Sodium in PDB 7s9m: Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Da

All present enzymatic activity of Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Da:
2.7.7.7;

The structure of Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Da, PDB code: 7s9m 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)	24.87 / 2.31
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.303, 80.841, 56.507, 90, 109.04, 90
R / Rfree (%)	21.8 / 30

The binding sites of Sodium atom in the Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Da (pdb code 7s9m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Da, PDB code: 7s9m:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Da


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:23.5 occ:1.00 O A:THR101 2.3 25.9 1.0 O A:ILE106 2.4 20.5 1.0 O A:VAL103 2.4 26.6 1.0 OP1 P:DG9 2.5 22.0 1.0 O P:HOH206 2.5 23.3 1.0 O A:HOH518 2.7 30.1 1.0 C A:THR101 3.2 20.9 1.0 C A:VAL103 3.3 25.6 1.0 C A:ILE106 3.5 20.5 1.0 O A:HOH527 3.5 21.4 1.0 P P:DG9 3.5 21.4 1.0 OP2 P:DG9 3.7 23.4 1.0 NA A:NA403 3.7 30.1 1.0 CA A:THR101 3.8 17.2 1.0 N A:ILE106 3.8 19.6 1.0 CA A:SER104 3.9 18.9 1.0 N A:SER104 4.0 24.1 1.0 N A:VAL103 4.1 22.9 1.0 CA A:ILE106 4.1 15.7 1.0 N A:GLY105 4.2 20.7 1.0 C A:ARG102 4.2 23.8 1.0 N A:ARG102 4.2 24.1 1.0 CB A:THR101 4.3 19.9 1.0 CA A:VAL103 4.4 23.7 1.0 C A:SER104 4.4 19.7 1.0 CB A:ILE106 4.5 19.9 1.0 CA A:ARG102 4.5 21.4 1.0 N A:GLY107 4.5 18.1 1.0 O5' P:DG9 4.5 19.8 1.0 O A:ARG102 4.6 27.5 1.0 CA A:GLY107 4.8 17.9 1.0 O3' P:DC8 4.8 21.3 1.0 O A:LEU100 4.8 23.0 1.0 C A:GLY105 4.8 23.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Da


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:33.3 occ:1.00 O A:LYS60 2.6 33.7 1.0 O A:VAL65 2.7 32.4 1.0 O A:LEU62 2.7 32.2 1.0 OP1 D:DC3 3.0 27.8 1.0 OP2 D:DC3 3.3 28.4 1.0 P D:DC3 3.6 30.7 1.0 C A:LYS60 3.8 31.9 1.0 C A:VAL65 3.8 29.2 1.0 C A:LEU62 3.9 30.6 1.0 O A:LYS61 4.1 43.8 1.0 CG A:LYS60 4.3 30.4 1.0 C A:LYS61 4.3 30.5 1.0 CA A:PRO63 4.4 27.4 1.0 N A:GLY64 4.4 28.3 1.0 N A:VAL65 4.5 26.4 1.0 CA A:LYS60 4.5 29.4 1.0 N A:PRO63 4.6 26.2 1.0 N A:GLY66 4.7 29.4 1.0 O3' D:DT2 4.7 27.4 1.0 N A:LEU62 4.7 25.9 1.0 CA A:VAL65 4.7 22.4 1.0 CA A:GLY66 4.7 24.7 1.0 N A:LYS61 4.8 33.2 1.0 C A:PRO63 4.8 28.8 1.0 CA A:LYS61 4.9 32.8 1.0 O5' D:DC3 4.9 22.9 1.0 CA A:LEU62 4.9 25.6 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Da


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Dna Polymerase Beta with Ring Open Intermediate Fapy-Dg Base-Paired with A Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:30.1 occ:1.00 O A:HOH518 2.2 30.1 1.0 O P:HOH206 2.6 23.3 1.0 O A:HOH526 2.6 38.4 1.0 O A:THR101 2.8 25.9 1.0 NZ A:LYS27 3.2 28.8 1.0 NA A:NA401 3.7 23.5 1.0 C A:THR101 3.7 20.9 1.0 OG1 A:THR101 4.1 23.3 1.0 O A:HOH527 4.2 21.4 1.0 CB A:THR101 4.4 19.9 1.0 N A:ARG102 4.4 24.1 1.0 CA A:ARG102 4.4 21.4 1.0 OD1 A:ASN28 4.6 26.5 1.0 CA A:THR101 4.7 17.2 1.0 CE A:LYS27 4.7 30.0 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