Sodium in PDB 4tup: Structure of Human Dna Polymerase Beta Complexed with Gg As the Template (GG0B) in A 1-Nucleotide Gapped Dna

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with Gg As the Template (GG0B) in A 1-Nucleotide Gapped Dna:
2.7.7.7;

The structure of Structure of Human Dna Polymerase Beta Complexed with Gg As the Template (GG0B) in A 1-Nucleotide Gapped Dna, PDB code: 4tup 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)	19.81 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.354, 79.257, 54.927, 90.00, 105.42, 90.00
R / Rfree (%)	20.3 / 23.6

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with Gg As the Template (GG0B) in A 1-Nucleotide Gapped Dna (pdb code 4tup). 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 Gg As the Template (GG0B) in A 1-Nucleotide Gapped Dna, PDB code: 4tup:
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 Gg As the Template (GG0B) 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 Gg As the Template (GG0B) in A 1-Nucleotide Gapped Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:11.4 occ:1.00 O A:THR101 2.3 11.8 1.0 O A:ILE106 2.4 11.8 1.0 OP1 P:DG9 2.4 12.6 1.0 O A:HOH560 2.4 14.8 1.0 O A:VAL103 2.5 13.3 1.0 O P:HOH103 2.6 13.6 1.0 O A:HOH562 3.2 16.3 1.0 C A:THR101 3.3 13.8 1.0 C A:VAL103 3.4 14.5 1.0 C A:ILE106 3.4 13.4 1.0 P P:DG9 3.5 13.3 1.0 OP2 P:DG9 3.7 12.7 1.0 N A:ILE106 3.8 11.8 1.0 CA A:THR101 3.9 11.1 1.0 CA A:SER104 4.0 12.5 1.0 N A:SER104 4.1 12.2 1.0 N A:GLY105 4.1 11.4 1.0 CA A:ILE106 4.1 10.6 1.0 N A:VAL103 4.1 11.4 1.0 C A:ARG102 4.3 14.0 1.0 N A:ARG102 4.3 12.6 1.0 CB A:THR101 4.4 12.8 1.0 C A:SER104 4.4 11.8 1.0 CA A:VAL103 4.4 11.7 1.0 N A:GLY107 4.4 11.4 1.0 O3' P:DG8 4.5 11.4 1.0 CB A:ILE106 4.5 12.3 1.0 CA A:ARG102 4.6 12.8 1.0 O5' P:DG9 4.6 13.3 1.0 CA A:GLY107 4.7 14.7 1.0 O A:ARG102 4.7 14.4 1.0 C A:GLY105 4.7 12.8 1.0 O A:LEU100 4.9 11.7 1.0 CA A:GLY105 5.0 10.0 1.0

Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with Gg As the Template (GG0B) 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 Gg As the Template (GG0B) in A 1-Nucleotide Gapped Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:23.9 occ:1.00 O A:VAL65 2.4 23.4 1.0 O D:HOH106 2.4 26.2 1.0 O A:LYS60 2.4 25.9 1.0 O A:HOH606 2.4 26.2 1.0 O A:LEU62 2.5 24.5 1.0 OP1 D:DG3 2.7 24.2 1.0 C A:LEU62 3.5 25.0 1.0 C A:LYS60 3.5 28.0 1.0 C A:VAL65 3.5 20.3 1.0 P D:DG3 3.7 20.9 1.0 OP2 D:DG3 3.9 16.2 1.0 N A:VAL65 4.0 20.7 1.0 N A:LEU62 4.1 23.9 1.0 CA A:PRO63 4.2 22.5 1.0 N A:GLY64 4.2 20.2 1.0 CA A:VAL65 4.2 19.6 1.0 C A:LYS61 4.2 26.4 1.0 N A:PRO63 4.2 24.8 1.0 CA A:LYS60 4.2 22.6 1.0 CG A:LYS60 4.3 29.6 1.0 CA A:LEU62 4.4 23.9 1.0 N A:LYS61 4.5 25.4 1.0 CB A:VAL65 4.5 21.3 1.0 O A:LYS61 4.5 26.2 1.0 N A:GLY66 4.5 17.5 1.0 C A:PRO63 4.6 22.8 1.0 CA A:LYS61 4.6 25.9 1.0 O3' D:DT2 4.7 18.5 1.0 CA A:GLY66 4.7 18.8 1.0 CB A:LYS60 4.9 24.8 1.0 C A:GLY64 4.9 22.7 1.0 O A:ALA59 5.0 23.9 1.0 O5' D:DG3 5.0 23.3 1.0

M.C.Koag, L.Lai, S.Lee. Structural Basis For the Inefficient Nucleotide Incorporation Opposite Cisplatin-Dna Lesion By Human Dna Polymerase Beta J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25237188
DOI: 10.1074/JBC.M114.605451