Sodium in PDB 5db6: Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dc

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

The structure of Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dc, PDB code: 5db6 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)	19.71 / 2.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.138, 78.828, 54.764, 90.00, 105.92, 90.00
R / Rfree (%)	18.5 / 26.6

The structure of Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dc 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 Dc (pdb code 5db6). 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 Dc, PDB code: 5db6:
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 Dc


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 Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:13.0 occ:1.00 O A:THR101 2.3 10.1 1.0 OP1 P:DG9 2.3 14.5 1.0 O A:HOH505 2.5 15.6 1.0 O A:ILE106 2.6 10.1 1.0 O A:VAL103 3.0 13.4 1.0 O A:HOH550 3.1 9.4 1.0 P P:DG9 3.2 11.8 1.0 OP2 P:DG9 3.2 15.8 1.0 C A:THR101 3.4 12.8 1.0 C A:ILE106 3.6 9.0 1.0 C A:VAL103 3.9 10.0 1.0 CA A:THR101 4.0 8.3 1.0 CA A:SER104 4.1 9.5 1.0 O A:HOH538 4.2 17.7 1.0 O5' P:DG9 4.2 8.3 1.0 N A:ILE106 4.2 10.0 1.0 N A:GLY105 4.3 8.2 1.0 O3' P:DC8 4.4 8.5 1.0 N A:SER104 4.4 11.2 1.0 CB A:THR101 4.4 11.2 1.0 CA A:ILE106 4.5 10.0 1.0 N A:ARG102 4.5 11.1 1.0 N A:GLY107 4.5 11.7 1.0 C A:ARG102 4.6 10.3 1.0 CA A:GLY107 4.6 8.7 1.0 C A:SER104 4.6 8.1 1.0 N A:VAL103 4.7 6.5 1.0 CA A:ARG102 4.7 11.8 1.0 O A:ARG102 4.9 9.0 1.0 CB A:ILE106 5.0 12.4 1.0 CA A:VAL103 5.0 8.0 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 Dc


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 Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:19.6 occ:1.00 O A:LYS60 2.6 17.8 1.0 O A:VAL65 2.6 14.6 1.0 OP1 D:DC3 2.7 16.6 1.0 O A:LEU62 3.4 16.8 1.0 OP2 D:DC3 3.4 7.7 1.0 P D:DC3 3.6 11.3 1.0 C A:LYS60 3.7 14.1 1.0 C A:VAL65 3.8 10.7 1.0 CG A:LYS60 4.2 11.6 1.0 C A:LEU62 4.3 15.1 1.0 NZ A:LYS60 4.4 22.6 1.0 CA A:LYS60 4.5 11.6 1.0 CA A:GLY66 4.5 7.8 1.0 C A:LYS61 4.6 12.6 1.0 N A:GLY66 4.6 10.3 1.0 N A:VAL65 4.6 10.4 1.0 O5' D:DC3 4.7 10.1 1.0 N A:LEU62 4.7 10.4 1.0 O3' D:DT2 4.7 10.4 1.0 CA A:VAL65 4.7 8.6 1.0 N A:LYS61 4.7 13.9 1.0 O A:LYS61 4.8 16.1 1.0 CA A:LYS61 4.9 12.7 1.0 CB A:LYS60 4.9 12.6 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