Sodium in PDB 5db7: Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dt

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

The structure of Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dt, PDB code: 5db7 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)	19.87 / 2.21
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.396, 79.480, 54.912, 90.00, 105.36, 90.00
R / Rfree (%)	22.1 / 27.3

The structure of Structure of Human Dna Polymerase Beta Host-Guest Complex with the N7MG Base Paired with A Dt 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 Dt (pdb code 5db7). 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 Dt, PDB code: 5db7:
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 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 N7MG Base Paired with A Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:25.2 occ:1.00 O A:THR101 2.3 23.7 1.0 OP1 P:DG9 2.3 21.5 1.0 O A:VAL103 2.4 22.7 1.0 O A:ILE106 2.5 18.3 1.0 O A:HOH565 2.7 22.1 1.0 C A:THR101 3.3 18.8 1.0 C A:VAL103 3.3 24.7 1.0 O A:HOH509 3.3 23.0 1.0 P P:DG9 3.4 20.9 1.0 C A:ILE106 3.4 18.2 1.0 OP2 P:DG9 3.6 23.1 1.0 N A:ILE106 3.8 14.8 1.0 CA A:SER104 3.9 20.0 1.0 N A:GLY105 3.9 19.6 1.0 CA A:THR101 3.9 18.9 1.0 N A:SER104 4.0 23.4 1.0 N A:VAL103 4.1 22.6 1.0 CA A:ILE106 4.1 15.0 1.0 C A:SER104 4.3 21.4 1.0 C A:ARG102 4.3 25.0 1.0 N A:ARG102 4.3 21.2 1.0 N A:GLY107 4.3 19.4 1.0 CA A:VAL103 4.3 20.9 1.0 O3' P:DC8 4.5 18.9 1.0 CB A:THR101 4.5 22.1 1.0 O5' P:DG9 4.5 28.3 1.0 CB A:ILE106 4.5 21.1 1.0 CA A:ARG102 4.6 22.9 1.0 CA A:GLY107 4.6 17.8 1.0 C A:GLY105 4.6 15.7 1.0 O A:ARG102 4.8 27.9 1.0 CA A:GLY105 4.9 15.5 1.0 O A:LEU100 4.9 23.2 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 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 N7MG Base Paired with A Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:30.6 occ:1.00 O A:LYS60 2.4 32.0 1.0 O A:VAL65 2.4 28.4 1.0 O A:LEU62 2.5 31.1 1.0 OP1 D:DC3 2.5 27.3 1.0 O A:HOH544 2.6 30.9 1.0 C A:VAL65 3.5 24.5 1.0 C A:LEU62 3.5 27.6 1.0 C A:LYS60 3.5 31.0 1.0 P D:DC3 3.6 24.1 1.0 N A:VAL65 3.8 21.5 1.0 OP2 D:DC3 3.9 21.5 1.0 C A:LYS61 4.1 35.0 1.0 CA A:VAL65 4.1 20.4 1.0 N A:GLY64 4.1 27.4 1.0 N A:LEU62 4.2 29.5 1.0 O A:LYS61 4.2 39.9 1.0 CA A:PRO63 4.2 28.9 1.0 N A:PRO63 4.3 30.1 1.0 CA A:LYS60 4.4 22.5 1.0 CB A:VAL65 4.5 24.5 1.0 N A:LYS61 4.5 29.6 1.0 CG A:LYS60 4.5 24.5 1.0 CA A:LEU62 4.5 27.7 1.0 N A:GLY66 4.6 22.2 1.0 CA A:LYS61 4.6 34.5 1.0 C A:PRO63 4.6 28.9 1.0 O3' D:DT2 4.6 25.5 1.0 O5' D:DC3 4.8 23.5 1.0 CA A:GLY66 4.8 21.8 1.0 C A:GLY64 4.8 23.8 1.0 NZ A:LYS60 4.9 32.9 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