Atomistry » Fluorine » PDB 8smc-8t4v » 8sv4
Atomistry »
  Fluorine »
    PDB 8smc-8t4v »
      8sv4 »

Fluorine in PDB 8sv4: 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: 8sv4 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) 27.60 / 2.30
Space group P 62
Cell size a, b, c (Å), α, β, γ (°) 92.539, 92.539, 78.896, 90, 90, 120
R / Rfree (%) 21.4 / 25.4

Other elements in 8sv4:

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

Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex (pdb code 8sv4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex, PDB code: 8sv4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 8sv4

Go back to Fluorine Binding Sites List in 8sv4
Fluorine binding site 1 out of 8 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
B:F1

b:43.6
occ:1.00
 F8 B:B861 0.0 43.6 1.0
C6 B:B861 1.4 38.0 1.0
C1 B:B861 2.4 38.4 1.0
C5 B:B861 2.4 37.5 1.0
N7 B:B861 2.7 39.5 1.0
O B:HOH103 2.8 51.0 1.0
N4 B:B861 3.6 42.3 1.0
N2 B:B861 3.6 34.9 1.0
C3 B:B861 4.1 37.9 1.0
O16 B:B861 4.1 60.9 1.0
O6 B:7GU2 4.6 41.7 1.0
C10 B:B861 4.8 46.9 1.0
O11 B:B861 4.9 51.5 1.0

Fluorine binding site 2 out of 8 in 8sv4

Go back to Fluorine Binding Sites List in 8sv4
Fluorine binding site 2 out of 8 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
B:F3

b:41.3
occ:1.00
 F B:C373 0.0 41.3 1.0
C5 B:C373 1.3 39.0 1.0
C6 B:C373 2.3 42.6 1.0
C4 B:C373 2.4 41.0 1.0
N4 B:C373 2.8 37.7 1.0
N9 B:7GU2 3.4 41.6 1.0
C8 B:7GU2 3.5 41.0 1.0
C2' B:7GU2 3.5 47.4 1.0
N1 B:C373 3.5 42.7 1.0
N3 B:C373 3.6 42.2 1.0
C4 B:7GU2 3.7 41.2 1.0
C7 B:7GU2 3.7 42.9 1.0
C5 B:7GU2 3.8 41.1 1.0
C1' B:7GU2 4.0 45.4 1.0
O6 B:7GU4 4.1 38.9 1.0
C2 B:C373 4.1 42.5 1.0
C7 B:7GU4 4.1 44.5 1.0
N3 B:7GU2 4.3 43.9 1.0
C5 B:7GU4 4.6 40.6 1.0
C6 B:7GU4 4.6 41.4 1.0
C6 B:7GU2 4.7 44.1 1.0
C1' B:C373 4.7 41.2 1.0
O4' B:C373 4.8 34.6 1.0
C3' B:7GU2 4.9 46.8 1.0

Fluorine binding site 3 out of 8 in 8sv4

Go back to Fluorine Binding Sites List in 8sv4
Fluorine binding site 3 out of 8 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
B:F9

b:49.8
occ:1.00
 F B:C379 0.0 49.8 1.0
C5 B:C379 1.4 45.8 1.0
C4 B:C379 2.4 46.9 1.0
C6 B:C379 2.4 50.7 1.0
N4 B:C379 2.7 51.9 1.0
C6 B:UCL8 3.6 46.9 1.0
N3 B:C379 3.6 43.2 1.0
N1 B:C379 3.6 52.2 1.0
N1 B:UCL8 3.8 51.5 1.0
C2' B:UCL8 3.8 63.7 1.0
C5 B:UCL8 3.9 43.9 1.0
C2 B:C379 4.1 47.1 1.0
O6 B:7GU10 4.2 47.0 1.0
C2 B:UCL8 4.3 47.6 1.0
C1' B:UCL8 4.3 59.7 1.0
C4 B:UCL8 4.4 48.9 1.0
N3 B:UCL8 4.5 46.3 1.0
CL B:UCL8 4.6 57.9 1.0
C1' B:C379 4.9 70.5 1.0
C7 B:7GU10 5.0 53.9 1.0
O2 B:UCL8 5.0 50.1 1.0

Fluorine binding site 4 out of 8 in 8sv4

Go back to Fluorine Binding Sites List in 8sv4
Fluorine binding site 4 out of 8 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
B:F11

b:47.4
occ:1.00
 F B:C3711 0.0 47.4 1.0
C5 B:C3711 1.3 41.0 1.0
C4 B:C3711 2.3 43.8 1.0
C6 B:C3711 2.4 42.4 1.0
N4 B:C3711 2.7 44.8 1.0
O B:HOH101 2.9 52.8 0.6
C2' B:7GU10 3.2 80.3 1.0
N9 B:7GU10 3.5 61.4 1.0
N3 B:C3711 3.6 42.6 1.0
N1 B:C3711 3.6 49.8 1.0
C8 B:7GU10 3.7 58.2 1.0
C1' B:7GU10 3.8 76.0 1.0
C4 B:7GU10 3.9 49.0 1.0
O1P B:C3711 4.0 83.1 1.0
C2 B:C3711 4.1 47.2 1.0
C7 B:7GU10 4.2 53.9 1.0
C5 B:7GU10 4.4 48.3 1.0
O6 B:7GU12 4.4 47.7 1.0
N3 B:7GU10 4.6 47.0 1.0
O5' B:C3711 4.6 87.4 1.0
C3' B:7GU10 4.6 90.1 1.0
C1' B:C3711 4.8 68.3 1.0
P B:C3711 4.9 98.4 1.0
C7 B:7GU12 4.9 57.0 1.0

Fluorine binding site 5 out of 8 in 8sv4

Go back to Fluorine Binding Sites List in 8sv4
Fluorine binding site 5 out of 8 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
C:F1

b:46.4
occ:1.00
 F8 C:B861 0.0 46.4 1.0
C6 C:B861 1.3 41.5 1.0
C1 C:B861 2.3 44.6 1.0
C5 C:B861 2.4 41.9 1.0
N7 C:B861 2.7 45.2 1.0
N4 C:B861 3.6 45.8 1.0
N2 C:B861 3.6 42.5 1.0
O C:HOH111 3.7 51.3 1.0
C3 C:B861 4.1 47.0 1.0
O16 C:B861 4.3 64.3 1.0
C10 C:B861 4.8 53.8 1.0
O11 C:B861 4.9 62.4 1.0
O6 C:7GU2 4.9 52.8 1.0
C7 C:7GU2 5.0 43.9 1.0

Fluorine binding site 6 out of 8 in 8sv4

Go back to Fluorine Binding Sites List in 8sv4
Fluorine binding site 6 out of 8 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
C:F3

b:52.6
occ:1.00
 F C:C373 0.0 52.6 1.0
C5 C:C373 1.3 50.1 1.0
C4 C:C373 2.3 49.4 1.0
C6 C:C373 2.4 55.5 1.0
N4 C:C373 2.7 49.6 1.0
C2' C:7GU2 3.4 53.1 1.0
N1 C:C373 3.6 57.9 1.0
N3 C:C373 3.6 48.4 1.0
N9 C:7GU2 3.7 50.6 1.0
C8 C:7GU2 3.7 44.1 1.0
C1' C:7GU2 4.0 52.9 1.0
C4 C:7GU2 4.0 47.9 1.0
C2 C:C373 4.1 52.7 1.0
C7 C:7GU2 4.1 43.9 1.0
C5 C:7GU2 4.3 45.3 1.0
O6 C:7GU4 4.5 51.0 1.0
N3 C:7GU2 4.7 49.3 1.0
O1P C:C373 4.7 68.1 1.0
C3' C:7GU2 4.8 58.7 1.0
C1' C:C373 4.8 67.6 1.0
O5' C:C373 4.9 66.8 1.0

Fluorine binding site 7 out of 8 in 8sv4

Go back to Fluorine Binding Sites List in 8sv4
Fluorine binding site 7 out of 8 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
C:F9

b:52.9
occ:1.00
 F C:C379 0.0 52.9 1.0
C5 C:C379 1.4 48.1 1.0
C6 C:C379 2.4 47.5 1.0
C4 C:C379 2.4 46.4 1.0
N4 C:C379 2.7 43.0 1.0
O C:HOH108 3.1 58.4 1.0
O C:HOH105 3.2 54.9 1.0
C6 C:UCL8 3.4 44.5 1.0
N1 C:UCL8 3.5 50.5 1.0
N1 C:C379 3.6 50.5 1.0
N3 C:C379 3.6 44.2 1.0
C5 C:UCL8 3.7 38.7 1.0
C2' C:UCL8 3.8 66.8 1.0
C2 C:UCL8 3.9 45.7 1.0
C2 C:C379 4.1 48.9 1.0
C4 C:UCL8 4.1 41.4 1.0
C1' C:UCL8 4.1 61.2 1.0
N3 C:UCL8 4.2 38.3 1.0
CL C:UCL8 4.5 54.8 1.0
O6 C:7GU10 4.5 44.2 1.0
O2 C:UCL8 4.6 49.6 1.0
C7 C:7GU10 4.8 43.7 1.0
C1' C:C379 4.8 57.3 1.0
O4 C:UCL8 4.9 41.9 1.0

Fluorine binding site 8 out of 8 in 8sv4

Go back to Fluorine Binding Sites List in 8sv4
Fluorine binding site 8 out of 8 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
C:F11

b:50.2
occ:1.00
 F C:C3711 0.0 50.2 1.0
C5 C:C3711 1.3 48.9 1.0
C4 C:C3711 2.4 45.9 1.0
C6 C:C3711 2.4 43.5 1.0
N4 C:C3711 2.7 43.8 1.0
O C:HOH109 3.2 30.1 0.5
C7 C:7GU10 3.4 43.7 1.0
C8 C:7GU10 3.4 38.9 1.0
O C:HOH104 3.4 59.2 1.0
N3 C:C3711 3.6 44.5 1.0
N1 C:C3711 3.6 41.5 1.0
C5 C:7GU10 3.9 44.1 1.0
N9 C:7GU10 4.0 39.4 1.0
O6 C:7GU12 4.1 41.0 1.0
C2 C:C3711 4.1 44.4 1.0
C4 C:7GU10 4.3 43.0 1.0
C2' C:7GU10 4.7 43.5 1.0
C6 C:7GU10 4.7 46.1 1.0
C1' C:C3711 4.8 44.4 1.0
C1' C:7GU10 4.9 41.1 1.0
C6 C:7GU12 4.9 44.9 1.0
C7 C:7GU12 5.0 49.1 1.0
O6 C:7GU10 5.0 44.2 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: Wed Jul 16 08:19:29 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy