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Fluorine in PDB 3jps: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Methyl Methylene Triphosphate

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

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Methyl Methylene 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-Fluoro Methyl Methylene Triphosphate, PDB code: 3jps was solved by V.K.Batra, J.Upton, B.Kashmerov, W.A.Beard, S.H.Wilson, M.F.Goodman, C.E.Mckenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.98 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.570, 79.860, 55.550, 90.00, 107.84, 90.00
R / Rfree (%) 19.1 / 23.7

Other elements in 3jps:

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

Magnesium (Mg) 1 atom
Chlorine (Cl) 3 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-Fluoro Methyl Methylene Triphosphate (pdb code 3jps). 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-Fluoro Methyl Methylene Triphosphate, PDB code: 3jps:

Fluorine binding site 1 out of 1 in 3jps

Go back to Fluorine Binding Sites List in 3jps
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-Fluoro Methyl Methylene 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-Fluoro Methyl Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F338

b:18.3
occ:1.00
 F3B2 A:GFM338 0.0 18.3 1.0
C3B A:GFM338 1.4 16.6 1.0
C3B3 A:GFM338 2.4 17.5 1.0
PG A:GFM338 2.6 21.0 1.0
PB A:GFM338 2.8 13.2 1.0
O1B A:GFM338 2.8 16.2 1.0
O3G A:GFM338 2.9 20.3 1.0
NH2 A:ARG183 3.2 13.9 1.0
O2G A:GFM338 3.2 23.4 1.0
O A:HOH365 3.3 49.0 1.0
O A:HOH508 3.4 43.1 1.0
CB A:SER180 3.5 17.4 1.0
O2B A:GFM338 3.6 13.8 1.0
O A:HOH584 3.7 30.4 1.0
O A:HOH654 3.7 40.4 1.0
O1G A:GFM338 3.8 17.8 1.0
O3A A:GFM338 3.9 14.9 1.0
OG A:SER180 3.9 18.5 1.0
O A:HOH349 4.2 13.8 1.0
CZ A:ARG183 4.2 14.8 1.0
O A:HOH567 4.3 42.6 1.0
N A:SER180 4.3 15.8 1.0
CA A:SER180 4.4 15.0 1.0
NH1 A:ARG183 4.4 14.3 1.0
O A:HOH495 4.7 28.7 1.0
MG A:MG339 4.9 15.2 1.0

Reference:

V.K.Batra, L.C.Pedersen, W.A.Beard, S.H.Wilson, B.A.Kashemirov, T.G.Upton, M.F.Goodman, C.E.Mckenna. Halogenated Beta,Gamma-Methylene- and Ethylidene-Dgtp-Dna Ternary Complexes with Dna Polymerase Beta: Structural Evidence For Stereospecific Binding of the Fluoromethylene Analogues. J.Am.Chem.Soc. V. 132 7617 2010.
ISSN: ISSN 0002-7863
PubMed: 20465217
DOI: 10.1021/JA909370K
Page generated: Wed Jul 31 19:37:44 2024

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