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

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

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Difluoromethylene 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- Difluoromethylene Triphosphate, PDB code: 2iso was solved by C.A.Sucato, T.G.Upton, B.A.Kashemirov, V.Martinek, Y.Xiang, W.A.Beard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.35 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.700, 80.500, 55.400, 90.00, 108.00, 90.00
R / Rfree (%) 20.1 / 26

Other elements in 2iso:

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

Magnesium (Mg) 1 atom
Chlorine (Cl) 4 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- Difluoromethylene Triphosphate (pdb code 2iso). 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 of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Difluoromethylene Triphosphate, PDB code: 2iso:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 2iso

Go back to Fluorine Binding Sites List in 2iso
Fluorine binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Difluoromethylene 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- Difluoromethylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F338

b:21.0
occ:1.00
F1B A:GFF338 0.0 21.0 1.0
C3B A:GFF338 1.4 21.7 1.0
F2B A:GFF338 2.2 20.9 1.0
P2 A:GFF338 2.6 17.9 1.0
P3 A:GFF338 2.7 26.0 1.0
O1B A:GFF338 2.7 18.5 1.0
O3G A:GFF338 2.8 22.8 1.0
O A:HOH646 3.1 35.1 1.0
NH2 A:ARG183 3.3 16.7 1.0
O A:HOH515 3.3 36.0 1.0
O2G A:GFF338 3.3 27.4 1.0
O2B A:GFF338 3.4 15.5 1.0
CB A:SER180 3.4 16.6 1.0
O3A A:GFF338 3.7 18.1 1.0
OG A:SER180 3.8 19.5 1.0
O1G A:GFF338 3.8 21.9 1.0
O A:HOH363 4.1 16.4 1.0
O A:HOH510 4.1 42.5 1.0
N A:SER180 4.2 17.4 1.0
CZ A:ARG183 4.2 16.9 1.0
NH1 A:ARG183 4.2 13.4 1.0
CA A:SER180 4.3 17.4 1.0
O A:HOH473 4.3 40.5 1.0
O A:HOH347 4.8 24.8 1.0
MG A:MG339 4.8 13.5 1.0

Fluorine binding site 2 out of 2 in 2iso

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


Mono view


Stereo pair view

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

b:20.9
occ:1.00
F2B A:GFF338 0.0 20.9 1.0
C3B A:GFF338 1.4 21.7 1.0
F1B A:GFF338 2.2 21.0 1.0
P2 A:GFF338 2.6 17.9 1.0
P3 A:GFF338 2.7 26.0 1.0
O3A A:GFF338 2.8 18.1 1.0
O2G A:GFF338 2.9 27.4 1.0
O1B A:GFF338 3.3 18.5 1.0
O A:HOH363 3.3 16.4 1.0
O1G A:GFF338 3.4 21.9 1.0
O A:HOH515 3.5 36.0 1.0
O A:HOH413 3.6 24.7 1.0
O2B A:GFF338 3.8 15.5 1.0
O3G A:GFF338 3.8 22.8 1.0
P1 A:GFF338 3.8 20.4 1.0
O2A A:GFF338 3.9 17.6 1.0
O A:HOH646 4.1 35.1 1.0
O1A A:GFF338 4.2 15.2 1.0
O A:HOH388 4.3 35.9 1.0
O A:HOH531 4.3 26.5 1.0
MG A:MG339 4.6 13.5 1.0

Reference:

C.A.Sucato, T.G.Upton, B.A.Kashemirov, V.K.Batra, V.Martinek, Y.Xiang, W.A.Beard, L.C.Pedersen, S.H.Wilson, C.E.Mckenna, J.Florian, A.Warshel, M.F.Goodman. Modifying the Beta,Gamma Leaving-Group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, and the Catalytic Mechanism of Dna Polymerase Beta. Biochemistry V. 46 461 2007.
ISSN: ISSN 0006-2960
PubMed: 17209556
DOI: 10.1021/BI061517B
Page generated: Sun Dec 13 11:37:26 2020

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