Sodium in PDB 3lk9: Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P

All present enzymatic activity of Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P:
2.7.7.7;

The structure of Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P, PDB code: 3lk9 was solved by M.Zibinsky, G.K.Surya Prakash, T.G.Upton, B.A.Kashemirov, C.E.Mckenna, K.Oertell, M.F.Goodman, V.K.Batra, L.C.Pedersen, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.28 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.960, 79.800, 55.050, 90.00, 108.46, 90.00
R / Rfree (%)	19.8 / 28.1

The structure of Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P (pdb code 3lk9). 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 Gapped Dna Substrate and Dtmp(CF2)P(CF2)P, PDB code: 3lk9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P


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 Gapped Dna Substrate and Dtmp(CF2)P(CF2)P within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:42.8 occ:1.00 O A:THR101 2.2 35.0 1.0 OP1 P:DG9 2.3 34.9 1.0 O A:VAL103 2.4 33.1 1.0 O A:ILE106 2.6 27.6 1.0 O A:HOH364 2.7 29.5 1.0 O A:HOH442 2.8 36.0 1.0 P P:DG9 3.3 37.2 1.0 C A:VAL103 3.3 32.1 1.0 OP2 P:DG9 3.4 36.5 1.0 C A:THR101 3.4 33.0 1.0 C A:ILE106 3.6 28.6 1.0 CA A:SER104 3.9 32.5 1.0 N A:ILE106 3.9 27.7 1.0 N A:GLY105 4.0 30.9 1.0 N A:SER104 4.0 31.2 1.0 N A:VAL103 4.0 32.0 1.0 CA A:THR101 4.2 32.4 1.0 O3' P:DC8 4.3 38.9 1.0 C A:ARG102 4.3 32.2 1.0 C A:SER104 4.3 32.3 1.0 CA A:ILE106 4.3 28.1 1.0 CA A:VAL103 4.4 31.2 1.0 N A:ARG102 4.4 31.5 1.0 O5' P:DG9 4.5 36.0 1.0 CA A:ARG102 4.6 30.7 1.0 N A:GLY107 4.6 28.5 1.0 CB A:ILE106 4.8 28.7 1.0 CB A:THR101 4.8 29.3 1.0 C A:GLY105 4.8 29.6 1.0 CA A:GLY107 4.8 28.1 1.0 O A:ARG102 4.8 35.9 1.0 O A:LEU100 4.9 33.8 1.0 CA A:GLY105 5.0 30.2 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P


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 Gapped Dna Substrate and Dtmp(CF2)P(CF2)P within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:59.1 occ:1.00 O A:LEU62 2.1 44.0 1.0 O A:LYS60 2.2 51.2 1.0 O A:VAL65 2.7 36.8 1.0 OP1 D:DC3 2.7 46.8 1.0 C A:LEU62 2.9 45.1 1.0 C A:LYS60 3.3 50.5 1.0 N A:LEU62 3.5 47.0 1.0 N A:PRO63 3.6 44.6 1.0 CA A:PRO63 3.7 44.2 1.0 CA A:LEU62 3.8 45.6 1.0 C A:VAL65 3.8 37.3 1.0 CA A:LYS60 4.0 50.3 1.0 P D:DC3 4.0 48.0 1.0 N A:VAL65 4.0 37.3 1.0 C A:LYS61 4.1 48.2 1.0 N A:GLY64 4.2 42.1 1.0 N A:LYS61 4.3 50.8 1.0 C A:PRO63 4.3 43.8 1.0 OP2 D:DC3 4.3 47.6 1.0 CA A:VAL65 4.3 36.5 1.0 CB A:VAL65 4.4 34.6 1.0 CG A:LYS60 4.4 53.4 1.0 CA A:LYS61 4.5 50.3 1.0 O A:ALA59 4.6 43.9 1.0 O A:LYS61 4.7 48.5 1.0 CB A:LYS60 4.8 51.4 1.0 O3' D:DT2 4.8 48.3 1.0 CD A:PRO63 4.9 44.1 1.0 CB A:LEU62 4.9 45.0 1.0 N A:GLY66 5.0 39.8 1.0 CB A:PRO63 5.0 43.4 1.0

G.K.Surya Prakash, M.Zibinsky, T.G.Upton, B.A.Kashemirov, C.E.Mckenna, K.Oertell, M.F.Goodman, V.K.Batra, L.C.Pedersen, W.A.Beard, D.D.Shock, S.H.Wilson, G.A.Olah. Synthesis and Biological Evaluation of Fluorinated Deoxynucleotide Analogs Based on Bis-(Difluoromethylene)Triphosphoric Acid. Proc.Natl.Acad.Sci.Usa V. 107 15693 2010.
ISSN: ISSN 0027-8424
PubMed: 20724659
DOI: 10.1073/PNAS.1007430107