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

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

The structure of Structure of Human Dna Polymerase Beta Host-Guest Complex with the Dg Base Paired with A Dg, PDB code: 5dbc 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)	19.07 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.458, 79.352, 54.864, 90.00, 105.45, 90.00
R / Rfree (%)	21.4 / 27.9

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Host-Guest Complex with the Dg Base Paired with A Dg (pdb code 5dbc). 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 Dg Base Paired with A Dg, PDB code: 5dbc:
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 Dg 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 Dg Base Paired with A Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:19.0 occ:1.00 O A:THR101 2.4 27.0 1.0 OP1 P:DG9 2.4 13.3 1.0 O A:ILE106 2.5 15.1 1.0 O A:VAL103 2.5 17.1 1.0 O P:HOH107 2.6 16.1 1.0 O P:HOH102 2.6 18.1 1.0 C A:THR101 3.3 23.0 1.0 C A:VAL103 3.4 18.3 1.0 C A:ILE106 3.4 15.8 1.0 P P:DG9 3.5 15.4 1.0 OP2 P:DG9 3.8 18.0 1.0 N A:ILE106 3.8 13.8 1.0 CA A:SER104 3.8 11.9 1.0 N A:SER104 3.9 18.4 1.0 N A:GLY105 3.9 12.4 1.0 CA A:THR101 4.0 18.6 1.0 CA A:ILE106 4.1 12.4 1.0 N A:VAL103 4.2 18.0 1.0 C A:SER104 4.3 15.0 1.0 C A:ARG102 4.3 23.6 1.0 N A:GLY107 4.3 17.0 1.0 N A:ARG102 4.3 22.8 1.0 CA A:VAL103 4.4 17.7 1.0 CB A:ILE106 4.6 18.6 1.0 O3' P:DC8 4.6 16.1 1.0 CB A:THR101 4.6 21.4 1.0 O5' P:DG9 4.6 17.0 1.0 CA A:ARG102 4.6 22.9 1.0 CA A:GLY107 4.6 17.6 1.0 O A:ARG102 4.6 13.9 1.0 C A:GLY105 4.6 17.6 1.0 CA A:GLY105 4.9 15.6 1.0 O A:LEU100 4.9 23.4 1.0

Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Host-Guest Complex with the Dg 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 Dg Base Paired with A Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:31.8 occ:1.00 O A:LYS60 2.5 36.6 1.0 O A:LEU62 2.5 33.6 1.0 O D:HOH103 2.5 15.6 1.0 O A:VAL65 2.5 28.5 1.0 OP1 D:DC3 2.5 33.9 1.0 C A:LEU62 3.4 28.8 1.0 C A:VAL65 3.5 26.5 1.0 C A:LYS60 3.5 30.9 1.0 P D:DC3 3.7 28.2 1.0 N A:VAL65 3.7 27.3 1.0 OP2 D:DC3 3.9 20.5 1.0 N A:GLY64 4.0 35.2 1.0 C A:LYS61 4.0 32.8 1.0 CA A:VAL65 4.1 23.2 1.0 O A:LYS61 4.1 38.8 1.0 CA A:PRO63 4.1 25.9 1.0 N A:PRO63 4.1 28.6 1.0 N A:LEU62 4.2 34.6 1.0 CA A:LYS60 4.3 28.9 1.0 CB A:VAL65 4.4 26.5 1.0 CA A:LEU62 4.4 30.6 1.0 N A:LYS61 4.5 32.4 1.0 C A:PRO63 4.5 31.6 1.0 N A:GLY66 4.5 25.5 1.0 CA A:LYS61 4.6 31.8 1.0 CG A:LYS60 4.6 30.4 1.0 O3' D:DT2 4.6 29.3 1.0 C A:GLY64 4.7 25.5 1.0 O5' D:DC3 4.8 26.1 1.0 CA A:GLY66 4.9 22.0 1.0 O A:ALA59 4.9 28.1 1.0 CA A:GLY64 5.0 33.6 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