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

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

The structure of Structure of Human Dna Polymerase Beta Host-Guest Complex with the Dg Base Paired with A Da, PDB code: 5dbb 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)	19.84 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.389, 79.372, 54.938, 90.00, 105.45, 90.00
R / Rfree (%)	20.6 / 26.5

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Host-Guest Complex with the Dg Base Paired with A Da (pdb code 5dbb). 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 Da, PDB code: 5dbb:
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 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 Dg Base Paired with A Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:22.4 occ:1.00 O A:THR101 2.3 25.6 1.0 OP1 P:DG9 2.3 20.0 1.0 O A:ILE106 2.4 22.7 1.0 O A:VAL103 2.5 22.2 1.0 O P:HOH104 2.5 22.6 1.0 O A:HOH607 2.6 18.1 1.0 O A:HOH508 3.2 24.1 1.0 C A:THR101 3.3 22.9 1.0 C A:VAL103 3.3 22.2 1.0 C A:ILE106 3.4 19.5 1.0 P P:DG9 3.4 20.3 1.0 OP2 P:DG9 3.7 22.2 1.0 N A:ILE106 3.8 16.7 1.0 CA A:SER104 3.9 19.2 1.0 CA A:THR101 3.9 18.4 1.0 N A:GLY105 3.9 18.7 1.0 N A:SER104 3.9 18.9 1.0 CA A:ILE106 4.0 15.9 1.0 N A:VAL103 4.1 24.8 1.0 N A:GLY107 4.3 22.6 1.0 C A:SER104 4.3 17.1 1.0 N A:ARG102 4.3 23.5 1.0 C A:ARG102 4.4 23.8 1.0 CA A:VAL103 4.4 21.8 1.0 CB A:THR101 4.4 24.8 1.0 O3' P:DC8 4.5 19.8 1.0 CB A:ILE106 4.5 17.2 1.0 O5' P:DG9 4.5 23.6 1.0 CA A:GLY107 4.6 21.1 1.0 C A:GLY105 4.6 18.7 1.0 CA A:ARG102 4.6 21.9 1.0 O A:ARG102 4.8 19.3 1.0 CA A:GLY105 4.9 16.6 1.0 O A:LEU100 5.0 23.6 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 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 Dg Base Paired with A Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:38.3 occ:1.00 O A:LYS60 2.4 32.1 1.0 O A:HOH516 2.5 34.4 1.0 OP1 D:DC3 2.5 31.8 1.0 O D:HOH104 2.5 30.9 1.0 O A:VAL65 2.5 33.8 1.0 O A:LEU62 2.6 36.1 1.0 C A:LEU62 3.5 34.4 1.0 C A:LYS60 3.5 33.2 1.0 C A:VAL65 3.5 30.5 1.0 P D:DC3 3.7 27.1 1.0 N A:VAL65 3.8 27.7 1.0 O A:LYS61 3.9 40.2 1.0 C A:LYS61 4.0 35.5 1.0 OP2 D:DC3 4.0 25.1 1.0 CA A:PRO63 4.1 34.5 1.0 N A:GLY64 4.1 31.5 1.0 CA A:VAL65 4.1 25.8 1.0 N A:PRO63 4.1 34.8 1.0 N A:LEU62 4.2 31.1 1.0 CA A:LYS60 4.3 26.8 1.0 N A:LYS61 4.4 30.7 1.0 CB A:VAL65 4.4 28.6 1.0 CA A:LEU62 4.5 33.6 1.0 CA A:LYS61 4.5 31.1 1.0 C A:PRO63 4.5 29.6 1.0 CG A:LYS60 4.6 32.0 1.0 O3' D:DT2 4.6 27.5 1.0 N A:GLY66 4.6 24.0 1.0 C A:GLY64 4.8 29.6 1.0 O5' D:DC3 4.8 26.4 1.0 CA A:GLY66 4.9 24.5 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