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Fluorine in PDB 2pxi: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate, PDB code: 2pxi was solved by C.E.Mckenna, V.K.Batra, W.A.Beard, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.09 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.600, 80.200, 55.400, 90.00, 107.80, 90.00
R / Rfree (%) 20.6 / 27

Other elements in 2pxi:

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 5 atoms
Sodium (Na) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate (pdb code 2pxi). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate, PDB code: 2pxi:

Fluorine binding site 1 out of 1 in 2pxi

Go back to Fluorine Binding Sites List in 2pxi
Fluorine binding site 1 out of 1 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F338

b:23.0
occ:1.00
 F3B A:GFH338 0.0 23.0 1.0
C3B A:GFH338 1.4 21.6 1.0
PG A:GFH338 2.7 26.9 1.0
PB A:GFH338 2.7 16.9 1.0
O1B A:GFH338 2.8 21.3 1.0
O3G A:GFH338 2.9 22.7 1.0
NH2 A:ARG183 3.1 22.3 1.0
O2G A:GFH338 3.2 27.3 1.0
CB A:SER180 3.4 19.4 1.0
O A:HOH494 3.4 45.1 1.0
O A:HOH519 3.5 38.9 1.0
O2B A:GFH338 3.6 15.5 1.0
O3A A:GFH338 3.8 17.7 1.0
O1G A:GFH338 3.8 22.2 1.0
OG A:SER180 3.9 22.7 1.0
O A:HOH350 4.0 15.9 1.0
CZ A:ARG183 4.2 23.1 1.0
N A:SER180 4.3 20.5 1.0
CA A:SER180 4.3 19.8 1.0
NH1 A:ARG183 4.4 21.3 1.0
O A:HOH492 4.7 38.2 1.0
O A:HOH348 4.7 19.1 1.0
MG A:MG339 5.0 18.2 1.0

Reference:

C.E.Mckenna, B.A.Kashemirov, T.G.Upton, V.K.Batra, M.F.Goodman, L.C.Pedersen, W.A.Beard, S.H.Wilson. (R)-Beta,Gamma-Fluoromethylene-Dgtp-Dna Ternary Complex with Dna Polymerase Beta. J.Am.Chem.Soc. V. 129 15412 2007.
ISSN: ISSN 0002-7863
PubMed: 18031037
DOI: 10.1021/JA072127V
Page generated: Mon Jul 14 14:04:20 2025

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