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Fluorine in PDB 3lk9: Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P

Enzymatic activity of Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P

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

Protein crystallography data

The structure of Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P, PDB code: 3lk9 was solved by M.Zibinsky, G.K.Surya Prakash, T.G.Upton, B.A.Kashemirov, C.E.Mckenna, K.Oertell, M.F.Goodman, V.K.Batra, L.C.Pedersen, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.28 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.960, 79.800, 55.050, 90.00, 108.46, 90.00
R / Rfree (%) 19.8 / 28.1

Other elements in 3lk9:

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

Magnesium (Mg) 2 atoms
Chlorine (Cl) 3 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P (pdb code 3lk9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P, PDB code: 3lk9:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3lk9

Go back to Fluorine Binding Sites List in 3lk9
Fluorine binding site 1 out of 4 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F338

b:33.0
occ:1.00
 F1A A:TFF338 0.0 33.0 1.0
C3A A:TFF338 1.4 32.1 1.0
F2A A:TFF338 2.2 31.8 1.0
PA A:TFF338 2.6 30.1 1.0
PB A:TFF338 2.7 32.2 1.0
O1B A:TFF338 2.8 30.5 1.0
O A:HOH351 3.0 34.8 1.0
O2A A:TFF338 3.0 32.7 1.0
F2B A:TFF338 3.2 31.0 1.0
O5' A:TFF338 3.2 30.6 1.0
C3B A:TFF338 3.6 32.4 1.0
C5M A:TFF338 3.6 25.3 1.0
O2B A:TFF338 3.8 29.2 1.0
C5' A:TFF338 3.9 30.1 1.0
O1A A:TFF338 3.9 27.3 1.0
C3' A:TFF338 4.0 29.7 1.0
O A:HOH381 4.1 34.7 1.0
C6 A:TFF338 4.1 26.6 1.0
C5 A:TFF338 4.2 24.1 1.0
O3' A:TFF338 4.5 27.3 1.0
C4' A:TFF338 4.5 29.4 1.0
O3G A:TFF338 4.6 32.6 1.0
CB A:ASP276 4.6 41.7 1.0
F1B A:TFF338 4.6 33.7 1.0
MG A:MG339 4.6 29.4 1.0
PG A:TFF338 4.8 33.8 1.0
CG A:ASP276 4.9 44.5 1.0
N A:ASP276 5.0 39.9 1.0

Fluorine binding site 2 out of 4 in 3lk9

Go back to Fluorine Binding Sites List in 3lk9
Fluorine binding site 2 out of 4 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F338

b:33.7
occ:1.00
 F1B A:TFF338 0.0 33.7 1.0
C3B A:TFF338 1.4 32.4 1.0
F2B A:TFF338 2.2 31.0 1.0
PG A:TFF338 2.6 33.8 1.0
PB A:TFF338 2.7 32.2 1.0
O2G A:TFF338 2.8 32.0 1.0
NH2 A:ARG183 2.9 39.0 1.0
CB A:SER180 3.0 36.6 1.0
O1B A:TFF338 3.0 30.5 1.0
O2B A:TFF338 3.3 29.2 1.0
O1G A:TFF338 3.4 35.8 1.0
OG A:SER180 3.6 38.6 1.0
N A:SER180 3.6 35.4 1.0
CA A:SER180 3.8 34.6 1.0
O A:HOH420 3.8 45.1 1.0
O3G A:TFF338 3.8 32.6 1.0
CZ A:ARG183 3.9 38.5 1.0
C3A A:TFF338 4.1 32.1 1.0
F2A A:TFF338 4.1 31.8 1.0
O A:HOH351 4.2 34.8 1.0
O A:HOH438 4.3 39.2 1.0
NH1 A:ARG183 4.3 39.0 1.0
O A:HOH349 4.6 28.4 1.0
F1A A:TFF338 4.6 33.0 1.0
C A:GLY179 4.7 35.4 1.0
MG A:MG339 4.7 29.4 1.0
O A:HOH366 4.8 33.8 1.0
NE A:ARG183 5.0 36.5 1.0

Fluorine binding site 3 out of 4 in 3lk9

Go back to Fluorine Binding Sites List in 3lk9
Fluorine binding site 3 out of 4 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F338

b:31.8
occ:1.00
 F2A A:TFF338 0.0 31.8 1.0
C3A A:TFF338 1.4 32.1 1.0
F1A A:TFF338 2.2 33.0 1.0
O3G A:TFF338 2.6 32.6 1.0
F2B A:TFF338 2.6 31.0 1.0
PA A:TFF338 2.6 30.1 1.0
PB A:TFF338 2.6 32.2 1.0
C3B A:TFF338 2.8 32.4 1.0
O A:HOH381 2.9 34.7 1.0
O2A A:TFF338 3.1 32.7 1.0
PG A:TFF338 3.1 33.8 1.0
O1A A:TFF338 3.2 27.3 1.0
O A:HOH413 3.4 32.2 1.0
O2B A:TFF338 3.4 29.2 1.0
MG A:MG339 3.5 29.4 1.0
O1G A:TFF338 3.6 35.8 1.0
O1B A:TFF338 3.7 30.5 1.0
O5' A:TFF338 4.0 30.6 1.0
O A:HOH415 4.1 52.8 1.0
F1B A:TFF338 4.1 33.7 1.0
O A:HOH437 4.3 26.5 1.0
O2G A:TFF338 4.4 32.0 1.0
OD1 A:ASP190 4.5 27.8 1.0
O A:HOH351 4.6 34.8 1.0
C5' A:TFF338 4.7 30.1 1.0

Fluorine binding site 4 out of 4 in 3lk9

Go back to Fluorine Binding Sites List in 3lk9
Fluorine binding site 4 out of 4 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Dna Polymerase Beta with A Gapped Dna Substrate and Dtmp(CF2)P(CF2)P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F338

b:31.0
occ:1.00
 F2B A:TFF338 0.0 31.0 1.0
C3B A:TFF338 1.4 32.4 1.0
F1B A:TFF338 2.2 33.7 1.0
F2A A:TFF338 2.6 31.8 1.0
PB A:TFF338 2.7 32.2 1.0
PG A:TFF338 2.7 33.8 1.0
O1G A:TFF338 2.9 35.8 1.0
C3A A:TFF338 3.0 32.1 1.0
O1B A:TFF338 3.2 30.5 1.0
F1A A:TFF338 3.2 33.0 1.0
O A:HOH351 3.4 34.8 1.0
O3G A:TFF338 3.4 32.6 1.0
O2G A:TFF338 3.9 32.0 1.0
O2B A:TFF338 3.9 29.2 1.0
O A:HOH420 3.9 45.1 1.0
NH2 A:ARG183 4.3 39.0 1.0
PA A:TFF338 4.8 30.1 1.0
MG A:MG339 4.9 29.4 1.0
O A:HOH415 5.0 52.8 1.0

Reference:

G.K.Surya Prakash, M.Zibinsky, T.G.Upton, B.A.Kashemirov, C.E.Mckenna, K.Oertell, M.F.Goodman, V.K.Batra, L.C.Pedersen, W.A.Beard, D.D.Shock, S.H.Wilson, G.A.Olah. Synthesis and Biological Evaluation of Fluorinated Deoxynucleotide Analogs Based on Bis-(Difluoromethylene)Triphosphoric Acid. Proc.Natl.Acad.Sci.Usa V. 107 15693 2010.
ISSN: ISSN 0027-8424
PubMed: 20724659
DOI: 10.1073/PNAS.1007430107
Page generated: Wed Jul 31 20:31:23 2024

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