Sodium in PDB 4o5c: Structure of Human Dna Polymerase Complexed with N7-Mg As the Template Base in A 1-Nucleotide Gapped Dna

All present enzymatic activity of Structure of Human Dna Polymerase Complexed with N7-Mg As the Template Base in A 1-Nucleotide Gapped Dna:
2.7.7.7;

The structure of Structure of Human Dna Polymerase Complexed with N7-Mg As the Template Base in A 1-Nucleotide Gapped Dna, PDB code: 4o5c 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)	19.94 / 2.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.396, 79.758, 54.830, 90.00, 105.54, 90.00
R / Rfree (%)	20 / 24.5

The structure of Structure of Human Dna Polymerase Complexed with N7-Mg As the Template Base in A 1-Nucleotide Gapped Dna also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Complexed with N7-Mg As the Template Base in A 1-Nucleotide Gapped Dna (pdb code 4o5c). 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 Complexed with N7-Mg As the Template Base in A 1-Nucleotide Gapped Dna, PDB code: 4o5c:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Complexed with N7-Mg 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 Complexed with N7-Mg As the Template Base in A 1-Nucleotide Gapped Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:19.3 occ:1.00 O A:THR101 2.3 20.2 1.0 OP1 P:DG9 2.3 13.4 1.0 O A:ILE106 2.5 13.0 1.0 O A:VAL103 2.5 14.6 1.0 O P:HOH101 2.8 10.5 1.0 C A:ILE106 3.3 14.7 1.0 C A:THR101 3.3 16.2 1.0 P P:DG9 3.3 10.6 1.0 O A:HOH506 3.4 21.6 1.0 C A:VAL103 3.5 15.7 1.0 OP2 P:DG9 3.5 16.0 1.0 N A:ILE106 3.7 11.6 1.0 CA A:THR101 4.0 14.1 1.0 N A:GLY105 4.0 9.1 1.0 CA A:SER104 4.0 12.0 1.0 CA A:ILE106 4.0 9.5 1.0 N A:SER104 4.1 16.5 1.0 N A:GLY107 4.2 13.5 1.0 N A:VAL103 4.3 12.5 1.0 C A:SER104 4.4 11.6 1.0 N A:ARG102 4.4 17.8 1.0 O3' P:DC8 4.4 15.4 1.0 C A:ARG102 4.4 17.1 1.0 CB A:ILE106 4.5 13.4 1.0 O5' P:DG9 4.5 11.7 1.0 CA A:VAL103 4.5 14.7 1.0 CA A:GLY107 4.5 14.7 1.0 CB A:THR101 4.5 15.2 1.0 C A:GLY105 4.6 10.5 1.0 CA A:ARG102 4.7 19.2 1.0 CA A:GLY105 4.9 9.4 1.0 O A:ARG102 4.9 15.7 1.0 O A:LEU100 5.0 14.7 1.0

Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Complexed with N7-Mg 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 Complexed with N7-Mg As the Template Base in A 1-Nucleotide Gapped Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:35.3 occ:1.00 O A:VAL65 2.6 29.0 1.0 OP1 D:DC3 2.6 25.9 1.0 O A:LYS60 2.6 32.7 1.0 OP2 D:DC3 3.3 19.1 1.0 O A:LEU62 3.3 32.4 1.0 P D:DC3 3.4 21.2 1.0 C A:VAL65 3.7 20.4 1.0 C A:LYS60 3.8 30.2 1.0 CG A:LYS60 4.3 26.9 1.0 C A:LEU62 4.3 29.4 1.0 N A:VAL65 4.4 16.4 1.0 NZ A:LYS60 4.5 30.4 1.0 N A:GLY66 4.5 19.1 1.0 CA A:GLY66 4.5 15.6 1.0 CA A:VAL65 4.6 17.3 1.0 O3' D:DT2 4.6 22.9 1.0 CA A:LYS60 4.6 23.5 1.0 O5' D:DC3 4.6 24.0 1.0 N A:GLY64 4.7 26.6 1.0 C A:LYS61 4.8 33.0 1.0 CA A:PRO63 4.8 28.4 1.0 N A:LYS61 4.9 32.5 1.0 O A:LYS61 4.9 34.1 1.0 N A:PRO63 5.0 29.0 1.0 N A:LEU62 5.0 29.4 1.0 CB A:VAL65 5.0 20.8 1.0

M.C.Koag, Y.Kou, H.Ouzon-Shubeita, S.Lee. Transition-State Destabilization Reveals How Human Dna Polymerase Beta Proceeds Across the Chemically Unstable Lesion N7-Methylguanine. Nucleic Acids Res. V. 42 8755 2014.
ISSN: ISSN 0305-1048
PubMed: 24966350
DOI: 10.1093/NAR/GKU554