Sodium in PDB 3gdx: Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp

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

The structure of Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp, PDB code: 3gdx was solved by S.H.Wilson, V.K.Batra, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.58 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.500, 79.700, 55.300, 90.00, 107.90, 90.00
R / Rfree (%)	20.8 / 26.6

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

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

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

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


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 Dnd Substrate and Dtmp(CF2)Pp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na349 b:21.2 occ:1.00 O A:ILE106 2.2 17.0 1.0 O P:HOH56 2.2 20.5 1.0 O A:THR101 2.3 19.7 1.0 OP1 P:DG9 2.4 22.1 1.0 O A:VAL103 2.7 14.8 1.0 O A:HOH510 2.7 27.1 1.0 C A:THR101 3.3 20.6 1.0 P P:DG9 3.3 23.0 1.0 C A:ILE106 3.3 19.0 1.0 OP2 P:DG9 3.4 23.7 1.0 C A:VAL103 3.6 16.1 1.0 N A:ILE106 3.8 19.7 1.0 CA A:THR101 3.9 20.3 1.0 N A:GLY105 4.0 18.8 1.0 CA A:ILE106 4.0 19.3 1.0 O3' P:DC8 4.1 23.2 1.0 CA A:SER104 4.1 16.9 1.0 N A:VAL103 4.1 18.4 1.0 N A:SER104 4.2 15.4 1.0 N A:ARG102 4.3 18.9 1.0 O A:HOH493 4.3 38.0 1.0 N A:GLY107 4.3 17.7 1.0 C A:ARG102 4.4 18.4 1.0 CB A:ILE106 4.5 19.1 1.0 C A:SER104 4.5 18.6 1.0 CB A:THR101 4.5 21.4 1.0 CA A:GLY107 4.6 16.7 1.0 CA A:ARG102 4.6 18.4 1.0 CA A:VAL103 4.6 17.3 1.0 O5' P:DG9 4.6 22.9 1.0 C A:GLY105 4.6 21.3 1.0 O A:LEU100 4.9 21.4 1.0 CA A:GLY105 5.0 19.8 1.0 O A:ARG102 5.0 19.6 1.0

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


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 Dnd Substrate and Dtmp(CF2)Pp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na350 b:26.6 occ:1.00 O A:LYS60 2.4 34.3 1.0 O A:LEU62 2.4 29.2 1.0 OP1 D:DC3 2.5 29.2 1.0 O D:HOH55 2.6 26.2 1.0 O A:VAL65 2.7 29.6 1.0 C A:LEU62 3.4 29.8 1.0 C A:LYS60 3.6 34.0 1.0 P D:DC3 3.6 30.6 1.0 C A:VAL65 3.7 29.0 1.0 OP2 D:DC3 3.8 30.2 1.0 CA A:PRO63 3.9 29.1 1.0 N A:VAL65 4.0 27.1 1.0 N A:PRO63 4.0 30.1 1.0 N A:GLY64 4.2 25.7 1.0 C A:LYS61 4.2 32.6 1.0 N A:LEU62 4.3 31.2 1.0 CA A:LYS60 4.3 33.2 1.0 CG A:LYS60 4.3 35.2 1.0 O A:LYS61 4.3 31.4 1.0 CA A:VAL65 4.3 27.9 1.0 C A:PRO63 4.4 28.1 1.0 CA A:LEU62 4.5 30.6 1.0 N A:LYS61 4.6 33.5 1.0 CB A:VAL65 4.6 28.4 1.0 O3' D:DT2 4.7 29.2 1.0 CA A:LYS61 4.7 33.6 1.0 O5' D:DC3 4.7 32.3 1.0 N A:GLY66 4.8 28.3 1.0 CB A:LYS60 4.9 34.1 1.0 C A:GLY64 5.0 28.0 1.0 CA A:GLY66 5.0 27.7 1.0

T.G.Upton, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, G.K.Prakash, R.Kultyshev, V.K.Batra, D.D.Shock, L.C.Pedersen, W.A.Beard, S.H.Wilson. Alpha,Beta-Difluoromethylene Deoxynucleoside 5'-Triphosphates: A Convenient Synthesis of Useful Probes For Dna Polymerase Beta Structure and Function Org.Lett. V. 11 1883 2009.
ISSN: ISSN 1523-7060
PubMed: 19351147
DOI: 10.1021/OL701755K