Sodium in PDB 6e3r: Structure of Human Dna Polymerase Beta Complexed with 8OA As the Template Base in A 1-Nucleotide Gapped Dna

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8OA As the Template Base in A 1-Nucleotide Gapped Dna:
2.7.7.7;

The structure of Structure of Human Dna Polymerase Beta Complexed with 8OA As the Template Base in A 1-Nucleotide Gapped Dna, PDB code: 6e3r was solved by M.-C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.76 / 2.26
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.572, 79.048, 54.966, 90.00, 105.75, 90.00
R / Rfree (%)	20.4 / 27.2

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with 8OA As the Template Base in A 1-Nucleotide Gapped Dna (pdb code 6e3r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Human Dna Polymerase Beta Complexed with 8OA As the Template Base in A 1-Nucleotide Gapped Dna, PDB code: 6e3r:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8OA As the Template Base in A 1-Nucleotide Gapped Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Dna Polymerase Beta Complexed with 8OA As the Template Base in A 1-Nucleotide Gapped Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:26.0 occ:1.00 O A:THR101 2.3 21.0 1.0 O P:HOH106 2.3 16.4 1.0 O A:ILE106 2.4 21.8 1.0 OP1 P:DG9 2.4 23.2 1.0 O A:VAL103 2.4 25.3 1.0 O P:HOH112 2.6 21.8 1.0 O A:HOH505 3.0 23.6 1.0 C A:THR101 3.3 21.0 1.0 C A:VAL103 3.4 25.2 1.0 C A:ILE106 3.4 20.5 1.0 P P:DG9 3.5 23.0 1.0 N A:ILE106 3.7 20.5 1.0 OP2 P:DG9 3.7 22.4 1.0 CA A:THR101 3.9 20.6 1.0 CA A:SER104 4.0 18.2 1.0 N A:SER104 4.0 22.0 1.0 N A:VAL103 4.1 22.6 1.0 CA A:ILE106 4.1 20.5 1.0 N A:GLY105 4.2 16.3 1.0 CB A:THR101 4.3 20.3 1.0 N A:GLY107 4.3 21.4 1.0 C A:ARG102 4.3 22.8 1.0 CA A:VAL103 4.3 23.4 1.0 N A:ARG102 4.4 22.4 1.0 C A:SER104 4.4 17.3 1.0 CA A:GLY107 4.5 22.2 1.0 O3' P:DC8 4.5 21.2 1.0 CB A:ILE106 4.6 21.7 1.0 CA A:ARG102 4.6 21.6 1.0 O5' P:DG9 4.6 21.6 1.0 C A:GLY105 4.6 19.1 1.0 O A:ARG102 4.7 22.7 1.0 CA A:GLY105 5.0 18.5 1.0

Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8OA As the Template Base in A 1-Nucleotide Gapped Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Dna Polymerase Beta Complexed with 8OA As the Template Base in A 1-Nucleotide Gapped Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:34.6 occ:1.00 O D:HOH105 2.1 32.4 1.0 O A:LYS60 2.4 38.9 1.0 O A:HOH547 2.4 34.9 1.0 O A:VAL65 2.4 32.4 1.0 O A:LEU62 2.5 38.9 1.0 OP1 D:DC3 2.6 27.8 1.0 C A:LYS60 3.5 35.8 1.0 C A:VAL65 3.5 26.6 1.0 C A:LEU62 3.6 36.4 1.0 P D:DC3 3.6 25.5 1.0 N A:VAL65 3.8 27.7 1.0 OP2 D:DC3 3.9 24.2 1.0 N A:GLY64 4.0 29.5 1.0 C A:LYS61 4.0 35.7 1.0 N A:LEU62 4.0 34.7 1.0 CA A:VAL65 4.1 26.8 1.0 O A:LYS61 4.2 43.1 1.0 CA A:LYS60 4.3 32.4 1.0 CB A:VAL65 4.3 27.2 1.0 CA A:PRO63 4.4 34.0 1.0 N A:LYS61 4.4 34.2 1.0 CG A:LYS60 4.5 36.1 1.0 CA A:LEU62 4.5 34.5 1.0 N A:PRO63 4.5 36.3 1.0 CA A:LYS61 4.5 35.2 1.0 O3' D:DT2 4.5 27.7 1.0 N A:GLY66 4.5 24.4 1.0 C A:PRO63 4.6 31.8 1.0 C A:GLY64 4.8 28.7 1.0 CA A:GLY66 4.8 23.1 1.0 O5' D:DC3 4.8 24.7 1.0 O A:ALA59 4.9 31.5 1.0 CA A:GLY64 4.9 29.5 1.0 NZ A:LYS60 5.0 38.1 1.0 CB A:LYS60 5.0 34.9 1.0

M.C.Koag, H.Jung, S.Lee. Mutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-Oxoadenine By Human Dna Polymerases. J. Am. Chem. Soc. V. 141 4584 2019.
ISSN: ESSN 1520-5126
PubMed: 30817143
DOI: 10.1021/JACS.8B08551