Fluorine in PDB 8sv3: 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex

Enzymatic activity of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex

All present enzymatic activity of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex:
3.1.26.4;

Protein crystallography data

The structure of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex, PDB code: 8sv3 was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.54 / 1.51
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.983, 89, 72.566, 90, 100.44, 90
R / Rfree (%) 17.7 / 21

Other elements in 8sv3:

The structure of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms
Magnesium (Mg) 1 atom
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex (pdb code 8sv3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex, PDB code: 8sv3:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 8sv3

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Fluorine binding site 1 out of 10 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1

b:18.4
occ:1.00
 F8 D:B861 0.0 18.4 1.0
C6 D:B861 1.3 14.1 1.0
C1 D:B861 2.4 14.5 1.0
C5 D:B861 2.4 13.5 1.0
N7 D:B861 2.7 15.0 1.0
O D:HOH312 3.2 27.8 1.0
O D:HOH353 3.3 26.2 1.0
O D:HOH330 3.4 21.3 1.0
N2 D:B861 3.6 13.9 1.0
N4 D:B861 3.6 13.7 1.0
C3 D:B861 4.1 12.3 1.0
O16 D:B861 4.5 22.0 1.0
O6 D:7GU2 4.6 13.6 1.0
O11 D:B861 4.8 16.2 1.0
C10 D:B861 4.8 15.6 1.0

Fluorine binding site 2 out of 10 in 8sv3

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Fluorine binding site 2 out of 10 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F3

b:14.0
occ:1.00
 F D:C373 0.0 14.0 1.0
C5 D:C373 1.4 12.1 1.0
C6 D:C373 2.4 12.3 1.0
C4 D:C373 2.4 10.5 1.0
N4 D:C373 2.7 11.1 1.0
O D:HOH358 3.0 23.8 1.0
O D:HOH334 3.1 19.5 1.0
O D:HOH341 3.2 17.8 1.0
N9 D:7GU2 3.4 13.5 1.0
C8 D:7GU2 3.5 12.7 1.0
C2' D:7GU2 3.6 15.1 1.0
N1 D:C373 3.6 12.3 1.0
O D:HOH338 3.6 18.5 1.0
N3 D:C373 3.6 11.0 1.0
C4 D:7GU2 3.7 13.0 1.0
O6 D:7GU4 3.8 12.0 1.0
C7 D:7GU2 3.8 16.4 1.0
C5 D:7GU2 3.9 13.1 1.0
C7 D:7GU4 4.0 15.0 1.0
C1' D:7GU2 4.0 14.0 1.0
C2 D:C373 4.1 11.6 1.0
C6 D:7GU4 4.2 11.5 1.0
C5 D:7GU4 4.3 11.9 1.0
N3 D:7GU2 4.4 12.8 1.0
C6 D:7GU2 4.8 12.7 1.0
C1' D:C373 4.8 12.6 1.0
O4' D:C373 4.9 13.7 1.0
C3' D:7GU2 5.0 15.6 1.0

Fluorine binding site 3 out of 10 in 8sv3

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Fluorine binding site 3 out of 10 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F9

b:16.1
occ:0.50
 F D:C379 0.0 16.1 0.5
F D:C379 0.7 22.2 0.5
C5 D:C379 1.1 21.0 0.5
C5 D:C379 1.3 14.5 0.5
C6 D:C379 1.8 20.6 0.5
C6 D:C379 2.3 16.3 0.5
C4 D:C379 2.4 14.8 0.5
C4 D:C379 2.4 18.9 0.5
N4 D:C379 2.8 14.0 0.5
N1 D:C379 3.0 22.9 0.5
N4 D:C379 3.1 17.9 0.5
O D:HOH307 3.2 41.1 1.0
N1 D:UCL8 3.3 18.8 0.5
C2' D:UCL8 3.3 20.7 0.5
N1 D:UCL8 3.4 15.5 0.5
O D:HOH326 3.4 23.2 1.0
C6 D:UCL8 3.4 16.9 0.5
C6 D:UCL8 3.4 16.1 0.5
N3 D:C379 3.5 18.6 0.5
N1 D:C379 3.5 15.9 0.5
C2' D:UCL8 3.6 18.6 0.5
N3 D:C379 3.6 16.3 0.5
C1' D:UCL8 3.7 19.3 0.5
O D:HOH303 3.7 25.4 1.0
C2 D:C379 3.7 20.0 0.5
C2 D:UCL8 3.7 15.4 0.5
O D:HOH356 3.7 37.2 1.0
C5 D:UCL8 3.8 13.8 0.5
O D:HOH359 3.8 37.5 1.0
C1' D:UCL8 3.9 18.5 0.5
C2 D:UCL8 3.9 18.4 0.5
C5 D:UCL8 4.0 15.8 0.5
C2 D:C379 4.0 16.6 0.5
N3 D:UCL8 4.1 14.2 0.5
C4 D:UCL8 4.1 14.4 0.5
C7 D:7GU10 4.2 14.3 0.5
C1' D:C379 4.2 24.8 0.5
O1P D:C379 4.3 25.3 0.5
O2 D:UCL8 4.3 15.1 0.5
O6 D:7GU10 4.4 13.7 0.5
N3 D:UCL8 4.4 15.7 0.5
O2 D:UCL8 4.4 19.5 0.5
C7 D:7GU10 4.5 25.7 0.5
C4 D:UCL8 4.5 16.0 0.5
C2' D:C379 4.5 26.2 0.5
O4' D:C379 4.5 27.0 0.5
C5 D:7GU10 4.6 13.0 0.5
CL D:UCL8 4.7 16.4 0.5
C6 D:7GU10 4.7 11.8 0.5
C1' D:C379 4.8 16.4 0.5
C3' D:UCL8 4.8 19.8 0.5
O4 D:UCL8 4.9 13.1 0.5
O6 D:7GU10 4.9 16.9 0.5
O5' D:C379 4.9 20.1 0.5
O4' D:UCL8 4.9 17.0 0.5
O2 D:C379 4.9 20.8 0.5
CL D:UCL8 5.0 16.5 0.5
C8 D:7GU10 5.0 14.1 0.5

Fluorine binding site 4 out of 10 in 8sv3

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Fluorine binding site 4 out of 10 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F9

b:22.2
occ:0.50
 F D:C379 0.0 22.2 0.5
F D:C379 0.7 16.1 0.5
C5 D:C379 1.3 21.0 0.5
C5 D:C379 1.8 14.5 0.5
C4 D:C379 2.4 18.9 0.5
C6 D:C379 2.4 20.6 0.5
C4 D:C379 2.5 14.8 0.5
N4 D:C379 2.5 14.0 0.5
O D:HOH326 2.6 23.2 1.0
N4 D:C379 2.7 17.9 0.5
C6 D:C379 3.0 16.3 0.5
O D:HOH303 3.2 25.4 1.0
O D:HOH359 3.3 37.5 1.0
C6 D:UCL8 3.4 16.9 0.5
C6 D:UCL8 3.5 16.1 0.5
N1 D:UCL8 3.5 18.8 0.5
N1 D:C379 3.6 22.9 0.5
N3 D:C379 3.6 18.6 0.5
C5 D:UCL8 3.6 13.8 0.5
O D:HOH356 3.6 37.2 1.0
O D:HOH307 3.6 41.1 1.0
N1 D:UCL8 3.7 15.5 0.5
C5 D:UCL8 3.7 15.8 0.5
N3 D:C379 3.8 16.3 0.5
C2' D:UCL8 3.9 20.7 0.5
C4 D:UCL8 3.9 14.4 0.5
O6 D:7GU10 4.0 13.7 0.5
C2 D:UCL8 4.0 15.4 0.5
C2 D:C379 4.0 20.0 0.5
C2' D:UCL8 4.1 18.6 0.5
C2 D:UCL8 4.1 18.4 0.5
C1' D:UCL8 4.1 19.3 0.5
N1 D:C379 4.1 15.9 0.5
N3 D:UCL8 4.2 14.2 0.5
C4 D:UCL8 4.2 16.0 0.5
C7 D:7GU10 4.3 14.3 0.5
CL D:UCL8 4.3 16.4 0.5
C1' D:UCL8 4.4 18.5 0.5
N3 D:UCL8 4.4 15.7 0.5
C2 D:C379 4.4 16.6 0.5
CL D:UCL8 4.5 16.5 0.5
C6 D:7GU10 4.5 11.8 0.5
C7 D:7GU10 4.5 25.7 0.5
O6 D:7GU10 4.5 16.9 0.5
C5 D:7GU10 4.6 13.0 0.5
O4 D:UCL8 4.6 13.1 0.5
O2 D:UCL8 4.8 15.1 0.5
O2 D:UCL8 4.8 19.5 0.5
C1' D:C379 4.8 24.8 0.5
O1P D:C379 4.8 25.3 0.5

Fluorine binding site 5 out of 10 in 8sv3

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Fluorine binding site 5 out of 10 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F11

b:18.6
occ:0.50
 F D:C3711 0.0 18.6 0.5
C5 D:C3711 1.3 15.3 0.5
F D:C3711 1.6 30.1 0.5
C4 D:C3711 2.3 15.4 0.5
C6 D:C3711 2.4 14.4 0.5
C5 D:C3711 2.6 25.2 0.5
N4 D:C3711 2.7 16.3 0.5
N4 D:C3711 2.7 22.5 0.5
C4 D:C3711 3.0 22.0 0.5
N3 D:C3711 3.6 12.1 0.5
N1 D:C3711 3.6 14.0 0.5
O D:HOH355 3.6 35.2 1.0
O D:HOH308 3.6 26.1 1.0
C7 D:7GU10 3.8 14.3 0.5
C6 D:C3711 3.8 24.7 0.5
C8 D:7GU10 3.8 14.1 0.5
C2 D:C3711 4.0 13.7 0.5
O6 D:7GU12 4.2 11.9 0.5
C7 D:7GU10 4.3 25.7 0.5
N3 D:C3711 4.4 22.4 0.5
C8 D:7GU10 4.4 27.2 0.5
C5 D:7GU10 4.4 13.0 0.5
N9 D:7GU10 4.4 13.3 0.5
O6 D:7GU12 4.7 20.0 0.5
C4 D:7GU10 4.8 12.9 0.5
C1' D:C3711 4.8 14.3 0.5
O4' D:C3711 4.8 14.4 0.5
O D:HOH356 4.9 37.2 1.0
N1 D:C3711 4.9 24.3 0.5

Fluorine binding site 6 out of 10 in 8sv3

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Fluorine binding site 6 out of 10 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F11

b:30.1
occ:0.50
 F D:C3711 0.0 30.1 0.5
C6 D:C3711 1.0 14.4 0.5
C5 D:C3711 1.1 15.3 0.5
C5 D:C3711 1.3 25.2 0.5
F D:C3711 1.6 18.6 0.5
N1 D:C3711 2.3 14.0 0.5
C4 D:C3711 2.3 15.4 0.5
C6 D:C3711 2.4 24.7 0.5
C4 D:C3711 2.4 22.0 0.5
N4 D:C3711 2.8 22.5 0.5
C2 D:C3711 3.1 13.7 0.5
N3 D:C3711 3.1 12.1 0.5
C8 D:7GU10 3.1 14.1 0.5
N9 D:7GU10 3.3 13.3 0.5
N4 D:C3711 3.3 16.3 0.5
C7 D:7GU10 3.3 14.3 0.5
O4' D:C3711 3.3 14.4 0.5
C1' D:C3711 3.4 14.3 0.5
C8 D:7GU10 3.4 27.2 0.5
C7 D:7GU10 3.5 25.7 0.5
O D:HOH355 3.5 35.2 1.0
N1 D:C3711 3.6 24.3 0.5
C4 D:7GU10 3.6 12.9 0.5
N3 D:C3711 3.6 22.4 0.5
C5 D:7GU10 3.6 13.0 0.5
C2' D:7GU10 3.8 14.9 0.5
N9 D:7GU10 3.8 26.9 0.5
C1' D:7GU10 3.9 14.1 0.5
C5 D:7GU10 4.1 23.3 0.5
C2 D:C3711 4.1 21.9 0.5
C2' D:7GU10 4.2 29.9 0.5
C4 D:7GU10 4.2 24.8 0.5
O2 D:C3711 4.3 13.1 0.5
N3 D:7GU10 4.4 12.2 0.5
C4' D:C3711 4.4 14.6 0.5
O D:HOH308 4.4 26.1 1.0
C2' D:C3711 4.5 13.7 0.5
C6 D:7GU10 4.5 11.8 0.5
C1' D:7GU10 4.6 28.1 0.5
C5' D:C3711 4.6 14.5 0.5
O6 D:7GU12 4.7 11.9 0.5
O5' D:C3711 4.7 15.7 0.5
O4' D:C3711 4.8 29.4 0.5
C1' D:C3711 4.8 28.1 0.5
C7 D:7GU12 4.8 13.0 0.5
C3' D:C3711 4.8 13.5 0.5
O6 D:7GU12 4.9 20.0 0.5
C6 D:7GU10 4.9 20.9 0.5
C7 D:7GU12 5.0 21.2 0.5
O5' D:C3711 5.0 38.8 0.5

Fluorine binding site 7 out of 10 in 8sv3

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Fluorine binding site 7 out of 10 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1

b:20.4
occ:1.00
 F8 E:B861 0.0 20.4 1.0
C6 E:B861 1.3 14.4 1.0
C1 E:B861 2.4 14.6 1.0
C5 E:B861 2.4 15.1 1.0
N7 E:B861 2.7 15.5 1.0
N2 E:B861 3.6 14.7 1.0
N4 E:B861 3.6 15.6 1.0
O E:HOH119 3.8 30.9 1.0
C3 E:B861 4.1 14.3 1.0
O16 E:B861 4.4 18.7 1.0
O6 E:7GU2 4.5 21.4 1.0
O11 E:B861 4.8 18.5 1.0
C10 E:B861 4.8 16.9 1.0

Fluorine binding site 8 out of 10 in 8sv3

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Fluorine binding site 8 out of 10 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F3

b:20.5
occ:1.00
 F E:C373 0.0 20.5 1.0
C5 E:C373 1.3 17.7 1.0
C4 E:C373 2.4 16.3 1.0
C6 E:C373 2.4 17.5 1.0
N4 E:C373 2.7 18.7 1.0
O E:HOH130 3.2 22.1 1.0
C2' E:7GU2 3.3 23.4 1.0
O E:HOH142 3.3 31.6 1.0
N9 E:7GU2 3.4 19.4 1.0
O E:HOH135 3.5 35.6 1.0
N3 E:C373 3.6 17.3 1.0
N1 E:C373 3.6 18.4 1.0
C4 E:7GU2 3.7 19.9 1.0
C1' E:7GU2 3.7 20.7 1.0
C8 E:7GU2 3.7 18.3 1.0
C2 E:C373 4.1 17.2 1.0
C5 E:7GU2 4.1 17.4 1.0
N3 E:7GU2 4.1 21.1 1.0
C7 E:7GU2 4.2 22.1 1.0
O D:HOH305 4.4 26.2 1.0
O6 E:7GU4 4.6 17.2 1.0
C3' E:7GU2 4.7 25.0 1.0
C1' E:C373 4.8 22.4 1.0
O4' E:C373 4.8 21.0 1.0
C2 E:7GU2 4.9 17.0 1.0
C6 E:7GU2 4.9 17.9 1.0
C7 E:7GU4 5.0 15.9 1.0
O2P E:C373 5.0 30.7 1.0

Fluorine binding site 9 out of 10 in 8sv3

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Fluorine binding site 9 out of 10 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F9

b:14.2
occ:1.00
 F E:C379 0.0 14.2 1.0
C5 E:C379 1.4 12.1 1.0
C4 E:C379 2.4 11.8 1.0
C6 E:C379 2.4 11.8 1.0
N4 E:C379 2.7 12.3 1.0
O E:HOH134 3.1 24.4 1.0
O E:HOH126 3.2 17.6 1.0
O E:HOH123 3.3 21.7 1.0
N3 E:C379 3.6 12.8 1.0
N1 E:C379 3.6 13.7 1.0
O1P E:C379 3.6 15.3 1.0
C6 E:UCL8 3.7 12.2 1.0
O E:HOH144 3.7 23.0 1.0
N1 E:UCL8 3.7 11.1 1.0
C5 E:UCL8 3.8 12.9 1.0
C2 E:UCL8 3.9 12.0 1.0
N3 E:UCL8 3.9 12.7 1.0
C2' E:UCL8 4.0 12.4 1.0
C4 E:UCL8 4.0 13.3 1.0
C3' E:UCL8 4.0 13.1 1.0
C2 E:C379 4.1 13.5 1.0
O E:HOH148 4.2 20.8 1.0
O5' E:C379 4.3 13.3 1.0
O2 E:UCL8 4.4 13.1 1.0
C1' E:UCL8 4.4 12.7 1.0
P E:C379 4.5 13.9 1.0
O E:HOH109 4.6 18.6 1.0
O6 E:7GU10 4.7 13.6 1.0
CL E:UCL8 4.7 15.8 1.0
O4 E:UCL8 4.7 14.0 1.0
O3' E:UCL8 4.8 15.1 1.0
O4' E:C379 4.8 14.5 1.0
C1' E:C379 4.8 14.9 1.0

Fluorine binding site 10 out of 10 in 8sv3

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Fluorine binding site 10 out of 10 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F11

b:16.8
occ:1.00
 F E:C3711 0.0 16.8 1.0
C5 E:C3711 1.4 14.4 1.0
C6 E:C3711 2.4 14.2 1.0
C4 E:C3711 2.4 14.5 1.0
N4 E:C3711 2.8 15.4 1.0
O E:HOH133 3.1 30.6 1.0
O E:HOH143 3.5 25.5 1.0
C8 E:7GU10 3.6 15.1 1.0
N1 E:C3711 3.6 14.0 1.0
C7 E:7GU10 3.6 17.5 1.0
N3 E:C3711 3.6 13.8 1.0
O E:HOH129 3.9 25.2 1.0
N9 E:7GU10 4.0 13.6 1.0
C5 E:7GU10 4.1 13.0 1.0
C2 E:C3711 4.1 14.0 1.0
C4 E:7GU10 4.3 14.1 1.0
O6 E:7GU12 4.4 15.0 1.0
C2' E:7GU10 4.4 14.2 1.0
O E:HOH127 4.6 17.5 0.5
C1' E:C3711 4.8 14.5 1.0
C1' E:7GU10 4.8 14.6 1.0
C6 E:7GU10 4.9 13.9 1.0
C7 E:7GU12 5.0 17.6 1.0
O4' E:C3711 5.0 14.6 1.0

Reference:

P.S.Pallan, T.P.Lybrand, E.Rozners, M.Abramov, G.Schepers, E.Eremeeva, P.Herdewijn, M.Egli. Conformational Morphing By A Dna Analogue Featuring 7-Deazapurines and 5-Halogenpyrimidines and the Origins of Adenine-Tract Geometry. Biochemistry 2023.
ISSN: ISSN 0006-2960
PubMed: 37694722
DOI: 10.1021/ACS.BIOCHEM.3C00327
Page generated: Sat Aug 3 00:09:38 2024

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