Sodium in PDB 4tuq: Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B).

All present enzymatic activity of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B).:
2.7.7.7;

The structure of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B)., PDB code: 4tuq 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)	19.85 / 2.37
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.820, 80.542, 55.535, 90.00, 107.69, 90.00
R / Rfree (%)	19.8 / 25.9

The structure of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B). also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B). (pdb code 4tuq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B)., PDB code: 4tuq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B).


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B). within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:28.1 occ:1.00 O A:THR101 2.4 31.2 1.0 OP1 P:DG9 2.4 26.2 1.0 O P:HOH101 2.5 30.5 1.0 O A:VAL103 2.6 26.3 1.0 O A:ILE106 2.6 25.8 1.0 O A:HOH539 2.6 24.2 1.0 C A:THR101 3.3 26.9 1.0 P P:DG9 3.3 23.2 1.0 C A:VAL103 3.4 18.8 1.0 OP2 P:DG9 3.4 31.9 1.0 C A:ILE106 3.5 26.7 1.0 N A:ILE106 3.8 25.3 1.0 CA A:SER104 3.8 22.4 1.0 N A:GLY105 3.9 21.6 1.0 N A:SER104 4.0 18.5 1.0 CA A:THR101 4.0 26.1 1.0 CA A:ILE106 4.1 22.2 1.0 N A:VAL103 4.2 22.6 1.0 C A:SER104 4.2 23.3 1.0 C A:ARG102 4.3 22.2 1.0 N A:ARG102 4.3 23.0 1.0 O3' P:DG8 4.4 23.6 1.0 CA A:VAL103 4.4 22.8 1.0 CB A:ILE106 4.5 24.6 1.0 N A:GLY107 4.5 23.5 1.0 O5' P:DG9 4.5 26.0 1.0 CA A:ARG102 4.5 26.6 1.0 C A:GLY105 4.6 24.2 1.0 CB A:THR101 4.7 22.3 1.0 O A:ARG102 4.8 22.4 1.0 CA A:GLY105 4.8 24.6 1.0 CA A:GLY107 4.9 24.4 1.0 O A:LEU100 4.9 23.4 1.0

Sodium binding site 2 out of 2 in the Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B).


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Dna Polymerase Beta Inserting Dcmpnpp Opposite Gg Template (GG0B). within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:29.4 occ:1.00 O A:LYS60 2.4 35.2 1.0 O A:HOH521 2.5 28.1 1.0 O A:LEU62 2.5 33.0 1.0 OP1 D:DG3 2.5 30.0 1.0 O A:VAL65 2.5 29.8 1.0 C A:VAL65 3.5 30.2 1.0 C A:LEU62 3.5 32.0 1.0 C A:LYS60 3.5 32.2 1.0 P D:DG3 3.6 31.9 1.0 OP2 D:DG3 3.8 34.2 1.0 N A:VAL65 3.8 23.4 1.0 O D:HOH102 4.0 30.8 1.0 N A:GLY64 4.1 25.9 1.0 CA A:VAL65 4.1 29.8 1.0 CA A:PRO63 4.1 27.8 1.0 N A:LEU62 4.2 33.5 1.0 N A:PRO63 4.2 32.6 1.0 CA A:LYS60 4.3 32.9 1.0 C A:LYS61 4.3 34.4 1.0 CG A:LYS60 4.4 37.3 1.0 N A:GLY66 4.5 29.9 1.0 CA A:LEU62 4.5 31.6 1.0 CB A:VAL65 4.5 30.3 1.0 N A:LYS61 4.5 31.7 1.0 C A:PRO63 4.6 25.0 1.0 O A:LYS61 4.6 37.9 1.0 O3' D:DT2 4.6 28.3 1.0 CA A:GLY66 4.7 28.1 1.0 CA A:LYS61 4.7 32.9 1.0 O5' D:DG3 4.7 38.4 1.0 C A:GLY64 4.8 24.4 1.0 CB A:LYS60 5.0 31.8 1.0 O A:ALA59 5.0 30.4 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