Atomistry » Fluorine » PDB 2ihk-2jxr » 2iso
Atomistry »
  Fluorine »
    PDB 2ihk-2jxr »
      2iso »

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: Wed Jul 31 14:56:18 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy