Sodium in PDB 7s9o: Binary Complex of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg in the Template Position

All present enzymatic activity of Binary Complex of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg in the Template Position:
2.7.7.7;

The structure of Binary Complex of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg in the Template Position, PDB code: 7s9o was solved by B.D.Freudenthal, B.J.Ryan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.55 / 2.23
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.727, 78.826, 54.949, 90, 105.89, 90
R / Rfree (%)	20.2 / 27.8

The binding sites of Sodium atom in the Binary Complex of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg in the Template Position (pdb code 7s9o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Binary Complex of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg in the Template Position, PDB code: 7s9o:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Binary Complex of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg in the Template Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Binary Complex of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg in the Template Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:26.1 occ:1.00 OP1 P:DG9 2.3 24.4 1.0 O A:THR101 2.4 27.8 1.0 O A:ILE106 2.6 23.1 1.0 NA A:NA403 2.6 35.3 1.0 NA A:NA402 2.8 30.1 1.0 O P:HOH105 2.8 12.6 1.0 O A:VAL103 2.8 25.5 1.0 P P:DG9 3.3 21.8 1.0 OP2 P:DG9 3.4 25.8 1.0 C A:THR101 3.5 24.0 1.0 C A:VAL103 3.5 24.2 1.0 CA A:SER104 3.7 21.7 1.0 C A:ILE106 3.7 20.3 1.0 N A:SER104 3.9 25.3 1.0 N A:GLY105 4.0 23.1 1.0 N A:ILE106 4.1 17.6 1.0 CA A:THR101 4.1 26.3 1.0 C A:SER104 4.3 20.9 1.0 O5' P:DG9 4.3 22.9 1.0 N A:VAL103 4.4 24.2 1.0 C A:ARG102 4.4 22.7 1.0 CA A:ILE106 4.5 16.6 1.0 O3' P:DC8 4.5 18.9 1.0 N A:ARG102 4.5 24.0 1.0 N A:GLY107 4.6 19.6 1.0 CB A:THR101 4.6 23.0 1.0 CA A:VAL103 4.6 23.4 1.0 O A:ARG102 4.6 22.2 1.0 O A:HOH510 4.6 27.8 1.0 CA A:ARG102 4.7 22.7 1.0 CA A:GLY107 4.8 20.9 1.0 CB A:SER104 4.8 28.5 1.0 C A:GLY105 4.8 20.5 1.0 CB A:ILE106 4.9 20.6 1.0 CA A:GLY105 5.0 22.2 1.0

Sodium binding site 2 out of 3 in the Binary Complex of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg in the Template Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Binary Complex of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg in the Template Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:30.1 occ:1.00 O P:HOH105 2.3 12.6 1.0 O A:HOH528 2.6 26.9 1.0 NA A:NA401 2.8 26.1 1.0 O A:THR101 2.8 27.8 1.0 O A:HOH510 2.9 27.8 1.0 NA A:NA403 3.0 35.3 1.0 C A:THR101 3.9 24.0 1.0 CA A:ARG102 4.4 22.7 1.0 OP1 P:DG9 4.4 24.4 1.0 OP2 P:DG9 4.5 25.8 1.0 O A:ARG102 4.6 22.2 1.0 C A:ARG102 4.6 22.7 1.0 N A:ARG102 4.6 24.0 1.0 OG1 A:THR101 4.7 17.2 1.0 CB A:THR101 4.8 23.0 1.0 NZ A:LYS27 4.9 30.6 1.0 P P:DG9 4.9 21.8 1.0 CA A:THR101 5.0 26.3 1.0 O A:ILE106 5.0 23.1 1.0

Sodium binding site 3 out of 3 in the Binary Complex of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg in the Template Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Binary Complex of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg in the Template Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:35.3 occ:1.00 NA A:NA401 2.6 26.1 1.0 OP2 P:DG9 2.6 25.8 1.0 NA A:NA402 3.0 30.1 1.0 O A:ILE106 3.2 23.1 1.0 O A:THR101 3.3 27.8 1.0 O A:HOH510 3.5 27.8 1.0 CB A:THR101 3.7 23.0 1.0 P P:DG9 3.7 21.8 1.0 CA A:GLY107 3.7 20.9 1.0 OP1 P:DG9 3.8 24.4 1.0 C A:THR101 4.1 24.0 1.0 C A:ILE106 4.1 20.3 1.0 CA A:THR101 4.2 26.3 1.0 OG1 A:THR101 4.2 17.2 1.0 CE A:LYS27 4.3 39.3 1.0 N A:GLY107 4.4 19.6 1.0 O P:HOH105 4.4 12.6 1.0 C A:GLY107 4.6 24.5 1.0 CG2 A:THR101 4.7 20.6 1.0 OD1 A:ASN28 4.7 28.7 1.0 O5' P:DG9 4.8 22.9 1.0 O3' P:DC8 4.8 18.9 1.0 CD A:PRO108 4.8 24.5 1.0 N A:PRO108 4.9 28.0 1.0 NZ A:LYS27 5.0 30.6 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