Atomistry » Fluorine » PDB 8aek-8b98 » 8ahf
Atomistry »
  Fluorine »
    PDB 8aek-8b98 »
      8ahf »

Fluorine in PDB 8ahf: Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery

Enzymatic activity of Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery

All present enzymatic activity of Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery:
5.1.3.14;

Protein crystallography data

The structure of Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery, PDB code: 8ahf was solved by L.M.Baker, J.B.Murray, R.E.Hubbard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.17 / 2.27
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 109.315, 109.315, 135.866, 90, 90, 90
R / Rfree (%) 17.7 / 23.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery (pdb code 8ahf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery, PDB code: 8ahf:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 8ahf

Go back to Fluorine Binding Sites List in 8ahf
Fluorine binding site 1 out of 4 in the Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:62.8
occ:1.00
F1 A:M3U401 0.0 62.8 1.0
C6 A:M3U401 1.3 59.7 1.0
H9 A:M3U401 1.9 60.1 1.0
F2 A:M3U401 2.1 56.0 1.0
O2 A:M3U401 2.3 62.8 1.0
HA A:VAL289 2.3 37.2 1.0
HB2 A:GLU292 2.6 45.1 1.0
HB2 A:ALA293 2.9 40.4 1.0
H A:ALA293 2.9 42.8 1.0
HE2 A:PHE272 3.0 42.0 1.0
HG23 A:VAL289 3.1 40.5 1.0
CA A:VAL289 3.2 34.5 1.0
HG11 A:VAL289 3.3 41.0 1.0
N A:ALA293 3.3 43.1 1.0
CB A:GLU292 3.5 45.3 1.0
HB3 A:GLU292 3.6 45.1 1.0
C5 A:M3U401 3.6 61.7 1.0
HA A:ALA293 3.7 42.3 1.0
CB A:ALA293 3.7 38.7 1.0
H8 A:M3U401 3.7 63.4 1.0
CG2 A:VAL289 3.8 41.0 1.0
CA A:ALA293 3.8 44.5 1.0
CB A:VAL289 3.8 39.0 1.0
O A:VAL289 3.9 42.3 1.0
O A:GLY288 3.9 43.5 1.0
HG22 A:VAL289 4.0 40.4 1.0
CE2 A:PHE272 4.0 40.4 1.0
H6 A:M3U401 4.0 63.7 1.0
N A:VAL289 4.0 41.4 1.0
OE1 A:GLU292 4.0 58.7 1.0
CG1 A:VAL289 4.0 41.9 1.0
C A:VAL289 4.1 37.5 1.0
C A:GLU292 4.1 40.4 1.0
H A:GLU292 4.1 44.1 1.0
CA A:GLU292 4.2 41.2 1.0
HB3 A:ALA293 4.2 40.4 1.0
C A:GLY288 4.2 46.1 1.0
C4 A:M3U401 4.3 65.1 1.0
HD2 A:PHE272 4.3 44.8 1.0
HB1 A:ALA293 4.4 40.4 1.0
CG A:GLU292 4.5 48.6 1.0
CD A:GLU292 4.5 55.0 1.0
H11 A:M3U401 4.6 64.1 1.0
N A:GLU292 4.6 44.5 1.0
H5 A:M3U401 4.6 64.3 1.0
CD2 A:PHE272 4.6 47.2 1.0
H A:VAL289 4.6 40.7 1.0
HG12 A:VAL289 4.6 41.0 1.0
HG21 A:VAL289 4.6 40.4 1.0
C7 A:M3U401 4.7 66.4 1.0
HG13 A:VAL289 4.7 41.0 1.0
HB A:VAL289 4.8 39.0 1.0
HD13 A:LEU296 4.9 43.1 1.0
HD2 A:HIS273 4.9 45.0 1.0
HZ A:PHE272 4.9 41.2 1.0
CZ A:PHE272 5.0 40.0 1.0
C3 A:M3U401 5.0 62.5 1.0
HG3 A:GLU292 5.0 49.2 1.0

Fluorine binding site 2 out of 4 in 8ahf

Go back to Fluorine Binding Sites List in 8ahf
Fluorine binding site 2 out of 4 in the Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:56.0
occ:1.00
F2 A:M3U401 0.0 56.0 1.0
C6 A:M3U401 1.3 59.7 1.0
H9 A:M3U401 1.9 60.1 1.0
F1 A:M3U401 2.1 62.8 1.0
O2 A:M3U401 2.2 62.8 1.0
HE2 A:PHE272 2.5 42.0 1.0
H8 A:M3U401 2.5 63.4 1.0
HD2 A:PHE272 2.5 44.8 1.0
HD2 A:HIS273 2.8 45.0 1.0
C5 A:M3U401 2.8 61.7 1.0
CE2 A:PHE272 3.1 40.4 1.0
CD2 A:PHE272 3.1 47.2 1.0
CD2 A:HIS273 3.5 43.6 1.0
H11 A:M3U401 3.7 64.1 1.0
HE2 A:HIS273 3.8 45.7 0.0
C7 A:M3U401 3.8 66.4 1.0
HB2 A:GLU292 3.9 45.1 1.0
HA A:HIS273 3.9 41.7 1.0
NE2 A:HIS273 4.0 47.3 1.0
OE1 A:GLU292 4.0 58.7 1.0
HG23 A:VAL289 4.0 40.5 1.0
C4 A:M3U401 4.1 65.1 1.0
H6 A:M3U401 4.1 63.7 1.0
HB3 A:GLU292 4.2 45.1 1.0
HA A:VAL289 4.2 37.2 1.0
H10 A:M3U401 4.4 64.2 1.0
HB3 A:ALA276 4.5 42.9 1.0
CZ A:PHE272 4.5 40.0 1.0
CG A:PHE272 4.5 44.9 1.0
HB2 A:ALA293 4.5 40.4 1.0
CB A:GLU292 4.5 45.3 1.0
HB2 A:ALA276 4.5 42.9 1.0
HD23 A:LEU182 4.6 47.2 1.0
CG A:HIS273 4.6 45.1 1.0
H7 A:M3U401 4.6 63.7 1.0
HD11 A:LEU296 4.6 43.1 1.0
HB3 A:PHE272 4.7 41.3 1.0
HA A:ALA293 4.7 42.3 1.0
CA A:HIS273 4.7 40.3 1.0
N A:HIS273 4.8 44.3 1.0
HZ A:PHE272 4.8 41.2 1.0
HD13 A:LEU296 4.8 43.1 1.0
CB A:ALA276 4.8 45.1 1.0
HB1 A:ALA276 4.8 42.9 1.0
H A:ALA293 4.9 42.8 1.0
CG2 A:VAL289 4.9 41.0 1.0
N2 A:M3U401 4.9 62.1 1.0
HG22 A:VAL289 4.9 40.4 1.0
HG11 A:VAL289 4.9 41.0 1.0

Fluorine binding site 3 out of 4 in 8ahf

Go back to Fluorine Binding Sites List in 8ahf
Fluorine binding site 3 out of 4 in the Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:53.2
occ:1.00
F1 B:M3U401 0.0 53.2 1.0
C6 B:M3U401 1.3 57.6 1.0
H9 B:M3U401 1.9 55.9 1.0
F2 B:M3U401 2.2 60.2 1.0
O2 B:M3U401 2.2 51.4 1.0
HA B:VAL289 2.4 40.7 1.0
HB2 B:GLU292 2.5 42.2 1.0
HB2 B:ALA293 3.0 44.2 1.0
HG11 B:VAL289 3.1 41.6 1.0
HE2 B:PHE272 3.2 46.5 1.0
H B:ALA293 3.2 42.6 1.0
HG23 B:VAL289 3.3 43.5 1.0
CB B:GLU292 3.3 42.3 1.0
CA B:VAL289 3.3 39.6 1.0
HB3 B:GLU292 3.4 42.1 1.0
N B:ALA293 3.4 41.1 1.0
C5 B:M3U401 3.5 47.9 1.0
HA B:ALA293 3.6 41.9 1.0
H8 B:M3U401 3.7 49.6 1.0
CB B:ALA293 3.7 45.1 1.0
CA B:ALA293 3.8 42.3 1.0
O B:VAL289 3.8 43.5 1.0
CB B:VAL289 3.9 41.2 1.0
CG1 B:VAL289 3.9 41.8 1.0
CG2 B:VAL289 3.9 44.5 1.0
H6 B:M3U401 3.9 51.2 1.0
C B:GLU292 4.0 46.1 1.0
O B:GLY288 4.0 45.2 1.0
HG22 B:VAL289 4.0 43.5 1.0
OE1 B:GLU292 4.0 46.7 1.0
CE2 B:PHE272 4.1 46.1 1.0
C B:VAL289 4.1 41.7 1.0
H B:GLU292 4.1 46.0 1.0
CA B:GLU292 4.1 45.2 1.0
HB3 B:ALA293 4.1 44.2 1.0
N B:VAL289 4.2 41.8 1.0
C4 B:M3U401 4.3 51.6 1.0
HG13 B:VAL289 4.3 41.6 1.0
CG B:GLU292 4.4 38.6 1.0
HD2 B:PHE272 4.4 45.9 1.0
CD B:GLU292 4.4 41.8 1.0
C B:GLY288 4.5 41.7 1.0
HB1 B:ALA293 4.5 44.2 1.0
H5 B:M3U401 4.5 53.4 1.0
H11 B:M3U401 4.5 48.9 1.0
N B:GLU292 4.6 48.1 1.0
C7 B:M3U401 4.6 49.3 1.0
HG12 B:VAL289 4.6 41.6 1.0
HD2 B:HIS273 4.7 44.5 1.0
CD2 B:PHE272 4.7 46.5 1.0
HG3 B:GLU292 4.8 40.2 1.0
HG21 B:VAL289 4.8 43.5 1.0
O B:GLU292 4.8 52.4 1.0
HB B:VAL289 4.8 41.6 1.0
H B:VAL289 4.8 41.3 1.0
C3 B:M3U401 4.9 53.7 1.0
HZ B:PHE272 5.0 46.0 1.0

Fluorine binding site 4 out of 4 in 8ahf

Go back to Fluorine Binding Sites List in 8ahf
Fluorine binding site 4 out of 4 in the Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Pac-Fragmentdel: Photoactivated Covalent Capture of Dna Encoded Fragments For Hit Discovery within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:60.2
occ:1.00
F2 B:M3U401 0.0 60.2 1.0
C6 B:M3U401 1.4 57.6 1.0
H9 B:M3U401 1.9 55.9 1.0
F1 B:M3U401 2.2 53.2 1.0
O2 B:M3U401 2.3 51.4 1.0
H8 B:M3U401 2.4 49.6 1.0
HD2 B:HIS273 2.6 44.5 1.0
C5 B:M3U401 2.8 47.9 1.0
HD2 B:PHE272 2.8 45.9 1.0
HE2 B:PHE272 2.8 46.5 1.0
CD2 B:HIS273 3.4 43.8 1.0
CE2 B:PHE272 3.5 46.1 1.0
CD2 B:PHE272 3.5 46.5 1.0
HE2 B:HIS273 3.5 46.1 0.0
H11 B:M3U401 3.7 48.9 1.0
HB2 B:GLU292 3.8 42.2 1.0
NE2 B:HIS273 3.8 48.6 1.0
OE1 B:GLU292 3.8 46.7 1.0
C7 B:M3U401 3.8 49.3 1.0
H6 B:M3U401 3.9 51.2 1.0
HB3 B:GLU292 3.9 42.1 1.0
C4 B:M3U401 4.0 51.6 1.0
HA B:HIS273 4.0 41.6 1.0
HG23 B:VAL289 4.3 43.5 1.0
CB B:GLU292 4.3 42.3 1.0
HA B:VAL289 4.3 40.7 1.0
H10 B:M3U401 4.4 48.9 1.0
HD23 B:LEU182 4.4 43.3 1.0
H7 B:M3U401 4.5 51.2 1.0
HB2 B:ALA293 4.5 44.2 1.0
CG B:HIS273 4.6 41.3 1.0
HA B:ALA293 4.7 41.9 1.0
HD11 B:LEU296 4.7 41.8 1.0
HB3 B:ALA276 4.7 45.5 1.0
CD B:GLU292 4.8 41.8 1.0
CG B:PHE272 4.8 44.5 1.0
CZ B:PHE272 4.8 47.9 1.0
N2 B:M3U401 4.8 49.0 1.0
HB3 B:PHE272 4.9 44.5 1.0
CA B:HIS273 4.9 40.1 1.0
HB2 B:ALA276 4.9 45.5 1.0
HG11 B:VAL289 4.9 41.6 1.0
C3 B:M3U401 5.0 53.7 1.0

Reference:

H.Ma, J.B.Murray, H.Luo, X.Cheng, Q.Chen, C.Song, C.Duan, P.Tan, L.Zhang, J.Liu, B.A.Morgan, J.Li, J.Wan, L.M.Baker, W.Finnie, L.Guetzoyan, R.Harris, N.Hendrickson, N.Matassova, H.Simmonite, J.Smith, R.E.Hubbard, G.Liu. Pac-Fragmentdel - Photoactivated Covalent Capture of Dna-Encoded Fragments For Hit Discovery. Rsc Med Chem V. 13 1341 2022.
ISSN: ESSN 2632-8682
PubMed: 36426238
DOI: 10.1039/D2MD00197G
Page generated: Wed Jul 16 02:40:42 2025

Last articles

Na in 2GTW
Na in 2GT9
Na in 2GN0
Na in 2GNO
Na in 2GJU
Na in 2GN1
Na in 2GN2
Na in 2GMH
Na in 2GLN
Na in 2GL3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy