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: Sat Aug 3 00:09:40 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy