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Fluorine in PDB 3tfr: Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site

Enzymatic activity of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site

All present enzymatic activity of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site, PDB code: 3tfr was solved by B.T.Chamberlain, V.K.Batra, W.A.Beard, A.P.Kadina, D.D.Shock, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.69 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.890, 79.380, 55.650, 90.00, 107.64, 90.00
R / Rfree (%) 18.8 / 25.1

Other elements in 3tfr:

The structure of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site (pdb code 3tfr). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site, PDB code: 3tfr:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3tfr

Go back to Fluorine Binding Sites List in 3tfr
Fluorine binding site 1 out of 2 in the Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F338

b:15.2
occ:1.00
 F1A A:F3A338 0.0 15.2 1.0
C3A A:F3A338 1.3 19.0 1.0
F2A A:F3A338 2.2 13.7 1.0
PA A:F3A338 2.6 13.5 1.0
PB A:F3A338 2.6 12.2 1.0
O1B A:F3A338 2.8 13.2 1.0
O A:HOH352 2.9 15.1 1.0
O5' A:F3A338 2.9 16.2 1.0
O2A A:F3A338 3.1 15.2 1.0
O A:HOH695 3.2 28.8 1.0
C3' A:F3A338 3.6 16.1 1.0
O3B A:F3A338 3.6 14.8 1.0
O A:HOH462 3.6 21.2 1.0
O2B A:F3A338 3.7 9.6 1.0
C5' A:F3A338 3.8 13.0 1.0
O3' A:F3A338 3.9 10.3 1.0
C8 A:F3A338 3.9 12.3 1.0
O1A A:F3A338 3.9 7.4 1.0
C4' A:F3A338 4.2 13.0 1.0
CB A:ASP276 4.3 13.3 1.0
CG A:ASP276 4.5 19.3 1.0
O3G A:F3A338 4.5 11.4 1.0
N A:ASP276 4.5 13.9 1.0
C2' A:F3A338 4.6 15.0 1.0
N7 A:F3A338 4.6 19.5 1.0
PG A:F3A338 4.7 14.4 1.0
N9 A:F3A338 4.7 14.0 1.0
OD2 A:ASP276 4.7 18.1 1.0
C1' A:F3A338 4.8 9.9 1.0
O A:HOH483 4.8 22.4 1.0
OD1 A:ASP276 4.8 21.0 1.0
MG A:MG339 4.9 14.0 1.0
O A:HOH533 4.9 31.4 1.0
O A:HOH641 4.9 27.1 1.0
CA A:ASP276 5.0 12.5 1.0

Fluorine binding site 2 out of 2 in 3tfr

Go back to Fluorine Binding Sites List in 3tfr
Fluorine binding site 2 out of 2 in the Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F338

b:13.7
occ:1.00
 F2A A:F3A338 0.0 13.7 1.0
C3A A:F3A338 1.3 19.0 1.0
F1A A:F3A338 2.2 15.2 1.0
PB A:F3A338 2.6 12.2 1.0
PA A:F3A338 2.6 13.5 1.0
O3B A:F3A338 2.7 14.8 1.0
O3G A:F3A338 2.8 11.4 1.0
O2A A:F3A338 3.0 15.2 1.0
PG A:F3A338 3.1 14.4 1.0
O1G A:F3A338 3.2 16.0 1.0
O1A A:F3A338 3.3 7.4 1.0
O A:HOH695 3.4 28.8 1.0
O A:HOH533 3.5 31.4 1.0
O A:HOH483 3.5 22.4 1.0
O A:HOH494 3.5 14.5 1.0
O1B A:F3A338 3.6 13.2 1.0
O2B A:F3A338 3.6 9.6 1.0
O5' A:F3A338 3.9 16.2 1.0
MG A:MG339 4.0 14.0 1.0
O A:HOH462 4.2 21.2 1.0
O A:HOH352 4.2 15.1 1.0
O A:HOH473 4.4 30.9 1.0
O2G A:F3A338 4.6 20.3 1.0
C5' A:F3A338 4.8 13.0 1.0

Reference:

B.T.Chamberlain, V.K.Batra, W.A.Beard, A.P.Kadina, D.D.Shock, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, S.H.Wilson. Stereospecific Formation of A Ternary Complex of (S)-Alpha, Beta-Fluoromethylene-Datp with Dna Pol Beta. Chembiochem V. 13 528 2012.
ISSN: ISSN 1439-4227
PubMed: 22315190
DOI: 10.1002/CBIC.201100738
Page generated: Sun Dec 13 11:55:49 2020

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