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

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

The structure of Structure of Human Dna Polymerase Beta Host-Guest Complex with the Dg Base Paired with A Dt, PDB code: 5dba 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)	19.08 / 1.97
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.344, 79.345, 54.584, 90.00, 106.14, 90.00
R / Rfree (%)	20.2 / 24.5

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Host-Guest Complex with the Dg Base Paired with A Dt (pdb code 5dba). 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 Dt, PDB code: 5dba:
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 Dt


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 Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:20.0 occ:1.00 O A:THR101 2.3 22.8 1.0 OP1 P:DG9 2.4 20.2 1.0 O P:HOH110 2.4 21.0 1.0 O A:ILE106 2.4 20.4 1.0 O A:VAL103 2.4 21.9 1.0 O A:HOH600 2.5 26.3 1.0 C A:THR101 3.3 21.7 1.0 C A:ILE106 3.4 20.9 1.0 C A:VAL103 3.4 24.8 1.0 P P:DG9 3.4 24.2 1.0 OP2 P:DG9 3.7 20.4 1.0 N A:ILE106 3.7 18.9 1.0 CA A:THR101 3.9 20.4 1.0 N A:GLY105 4.0 20.5 1.0 CA A:SER104 4.0 21.4 1.0 CA A:ILE106 4.1 17.9 1.0 N A:SER104 4.1 22.6 1.0 N A:VAL103 4.1 22.7 1.0 N A:GLY107 4.3 19.6 1.0 C A:SER104 4.3 21.4 1.0 CB A:THR101 4.4 24.7 1.0 C A:ARG102 4.4 24.7 1.0 CA A:VAL103 4.4 24.2 1.0 N A:ARG102 4.4 26.2 1.0 O3' P:DC8 4.5 22.4 1.0 CB A:ILE106 4.5 21.9 1.0 O5' P:DG9 4.6 24.1 1.0 C A:GLY105 4.6 19.7 1.0 CA A:GLY107 4.6 21.7 1.0 CA A:ARG102 4.7 23.3 1.0 O A:ARG102 4.9 22.8 1.0 CA A:GLY105 4.9 21.6 1.0 O A:LEU100 5.0 22.1 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 Dt


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 Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:35.5 occ:1.00 O D:HOH107 2.3 31.9 1.0 O A:LYS60 2.3 38.8 1.0 O A:VAL65 2.4 34.5 1.0 O A:LEU62 2.5 33.8 1.0 O A:HOH572 2.7 46.0 1.0 OP1 D:DC3 2.8 32.1 1.0 C A:LYS60 3.5 35.9 1.0 C A:VAL65 3.5 29.6 1.0 C A:LEU62 3.5 31.9 1.0 P D:DC3 3.7 32.3 1.0 OP2 D:DC3 3.9 25.9 1.0 N A:VAL65 3.9 29.4 1.0 C A:LYS61 4.1 35.8 1.0 N A:LEU62 4.1 30.8 1.0 CA A:VAL65 4.1 27.2 1.0 CA A:PRO63 4.2 34.7 1.0 CA A:LYS60 4.2 32.3 1.0 N A:GLY64 4.2 37.2 1.0 N A:PRO63 4.2 35.0 1.0 CG A:LYS60 4.3 35.7 1.0 O A:LYS61 4.3 39.4 1.0 N A:LYS61 4.4 35.6 1.0 CB A:VAL65 4.4 28.8 1.0 CA A:LEU62 4.5 32.0 1.0 N A:GLY66 4.5 28.1 1.0 CA A:LYS61 4.6 34.9 1.0 O3' D:DT2 4.6 27.7 1.0 C A:PRO63 4.6 34.8 1.0 CA A:GLY66 4.7 28.4 1.0 CB A:LYS60 4.9 33.4 1.0 C A:GLY64 4.9 32.7 1.0 O A:ALA59 4.9 33.3 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