N A:SER104 4.0 11.6 1.0 N A:VAL103 4.1 13.1 1.0 CA A:ILE106 4.1 12.9 1.0 C A:ARG102 4.3 17.0 1.0 C A:SER104 4.3 13.0 1.0 N A:ARG102 4.4 12.4 1.0 O3' P:DC8 4.4 14.6 1.0 CA A:VAL103 4.4 14.6 1.0 N A:GLY107 4.5 13.8 1.0 CB A:THR101 4.5 14.7 1.0 CB A:ILE106 4.5 12.3 1.0 CA A:ARG102 4.6 14.3 1.0 C A:GLY105 4.6 16.0 1.0 O5' P:DG9 4.7 16.4 1.0 O A:ARG102 4.7 16.1 1.0 CA A:GLY107 4.8 15.4 1.0 O A:LEU100 4.9 11.2 1.0 CA A:GLY105 4.9 14.9 1.0

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