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: Fri Aug 2 16:30:20 2024

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