Sodium in PDB 2i9g: Dna Polymerase Beta with A Benzo[C]Phenanthrene Diol Epoxide Adducted Guanine Base

All present enzymatic activity of Dna Polymerase Beta with A Benzo[C]Phenanthrene Diol Epoxide Adducted Guanine Base:
2.7.7.7;

The structure of Dna Polymerase Beta with A Benzo[C]Phenanthrene Diol Epoxide Adducted Guanine Base, PDB code: 2i9g was solved by V.K.Batra, S.H.Wilson, W.A.Beard, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.63 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.550, 78.900, 54.950, 90.00, 105.63, 90.00
R / Rfree (%)	20 / 25.2

The structure of Dna Polymerase Beta with A Benzo[C]Phenanthrene Diol Epoxide Adducted Guanine Base also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta with A Benzo[C]Phenanthrene Diol Epoxide Adducted Guanine Base (pdb code 2i9g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Beta with A Benzo[C]Phenanthrene Diol Epoxide Adducted Guanine Base, PDB code: 2i9g:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta with A Benzo[C]Phenanthrene Diol Epoxide Adducted Guanine Base


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 with A Benzo[C]Phenanthrene Diol Epoxide Adducted Guanine Base within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:15.0 occ:1.00 O A:THR101 2.2 20.1 1.0 OP1 P:DG9 2.3 13.4 1.0 O A:ILE106 2.3 15.2 1.0 O P:HOH508 2.4 19.0 1.0 O A:VAL103 2.4 17.0 1.0 O A:HOH512 2.6 19.2 1.0 C A:THR101 3.2 17.6 1.0 C A:VAL103 3.3 17.4 1.0 C A:ILE106 3.3 13.9 1.0 O A:HOH514 3.4 23.7 1.0 P P:DG9 3.4 16.8 1.0 N A:ILE106 3.7 13.5 1.0 OP2 P:DG9 3.7 13.6 1.0 CA A:THR101 3.8 16.0 1.0 CA A:SER104 3.9 14.3 1.0 N A:SER104 4.0 16.6 1.0 N A:VAL103 4.0 16.3 1.0 CA A:ILE106 4.0 12.0 1.0 N A:GLY105 4.0 12.1 1.0 C A:ARG102 4.2 17.5 1.0 N A:ARG102 4.2 17.7 1.0 N A:GLY107 4.3 13.6 1.0 C A:SER104 4.3 13.6 1.0 CB A:THR101 4.3 15.9 1.0 CA A:VAL103 4.3 15.7 1.0 CB A:ILE106 4.5 12.1 1.0 O3' P:DC8 4.5 15.1 1.0 CA A:GLY107 4.5 14.4 1.0 CA A:ARG102 4.6 17.1 1.0 O5' P:DG9 4.6 16.9 1.0 C A:GLY105 4.6 11.2 1.0 O A:ARG102 4.7 17.0 1.0 O A:HOH848 4.8 33.4 1.0 O A:LEU100 4.9 16.6 1.0 CA A:GLY105 5.0 11.2 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta with A Benzo[C]Phenanthrene Diol Epoxide Adducted Guanine Base


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 with A Benzo[C]Phenanthrene Diol Epoxide Adducted Guanine Base within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:23.7 occ:1.00 O D:HOH507 2.3 28.2 1.0 O A:LEU62 2.3 26.1 1.0 O A:VAL65 2.3 22.5 1.0 O A:LYS60 2.4 30.2 1.0 OP1 D:DC3 2.6 22.9 1.0 O A:HOH584 2.6 36.5 1.0 C A:LEU62 3.3 28.4 1.0 C A:VAL65 3.4 20.5 1.0 C A:LYS60 3.5 29.8 1.0 P D:DC3 3.7 21.4 1.0 N A:VAL65 3.7 20.0 1.0 O D:HOH740 3.8 34.7 1.0 OP2 D:DC3 3.9 21.0 1.0 CA A:VAL65 4.0 20.1 1.0 CA A:PRO63 4.0 28.2 1.0 N A:GLY64 4.0 25.0 1.0 N A:PRO63 4.0 28.4 1.0 N A:LEU62 4.1 28.2 1.0 C A:LYS61 4.2 29.1 1.0 CB A:VAL65 4.2 20.1 1.0 CA A:LYS60 4.3 27.4 1.0 CA A:LEU62 4.3 27.2 1.0 CG A:LYS60 4.4 32.1 1.0 C A:PRO63 4.4 26.5 1.0 O A:LYS61 4.4 29.9 1.0 N A:GLY66 4.5 19.5 1.0 O3' D:DT2 4.5 20.8 1.0 N A:LYS61 4.5 29.4 1.0 CA A:LYS61 4.6 30.5 1.0 C A:GLY64 4.7 22.7 1.0 CA A:GLY66 4.8 19.5 1.0 O5' D:DC3 4.9 22.9 1.0 O A:ALA59 4.9 26.5 1.0 CB A:LYS60 4.9 29.3 1.0 NZ A:LYS60 5.0 37.4 1.0

V.K.Batra, D.D.Shock, R.Prasad, W.A.Beard, E.W.Hou, L.C.Pedersen, J.M.Sayer, H.Yagi, S.Kumar, D.M.Jerina, S.H.Wilson. Structure of Dna Polymerase Beta with A Benzo[C]Phenanthrene Diol Epoxide-Adducted Template Exhibits Mutagenic Features. Proc.Natl.Acad.Sci.Usa V. 103 17231 2006.
ISSN: ISSN 0027-8424
PubMed: 17079493
DOI: 10.1073/PNAS.0605069103