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Fluorine in PDB 4zum: Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor

Protein crystallography data

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor, PDB code: 4zum was solved by C.Decroos, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.89 / 1.42
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.119, 121.351, 64.295, 90.00, 96.76, 90.00
R / Rfree (%) 13.3 / 15.3

Other elements in 4zum:

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor also contains other interesting chemical elements:

Potassium (K) 2 atoms
Zinc (Zn) 2 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor (pdb code 4zum). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor, PDB code: 4zum:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4zum

Go back to Fluorine Binding Sites List in 4zum
Fluorine binding site 1 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:10.8
occ:1.00
F15 A:FKS404 0.0 10.8 1.0
C12 A:FKS404 1.3 10.7 1.0
F17 A:FKS404 2.1 12.3 1.0
F16 A:FKS404 2.2 10.9 1.0
C11 A:FKS404 2.3 9.0 1.0
O14 A:FKS404 2.8 7.2 1.0
C10 A:FKS404 2.8 10.3 1.0
SG A:CYS169 3.1 6.5 1.0
CD2 A:HIS159 3.2 5.8 1.0
CD2 A:HIS158 3.2 6.6 1.0
O A:GLY167 3.3 5.7 1.0
NE2 A:HIS158 3.4 6.9 1.0
O13 A:FKS404 3.5 7.2 1.0
NE2 A:HIS159 3.6 5.9 1.0
CG A:PRO156 3.8 5.8 1.0
CB A:PRO156 3.8 5.7 1.0
CG A:HIS159 4.3 4.8 1.0
C9 A:FKS404 4.3 9.6 1.0
OE1 A:GLU320 4.4 6.7 1.0
OH A:TYR323 4.5 8.4 1.0
C A:GLY167 4.5 5.5 1.0
CG A:HIS158 4.6 5.5 1.0
CE1 A:HIS158 4.7 5.6 1.0
N A:HIS158 4.7 5.5 1.0
CE1 A:HIS159 4.8 6.0 1.0
ZN A:ZN401 4.8 6.6 1.0
N A:HIS159 4.8 5.9 1.0
N A:GLY157 4.9 5.0 1.0
CB A:CYS169 4.9 5.3 1.0
CB A:TYR168 4.9 6.6 1.0
N A:GLY321 4.9 6.3 1.0

Fluorine binding site 2 out of 6 in 4zum

Go back to Fluorine Binding Sites List in 4zum
Fluorine binding site 2 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:10.9
occ:1.00
F16 A:FKS404 0.0 10.9 1.0
C12 A:FKS404 1.3 10.7 1.0
F17 A:FKS404 2.1 12.3 1.0
F15 A:FKS404 2.2 10.8 1.0
C11 A:FKS404 2.3 9.0 1.0
O14 A:FKS404 2.7 7.2 1.0
O13 A:FKS404 2.8 7.2 1.0
OD2 A:ASP195 3.0 7.2 1.0
NE2 A:HIS158 3.0 6.9 1.0
N A:GLY321 3.0 6.3 1.0
CD2 A:HIS158 3.3 6.6 1.0
CB A:GLU320 3.4 5.2 1.0
CA A:GLY321 3.6 6.7 1.0
C A:GLU320 3.6 6.7 1.0
CG A:ASP195 3.6 7.1 1.0
ZN A:ZN401 3.6 6.6 1.0
C10 A:FKS404 3.7 10.3 1.0
CA A:GLU320 3.8 6.4 1.0
OD1 A:ASP195 3.9 5.9 1.0
OE1 A:GLU320 3.9 6.7 1.0
CE1 A:HIS158 4.0 5.6 1.0
CB A:PRO156 4.1 5.7 1.0
OH A:TYR323 4.2 8.4 1.0
CG A:HIS158 4.4 5.5 1.0
O A:GLU320 4.5 7.3 1.0
CG A:GLU320 4.5 6.0 1.0
CG A:PRO156 4.5 5.8 1.0
CD A:GLU320 4.6 7.1 1.0
CB A:ASP195 4.6 5.6 1.0
NE2 A:HIS159 4.7 5.9 1.0
ND1 A:HIS158 4.7 5.6 1.0
CD2 A:HIS159 4.8 5.8 1.0
C9 A:FKS404 4.9 9.6 1.0
OD2 A:ASP284 4.9 6.6 1.0
SG A:CYS169 5.0 6.5 1.0
C A:GLY321 5.0 6.2 1.0

Fluorine binding site 3 out of 6 in 4zum

Go back to Fluorine Binding Sites List in 4zum
Fluorine binding site 3 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:12.3
occ:1.00
F17 A:FKS404 0.0 12.3 1.0
C12 A:FKS404 1.3 10.7 1.0
F15 A:FKS404 2.1 10.8 1.0
F16 A:FKS404 2.1 10.9 1.0
C11 A:FKS404 2.3 9.0 1.0
OH A:TYR323 2.7 8.4 1.0
O13 A:FKS404 2.7 7.2 1.0
C10 A:FKS404 2.9 10.3 1.0
CG A:PRO156 3.2 5.8 1.0
CB A:PRO156 3.4 5.7 1.0
CA A:GLY321 3.5 6.7 1.0
O14 A:FKS404 3.5 7.2 1.0
N A:GLY321 3.6 6.3 1.0
C A:GLU320 3.9 6.7 1.0
CZ A:TYR323 4.0 7.5 1.0
CD2 A:TYR168 4.2 6.9 1.0
O A:GLU320 4.2 7.3 1.0
O A:GLY167 4.3 5.7 1.0
C9 A:FKS404 4.3 9.6 1.0
ZN A:ZN401 4.5 6.6 1.0
CD A:PRO156 4.5 6.4 1.0
OD2 A:ASP195 4.6 7.2 1.0
CA A:GLU320 4.7 6.4 1.0
CB A:TYR168 4.7 6.6 1.0
SG A:CYS169 4.7 6.5 1.0
NE2 A:HIS158 4.8 6.9 1.0
CB A:GLU320 4.8 5.2 1.0
CE1 A:TYR323 4.8 7.1 1.0
CE2 A:TYR323 4.9 8.2 1.0
CG A:TYR168 4.9 6.5 1.0
CA A:PRO156 4.9 5.9 1.0
CD2 A:HIS158 4.9 6.6 1.0
C A:GLY321 5.0 6.2 1.0
CG A:GLU28 5.0 8.2 1.0

Fluorine binding site 4 out of 6 in 4zum

Go back to Fluorine Binding Sites List in 4zum
Fluorine binding site 4 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:9.9
occ:1.00
F15 B:FKS404 0.0 9.9 1.0
C12 B:FKS404 1.3 9.6 1.0
F16 B:FKS404 2.1 10.2 1.0
F17 B:FKS404 2.1 12.0 1.0
C11 B:FKS404 2.3 7.7 1.0
O14 B:FKS404 2.8 7.5 1.0
C10 B:FKS404 2.8 8.8 1.0
SG B:CYS169 3.2 6.3 1.0
CD2 B:HIS159 3.2 6.8 1.0
CD2 B:HIS158 3.2 6.3 1.0
O B:GLY167 3.3 6.5 1.0
NE2 B:HIS158 3.4 6.0 1.0
O13 B:FKS404 3.5 6.7 1.0
NE2 B:HIS159 3.6 6.3 1.0
CG B:PRO156 3.8 6.1 1.0
CB B:PRO156 3.8 7.1 1.0
CG B:HIS159 4.3 4.9 1.0
C9 B:FKS404 4.3 9.4 1.0
OE1 B:GLU320 4.4 6.3 1.0
OH B:TYR323 4.5 8.2 1.0
CG B:HIS158 4.5 5.3 1.0
C B:GLY167 4.5 5.9 1.0
CE1 B:HIS158 4.7 5.4 1.0
N B:HIS158 4.7 5.4 1.0
CE1 B:HIS159 4.7 6.0 1.0
ZN B:ZN401 4.8 6.6 1.0
N B:HIS159 4.9 5.9 1.0
N B:GLY157 4.9 4.7 1.0
CB B:CYS169 4.9 5.3 1.0
N B:GLY321 4.9 5.7 1.0
CB B:TYR168 4.9 6.8 1.0

Fluorine binding site 5 out of 6 in 4zum

Go back to Fluorine Binding Sites List in 4zum
Fluorine binding site 5 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:10.2
occ:1.00
F16 B:FKS404 0.0 10.2 1.0
C12 B:FKS404 1.3 9.6 1.0
F15 B:FKS404 2.1 9.9 1.0
F17 B:FKS404 2.1 12.0 1.0
C11 B:FKS404 2.3 7.7 1.0
O14 B:FKS404 2.7 7.5 1.0
O13 B:FKS404 2.8 6.7 1.0
NE2 B:HIS158 3.0 6.0 1.0
OD2 B:ASP195 3.0 6.5 1.0
N B:GLY321 3.0 5.7 1.0
CD2 B:HIS158 3.3 6.3 1.0
CB B:GLU320 3.4 5.1 1.0
CA B:GLY321 3.6 6.5 1.0
C B:GLU320 3.6 6.8 1.0
CG B:ASP195 3.6 6.7 1.0
ZN B:ZN401 3.6 6.6 1.0
C10 B:FKS404 3.7 8.8 1.0
CA B:GLU320 3.8 5.9 1.0
OD1 B:ASP195 3.9 5.4 1.0
OE1 B:GLU320 3.9 6.3 1.0
CE1 B:HIS158 4.0 5.4 1.0
CB B:PRO156 4.0 7.1 1.0
OH B:TYR323 4.3 8.2 1.0
CG B:HIS158 4.4 5.3 1.0
O B:GLU320 4.5 6.8 1.0
CG B:GLU320 4.5 5.8 1.0
CG B:PRO156 4.5 6.1 1.0
CD B:GLU320 4.6 7.0 1.0
NE2 B:HIS159 4.6 6.3 1.0
CB B:ASP195 4.7 5.6 1.0
ND1 B:HIS158 4.7 6.0 1.0
CD2 B:HIS159 4.8 6.8 1.0
C9 B:FKS404 4.9 9.4 1.0
SG B:CYS169 5.0 6.3 1.0
C B:GLY321 5.0 6.1 1.0
OD2 B:ASP284 5.0 6.8 1.0

Fluorine binding site 6 out of 6 in 4zum

Go back to Fluorine Binding Sites List in 4zum
Fluorine binding site 6 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:12.0
occ:1.00
F17 B:FKS404 0.0 12.0 1.0
C12 B:FKS404 1.3 9.6 1.0
F16 B:FKS404 2.1 10.2 1.0
F15 B:FKS404 2.1 9.9 1.0
C11 B:FKS404 2.4 7.7 1.0
OH B:TYR323 2.7 8.2 1.0
O13 B:FKS404 2.7 6.7 1.0
C10 B:FKS404 3.0 8.8 1.0
CG B:PRO156 3.2 6.1 1.0
CB B:PRO156 3.4 7.1 1.0
CA B:GLY321 3.5 6.5 1.0
O14 B:FKS404 3.6 7.5 1.0
N B:GLY321 3.6 5.7 1.0
C B:GLU320 3.9 6.8 1.0
CZ B:TYR323 4.0 7.3 1.0
O B:GLU320 4.2 6.8 1.0
CD2 B:TYR168 4.3 6.8 1.0
O B:GLY167 4.3 6.5 1.0
C9 B:FKS404 4.4 9.4 1.0
ZN B:ZN401 4.5 6.6 1.0
CD B:PRO156 4.5 6.4 1.0
OD2 B:ASP195 4.6 6.5 1.0
CA B:GLU320 4.6 5.9 1.0
SG B:CYS169 4.7 6.3 1.0
CB B:TYR168 4.7 6.8 1.0
NE2 B:HIS158 4.8 6.0 1.0
CE2 B:TYR323 4.8 7.7 1.0
CB B:GLU320 4.8 5.1 1.0
CE1 B:TYR323 4.9 7.0 1.0
CA B:PRO156 4.9 5.8 1.0
CD2 B:HIS158 4.9 6.3 1.0
CG B:TYR168 4.9 6.4 1.0
C B:GLY321 5.0 6.1 1.0

Reference:

C.Decroos, D.W.Christianson. Design, Synthesis, and Evaluation of Polyamine Deacetylase Inhibitors, and High-Resolution Crystal Structures of Their Complexes with Acetylpolyamine Amidohydrolase. Biochemistry V. 54 4692 2015.
ISSN: ISSN 0006-2960
PubMed: 26200446
DOI: 10.1021/ACS.BIOCHEM.5B00536
Page generated: Tue Jul 15 02:03:05 2025

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