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Fluorine in PDB 4qw9: Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)Ftc-Ppnp

Enzymatic activity of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)Ftc-Ppnp

All present enzymatic activity of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)Ftc-Ppnp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)Ftc-Ppnp, PDB code: 4qw9 was solved by V.Gaur, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.18 / 2.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.800, 101.900, 52.540, 90.00, 90.00, 90.00
R / Rfree (%) 24.2 / 27

Other elements in 4qw9:

The structure of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)Ftc-Ppnp also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)Ftc-Ppnp (pdb code 4qw9). 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 Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)Ftc-Ppnp, PDB code: 4qw9:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4qw9

Go back to Fluorine Binding Sites List in 4qw9
Fluorine binding site 1 out of 2 in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)Ftc-Ppnp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)Ftc-Ppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:97.5
occ:0.50
 F5 A:0G4701 0.0 97.5 0.5
F5 A:0G4701 0.4 97.5 0.5
C5 A:0G4701 1.1 89.0 0.5
C5 A:0G4701 1.3 89.5 0.5
C4 A:0G4701 2.1 99.5 0.5
C6 A:0G4701 2.3 85.9 0.5
C6 A:0G4701 2.4 86.7 0.5
C4 A:0G4701 2.4 0.1 0.5
N4 A:0G4701 2.6 0.1 0.5
N4 A:0G4701 2.8 0.4 0.5
C6 C:DC13 3.2 90.3 1.0
N3 A:0G4701 3.3 0.4 0.5
C5 C:DC13 3.3 86.5 1.0
N1 A:0G4701 3.4 91.5 0.5
O1A A:0G4701 3.4 0.2 0.5
N1 A:0G4701 3.6 92.8 0.5
O A:HOH818 3.6 63.6 1.0
N3 A:0G4701 3.6 0.2 0.5
N1 C:DC13 3.6 94.2 1.0
C2 A:0G4701 3.8 95.4 0.5
C4 C:DC13 3.8 85.6 1.0
C2 A:0G4701 4.0 96.6 0.5
C2' C:DC13 4.0 0.8 1.0
C2 C:DC13 4.1 90.3 1.0
CB A:ALA57 4.1 76.5 1.0
N3 C:DC13 4.1 86.9 1.0
C1' C:DC13 4.3 0.2 1.0
O5' A:0G4701 4.4 97.7 0.5
N4 C:DC13 4.5 84.3 1.0
PA A:0G4701 4.5 99.9 0.5
C1' A:0G4701 4.7 0.2 0.5
O A:ALA44 4.8 67.8 1.0
C1' A:0G4701 4.8 0.9 0.5
O4' A:0G4701 4.8 0.9 0.5
O1B A:0G4701 4.8 1.0 0.5
O4' A:0G4701 4.9 0.1 0.5
O2 C:DC13 4.9 90.5 1.0

Fluorine binding site 2 out of 2 in 4qw9

Go back to Fluorine Binding Sites List in 4qw9
Fluorine binding site 2 out of 2 in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)Ftc-Ppnp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)Ftc-Ppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:97.5
occ:0.50
 F5 A:0G4701 0.0 97.5 0.5
F5 A:0G4701 0.4 97.5 0.5
C5 A:0G4701 1.3 89.0 0.5
C5 A:0G4701 1.6 89.5 0.5
C6 A:0G4701 2.4 85.9 0.5
C4 A:0G4701 2.4 99.5 0.5
C6 A:0G4701 2.5 86.7 0.5
C4 A:0G4701 2.7 0.1 0.5
N4 A:0G4701 2.8 0.1 0.5
C6 C:DC13 3.0 90.3 1.0
N4 A:0G4701 3.1 0.4 0.5
C5 C:DC13 3.1 86.5 1.0
O1A A:0G4701 3.2 0.2 0.5
N1 C:DC13 3.4 94.2 1.0
N1 A:0G4701 3.6 91.5 0.5
N3 A:0G4701 3.6 0.4 0.5
O A:HOH818 3.6 63.6 1.0
C4 C:DC13 3.7 85.6 1.0
N1 A:0G4701 3.7 92.8 0.5
C2' C:DC13 3.8 0.8 1.0
N3 A:0G4701 3.9 0.2 0.5
C2 C:DC13 4.0 90.3 1.0
C2 A:0G4701 4.0 95.4 0.5
N3 C:DC13 4.1 86.9 1.0
C1' C:DC13 4.1 0.2 1.0
C2 A:0G4701 4.2 96.6 0.5
O5' A:0G4701 4.3 97.7 0.5
PA A:0G4701 4.4 99.9 0.5
CB A:ALA57 4.4 76.5 1.0
N4 C:DC13 4.5 84.3 1.0
O1B A:0G4701 4.7 1.0 0.5
C1' A:0G4701 4.8 0.2 0.5
O2 C:DC13 4.8 90.5 1.0
O4' A:0G4701 4.9 0.9 0.5
C1' A:0G4701 4.9 0.9 0.5
O4' A:0G4701 4.9 0.1 0.5

Reference:

V.Gaur, R.Vyas, J.D.Fowler, G.Efthimiopoulos, J.Y.Feng, Z.Suo. Structural and Kinetic Insights Into Binding and Incorporation of L-Nucleotide Analogs By A Y-Family Dna Polymerase. Nucleic Acids Res. V. 42 9984 2014.
ISSN: ISSN 0305-1048
PubMed: 25104018
DOI: 10.1093/NAR/GKU709
Page generated: Thu Aug 1 05:30:55 2024

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