Sodium in PDB 5db9: Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dg

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

The structure of Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dg, PDB code: 5db9 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)	19.82 / 2.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.201, 79.278, 54.720, 90.00, 105.63, 90.00
R / Rfree (%)	18.7 / 26

The structure of Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dg 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 Dg (pdb code 5db9). 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 Dg, PDB code: 5db9:
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 Dg


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 Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:24.1 occ:1.00 O A:THR101 2.2 22.5 1.0 OP1 P:DG9 2.4 18.2 1.0 O A:ILE106 2.5 19.2 1.0 O P:HOH104 2.6 16.9 1.0 O A:VAL103 2.6 21.5 1.0 O A:HOH511 3.1 17.7 1.0 C A:THR101 3.3 22.6 1.0 C A:VAL103 3.3 20.6 1.0 P P:DG9 3.5 18.0 1.0 C A:ILE106 3.5 20.6 1.0 OP2 P:DG9 3.6 20.9 1.0 CA A:SER104 3.7 16.3 1.0 N A:SER104 3.8 20.3 1.0 N A:ILE106 3.9 16.7 1.0 N A:GLY105 3.9 14.9 1.0 CA A:THR101 4.0 22.0 1.0 N A:VAL103 4.2 19.2 1.0 C A:SER104 4.2 16.8 1.0 CA A:ILE106 4.2 18.4 1.0 C A:ARG102 4.3 23.6 1.0 N A:ARG102 4.3 23.0 1.0 CA A:VAL103 4.4 18.2 1.0 CB A:THR101 4.5 22.0 1.0 N A:GLY107 4.5 19.5 1.0 CA A:ARG102 4.5 24.4 1.0 O5' P:DG9 4.6 21.5 1.0 O3' P:DC8 4.6 17.6 1.0 CB A:ILE106 4.7 20.0 1.0 O A:HOH517 4.7 17.6 1.0 C A:GLY105 4.7 17.2 1.0 CA A:GLY107 4.7 20.2 1.0 O A:ARG102 4.7 19.8 1.0 CA A:GLY105 4.9 14.3 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 Dg


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 Dg within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:31.1 occ:1.00 OP2 D:DC3 2.8 22.0 1.0 O A:VAL65 3.1 32.3 1.0 OP1 D:DC3 3.2 28.3 1.0 O A:LYS60 3.3 32.3 1.0 P D:DC3 3.4 25.4 1.0 NZ A:LYS60 3.5 34.4 1.0 CG A:LYS60 4.0 29.2 1.0 C A:VAL65 4.2 28.5 1.0 CA A:GLY66 4.3 24.0 1.0 CE A:LYS60 4.4 34.3 1.0 O A:LEU62 4.5 31.3 1.0 O5' D:DC3 4.5 24.0 1.0 C A:LYS60 4.5 28.6 1.0 O3' D:DT2 4.7 26.1 1.0 N A:GLY66 4.7 24.5 1.0 CD A:LYS60 4.9 31.0 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