Sodium in PDB 5bom: Dna Polymerase Beta Binary Complex with A Templating 5CLC

All present enzymatic activity of Dna Polymerase Beta Binary Complex with A Templating 5CLC:
2.7.7.7;

The structure of Dna Polymerase Beta Binary Complex with A Templating 5CLC, PDB code: 5bom was solved by B.D.Freudenthal, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.67 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.944, 79.547, 55.133, 90.00, 109.23, 90.00
R / Rfree (%)	19 / 21.4

The structure of Dna Polymerase Beta Binary Complex with A Templating 5CLC also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Dna Polymerase Beta Binary Complex with A Templating 5CLC (pdb code 5bom). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Dna Polymerase Beta Binary Complex with A Templating 5CLC, PDB code: 5bom:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Beta Binary Complex with A Templating 5CLC


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Beta Binary Complex with A Templating 5CLC within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:30.0 occ:1.00 O A:THR101 2.4 20.4 1.0 OP1 P:DG9 2.4 17.5 1.0 O A:ILE106 2.5 20.2 1.0 O A:HOH661 2.5 13.3 1.0 O A:VAL103 2.5 18.2 1.0 O P:HOH105 2.5 23.6 1.0 C A:THR101 3.3 21.6 1.0 C A:ILE106 3.4 20.1 1.0 C A:VAL103 3.4 22.0 1.0 P P:DG9 3.5 21.0 1.0 OP2 P:DG9 3.6 25.5 1.0 N A:ILE106 3.7 17.6 1.0 O A:HOH554 3.8 30.0 1.0 CA A:THR101 3.8 18.2 1.0 CA A:SER104 4.0 19.6 1.0 N A:GLY105 4.1 19.7 1.0 N A:SER104 4.1 21.3 1.0 CA A:ILE106 4.1 18.8 1.0 N A:VAL103 4.2 25.1 1.0 CB A:THR101 4.3 28.2 1.0 N A:GLY107 4.3 19.3 1.0 C A:ARG102 4.4 24.1 1.0 C A:SER104 4.4 25.6 1.0 CA A:VAL103 4.4 23.3 1.0 N A:ARG102 4.4 21.5 1.0 O5' P:DG9 4.5 22.6 1.0 CB A:ILE106 4.5 14.2 1.0 CA A:GLY107 4.5 21.9 1.0 O3' P:DC8 4.6 22.4 1.0 C A:GLY105 4.6 18.3 1.0 CA A:ARG102 4.7 20.1 1.0 O A:ARG102 4.8 24.2 1.0 CA A:GLY105 4.9 19.9 1.0 O A:LEU100 4.9 18.5 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Beta Binary Complex with A Templating 5CLC


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Beta Binary Complex with A Templating 5CLC within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:30.0 occ:1.00 O A:VAL65 2.3 29.5 1.0 O A:LEU62 2.4 29.6 1.0 O D:HOH107 2.4 29.2 1.0 O A:HOH665 2.4 31.6 1.0 O A:LYS60 2.5 27.1 1.0 OP1 D:DC3 2.8 27.9 1.0 C A:VAL65 3.4 26.4 1.0 C A:LEU62 3.4 26.2 1.0 C A:LYS60 3.5 28.8 1.0 P D:DC3 3.7 26.4 1.0 OP2 D:DC3 3.7 24.0 1.0 N A:VAL65 3.8 30.0 1.0 CA A:VAL65 4.0 20.8 1.0 N A:LEU62 4.1 24.3 1.0 CA A:PRO63 4.1 31.0 1.0 N A:PRO63 4.1 30.1 1.0 N A:GLY64 4.2 32.9 1.0 C A:LYS61 4.2 31.7 1.0 CA A:LYS60 4.2 31.0 1.0 CB A:VAL65 4.3 30.5 1.0 CA A:LEU62 4.4 30.6 1.0 CG A:LYS60 4.4 40.9 1.0 N A:GLY66 4.4 21.8 1.0 N A:LYS61 4.5 31.8 1.0 O3' D:DT2 4.5 27.4 1.0 O A:LYS61 4.5 33.2 1.0 C A:PRO63 4.6 30.9 1.0 CA A:LYS61 4.7 33.9 1.0 CA A:GLY66 4.7 25.1 1.0 C A:GLY64 4.8 30.0 1.0 O A:ALA59 5.0 25.8 1.0 CB A:LYS60 5.0 35.9 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Beta Binary Complex with A Templating 5CLC


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dna Polymerase Beta Binary Complex with A Templating 5CLC within 5.0Å range: probe atom residue distance (Å) B Occ T:Na101 b:30.0 occ:1.00 O D:HOH115 2.2 39.6 1.0 O T:HOH222 2.2 34.5 1.0 O T:HOH227 2.2 40.4 1.0 O D:HOH116 2.3 30.0 1.0 O D:HOH101 2.9 32.1 1.0 O4' T:DA4 4.2 32.6 1.0 O D:HOH102 4.3 41.9 1.0 N2 T:DG3 4.6 24.2 1.0 N3 T:DA4 4.6 24.9 1.0 C1' T:DA4 4.6 32.0 1.0 C5' T:DC5 4.7 37.0 1.0 O3' T:DA4 4.8 29.9 1.0 O4' D:DG4 4.9 43.0 1.0 C4' T:DA4 5.0 33.5 1.0

B.I.Fedeles, B.D.Freudenthal, E.Yau, V.Singh, S.C.Chang, D.Li, J.C.Delaney, S.H.Wilson, J.M.Essigmann. Intrinsic Mutagenic Properties of 5-Chlorocytosine: A Mechanistic Connection Between Chronic Inflammation and Cancer. Proc.Natl.Acad.Sci.Usa V. 112 E4571 2015.
ISSN: ESSN 1091-6490
PubMed: 26243878
DOI: 10.1073/PNAS.1507709112