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Fluorine in PDB 2v9w: Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand

Enzymatic activity of Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand

All present enzymatic activity of Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand:
2.7.7.7;

Protein crystallography data

The structure of Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand, PDB code: 2v9w was solved by A.Irimia, P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.51 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.704, 186.744, 52.730, 90.00, 110.06, 90.00
R / Rfree (%) 21.8 / 29

Other elements in 2v9w:

The structure of Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand (pdb code 2v9w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand, PDB code: 2v9w:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 2v9w

Go back to Fluorine Binding Sites List in 2v9w
Fluorine binding site 1 out of 4 in the Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F6

b:46.8
occ:1.00
F4 D:DFT6 0.0 46.8 1.0
C4 D:DFT6 1.3 49.5 1.0
C3 D:DFT6 2.4 50.0 1.0
C5 D:DFT6 2.4 50.4 1.0
C5M D:DFT6 2.9 50.6 1.0
C6 D:DG5 3.1 55.6 1.0
O6 D:DG5 3.2 57.9 1.0
C5 D:DG5 3.5 54.5 1.0
N1 D:DG5 3.5 55.8 1.0
O C:HOH2012 3.6 25.9 1.0
N1 D:DA7 3.6 52.3 1.0
C2 D:DFT6 3.6 52.4 1.0
C6 D:DFT6 3.6 50.8 1.0
O4 C:DT12 3.7 0.8 1.0
N6 D:DA7 3.8 53.6 1.0
C6 D:DA7 3.8 53.0 1.0
N7 D:DG5 4.0 53.8 1.0
C4 D:DG5 4.1 55.6 1.0
C1 D:DFT6 4.1 51.8 1.0
C2 D:DG5 4.2 54.7 1.0
C2 D:DA7 4.3 53.2 1.0
N3 D:DG5 4.5 55.7 1.0
N3 A:DCT1347 4.6 48.0 1.0
C4 C:DT12 4.6 0.5 1.0
N3 C:DT12 4.6 0.6 1.0
C5 D:DA7 4.6 53.4 1.0
F2 D:DFT6 4.7 56.2 1.0
C8 D:DG5 4.8 55.2 1.0
N4 A:DCT1347 4.9 49.0 1.0
N9 D:DG5 4.9 55.7 1.0

Fluorine binding site 2 out of 4 in 2v9w

Go back to Fluorine Binding Sites List in 2v9w
Fluorine binding site 2 out of 4 in the Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F6

b:56.2
occ:1.00
F2 D:DFT6 0.0 56.2 1.0
C2 D:DFT6 1.3 52.4 1.0
C3 D:DFT6 2.4 50.0 1.0
C1 D:DFT6 2.4 51.8 1.0
C1' D:DFT6 2.8 50.6 1.0
C4 D:DFT6 3.6 49.5 1.0
C6 D:DFT6 3.6 50.8 1.0
O4' D:DA7 3.7 48.3 1.0
N2 D:DG5 3.7 54.8 1.0
C2' D:DFT6 3.9 49.5 1.0
O4' D:DFT6 4.0 49.6 1.0
C5 D:DFT6 4.1 50.4 1.0
C2 D:DG5 4.2 54.7 1.0
C5' D:DA7 4.3 48.2 1.0
C4 D:DA7 4.3 52.5 1.0
N9 D:DA7 4.4 51.0 1.0
N3 D:DA7 4.5 53.4 1.0
O2 A:DCT1347 4.5 50.7 1.0
N3 D:DG5 4.5 55.7 1.0
C4' D:DA7 4.5 47.0 1.0
C1' D:DA7 4.6 48.9 1.0
C5 D:DA7 4.7 53.4 1.0
O5' D:DA7 4.7 49.6 1.0
F4 D:DFT6 4.7 46.8 1.0
N1 D:DG5 4.8 55.8 1.0
NZ A:LYS78 4.8 53.0 1.0
C8 D:DA7 4.8 52.5 1.0
C4' D:DFT6 4.8 49.2 1.0
C3' D:DFT6 4.9 49.4 1.0
C2 D:DA7 5.0 53.2 1.0
N7 D:DA7 5.0 53.6 1.0

Fluorine binding site 3 out of 4 in 2v9w

Go back to Fluorine Binding Sites List in 2v9w
Fluorine binding site 3 out of 4 in the Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F6

b:65.8
occ:1.00
F4 F:DFT6 0.0 65.8 1.0
C4 F:DFT6 1.4 63.7 1.0
C3 F:DFT6 2.4 61.0 1.0
C5 F:DFT6 2.4 64.1 1.0
C5M F:DFT6 2.8 64.6 1.0
N7 F:DG5 3.5 61.5 1.0
C5 F:DG5 3.5 60.7 1.0
C6 F:DG5 3.6 60.4 1.0
O6 F:DG5 3.6 62.8 1.0
C6 F:DFT6 3.7 61.8 1.0
C2 F:DFT6 3.7 60.3 1.0
N6 F:DA7 3.7 41.4 1.0
C8 F:DG5 4.2 61.8 1.0
C1 F:DFT6 4.2 61.3 1.0
C4 F:DG5 4.2 61.0 1.0
N1 F:DG5 4.4 58.7 1.0
O4 E:DT12 4.5 96.4 1.0
N9 F:DG5 4.6 62.6 1.0
F2 F:DFT6 4.7 59.8 1.0
C6 F:DA7 4.8 41.0 1.0
N2 E:DG13 4.8 87.2 1.0
O F:HOH2003 4.9 38.5 1.0
N3 F:DG5 5.0 60.0 1.0
C2 F:DG5 5.0 58.7 1.0

Fluorine binding site 4 out of 4 in 2v9w

Go back to Fluorine Binding Sites List in 2v9w
Fluorine binding site 4 out of 4 in the Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F6

b:59.8
occ:1.00
F2 F:DFT6 0.0 59.8 1.0
C2 F:DFT6 1.3 60.3 1.0
C3 F:DFT6 2.4 61.0 1.0
C1 F:DFT6 2.4 61.3 1.0
C1' F:DFT6 2.9 62.6 1.0
N2 F:DG5 3.2 57.6 1.0
C2 F:DG5 3.3 58.7 1.0
C6 F:DFT6 3.6 61.8 1.0
C4 F:DFT6 3.6 63.7 1.0
N1 F:DG5 3.7 58.7 1.0
N3 F:DG5 3.7 60.0 1.0
O4' F:DFT6 3.7 63.9 1.0
C5 F:DA7 3.8 40.4 1.0
C6 F:DA7 3.9 41.0 1.0
N7 F:DA7 4.0 40.3 1.0
C5 F:DFT6 4.1 64.1 1.0
C4 F:DA7 4.1 41.1 1.0
C2' F:DFT6 4.2 63.6 1.0
O2 B:DCT1346 4.2 51.2 1.0
N6 F:DA7 4.3 41.4 1.0
C4 F:DG5 4.4 61.0 1.0
N1 F:DA7 4.4 44.2 1.0
C8 F:DA7 4.4 41.2 1.0
C6 F:DG5 4.5 60.4 1.0
N9 F:DA7 4.5 41.4 1.0
N3 F:DA7 4.6 44.6 1.0
C2 F:DA7 4.7 46.1 1.0
F4 F:DFT6 4.7 65.8 1.0
C5 F:DG5 4.8 60.7 1.0
O4' F:DA7 4.9 46.2 1.0
C2 B:DCT1346 4.9 51.1 1.0
C4' F:DFT6 5.0 63.4 1.0

Reference:

A.Irimia, R.L.Eoff, P.S.Pallan, F.P.Guengerich, M.Egli. Structure and Activity of Y-Class Dna Polymerase DPO4 From Sulfolobus Solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4- Difluorotoluene. J.Biol.Chem. V. 282 36421 2007.
ISSN: ISSN 0021-9258
PubMed: 17951245
DOI: 10.1074/JBC.M707267200
Page generated: Sun Dec 13 11:40:16 2020

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