Sodium in PDB 5db8: Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Da

All present enzymatic activity of Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Da:
2.7.7.7;

The structure of Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Da, PDB code: 5db8 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)	19.73 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.149, 78.904, 54.751, 90.00, 105.39, 90.00
R / Rfree (%)	18 / 25.8

The structure of Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Da also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Da (pdb code 5db8). 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 Host-Guest Complex with the N7MG Base Paired with A Da, PDB code: 5db8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG 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 Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:22.1 occ:1.00 O A:THR101 2.2 16.2 1.0 OP1 P:DG9 2.3 15.9 1.0 O P:HOH104 2.5 15.5 1.0 O A:ILE106 2.6 18.3 1.0 O A:VAL103 2.7 15.7 1.0 O A:HOH515 2.9 15.9 1.0 C A:THR101 3.4 15.8 1.0 P P:DG9 3.4 15.3 1.0 OP2 P:DG9 3.5 19.4 1.0 C A:VAL103 3.6 15.2 1.0 C A:ILE106 3.7 15.6 1.0 CA A:SER104 3.9 13.0 1.0 CA A:THR101 4.1 17.4 1.0 N A:SER104 4.1 15.3 1.0 N A:GLY105 4.2 14.3 1.0 N A:ILE106 4.2 13.8 1.0 C A:ARG102 4.3 16.5 1.0 O5' P:DG9 4.3 16.4 1.0 N A:VAL103 4.4 13.6 1.0 N A:ARG102 4.4 15.2 1.0 C A:SER104 4.5 14.7 1.0 CB A:THR101 4.5 16.9 1.0 CA A:ILE106 4.5 14.4 1.0 O A:ARG102 4.5 15.6 1.0 N A:GLY107 4.5 15.7 1.0 CA A:ARG102 4.5 15.8 1.0 O3' P:DC8 4.5 12.6 1.0 CA A:GLY107 4.6 14.4 1.0 CA A:VAL103 4.6 12.5 1.0 O A:HOH526 4.7 17.6 1.0 CB A:ILE106 5.0 15.8 1.0

Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG 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 Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Da within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:23.9 occ:1.00 OP2 D:DC3 2.8 19.2 1.0 O A:LYS60 2.9 23.4 1.0 OP1 D:DC3 3.0 17.9 1.0 O A:VAL65 3.0 23.4 1.0 P D:DC3 3.3 17.9 1.0 NZ A:LYS60 3.9 26.9 1.0 O A:LEU62 4.0 23.6 1.0 C A:VAL65 4.1 17.0 1.0 C A:LYS60 4.1 23.9 1.0 CG A:LYS60 4.2 18.3 1.0 CA A:GLY66 4.5 17.5 1.0 O3' D:DT2 4.5 17.3 1.0 O5' D:DC3 4.5 14.3 1.0 N A:GLY66 4.7 17.8 1.0 CA A:LYS60 4.8 20.6 1.0 N A:VAL65 4.9 13.9 1.0 O A:HOH520 4.9 22.2 1.0 C A:LEU62 5.0 19.9 1.0 CE A:LYS60 5.0 24.6 1.0

Y.Kou, M.C.Koag, S.Lee. N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex Dna. J.Am.Chem.Soc. V. 137 14067 2015.
ISSN: ESSN 1520-5126
PubMed: 26517568
DOI: 10.1021/JACS.5B10172