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Fluorine in PDB 4doa: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Non-Interactive Binding of S-Isomer

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Non-Interactive Binding of S-Isomer

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Non-Interactive Binding of S-Isomer:
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: Non-Interactive Binding of S-Isomer, PDB code: 4doa was solved by V.K.Batra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.27 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.638, 79.933, 55.519, 90.00, 107.70, 90.00
R / Rfree (%) 19.1 / 24.3

Other elements in 4doa:

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Non-Interactive Binding of S-Isomer 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: Non-Interactive Binding of S-Isomer (pdb code 4doa). 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: Non-Interactive Binding of S-Isomer, PDB code: 4doa:

Fluorine binding site 1 out of 1 in 4doa

Go back to Fluorine Binding Sites List in 4doa
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: Non-Interactive Binding of S-Isomer


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: Non-Interactive Binding of S-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F410

b:27.3
occ:1.00
 F2B A:FHG410 0.0 27.3 1.0
C3B A:FHG410 1.4 28.0 1.0
P2 A:FHG410 2.6 15.2 1.0
O3A A:FHG410 2.6 16.8 1.0
P3 A:FHG410 2.6 29.0 1.0
O2G A:FHG410 2.9 40.6 1.0
O1B A:FHG410 3.2 17.3 1.0
O A:HOH504 3.2 16.3 1.0
O1G A:FHG410 3.3 20.3 1.0
O A:HOH544 3.5 27.1 1.0
O A:HOH557 3.5 25.9 1.0
P1 A:FHG410 3.7 20.5 1.0
O3G A:FHG410 3.7 23.1 1.0
O2B A:FHG410 3.7 14.0 1.0
O2A A:FHG410 3.8 18.1 1.0
O A:HOH685 3.9 43.2 1.0
O1A A:FHG410 4.2 18.0 1.0
O A:HOH653 4.4 23.0 1.0
MG A:MG401 4.7 14.3 1.0
O A:HOH550 4.7 28.3 1.0
O5' A:FHG410 5.0 18.9 1.0

Reference:

Y.Wu, V.M.Zakharova, B.A.Kashemirov, M.F.Goodman, V.K.Batra, S.H.Wilson, C.E.Mckenna. Beta,Gamma-Chf- and Beta,Gamma-Chcl-Dgtp Diastereomers: Synthesis, Discrete (31)P uc(Nmr) Signatures, and Absolute Configurations of New Stereochemical Probes For Dna Polymerases J.Am.Chem.Soc. V. 134 8734 2012.
ISSN: ISSN 0002-7863
PubMed: 22397499
DOI: 10.1021/JA300218X
Page generated: Mon Jul 14 21:15:00 2025

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