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Fluorine in PDB 6phz: Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One

Protein crystallography data

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One, PDB code: 6phz was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.69 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.370, 82.360, 90.720, 90.00, 98.22, 90.00
R / Rfree (%) 16.1 / 21.2

Other elements in 6phz:

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Potassium (K) 4 atoms
Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One (pdb code 6phz). 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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One, PDB code: 6phz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6phz

Go back to Fluorine Binding Sites List in 6phz
Fluorine binding site 1 out of 6 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One


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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F406

b:27.1
occ:1.00
 F15 A:FKS406 0.0 27.1 1.0
C12 A:FKS406 1.3 21.8 1.0
F16 A:FKS406 2.1 24.2 1.0
F17 A:FKS406 2.2 28.4 1.0
C11 A:FKS406 2.5 18.4 1.0
O13 A:FKS406 2.8 13.2 1.0
C10 A:FKS406 3.0 17.7 1.0
CG A:PRO156 3.4 8.9 1.0
CD2 A:TYR168 3.6 9.8 1.0
CA A:GLY321 3.6 8.1 1.0
O14 A:FKS406 3.6 12.0 1.0
CB A:PRO156 4.1 6.6 1.0
N A:GLY321 4.1 8.0 1.0
O A:GLY167 4.1 4.8 1.0
CB A:TYR168 4.3 3.0 1.0
CE2 A:TYR168 4.4 6.8 1.0
CG A:TYR168 4.4 8.0 1.0
C A:GLU320 4.4 9.5 1.0
C9 A:FKS406 4.4 18.0 1.0
O A:GLU320 4.5 6.8 1.0
CD A:PRO156 4.6 3.7 1.0
ZN A:ZN403 4.6 13.4 0.4
CG A:GLU28 4.7 5.5 1.0
C A:GLY321 4.9 9.4 1.0

Fluorine binding site 2 out of 6 in 6phz

Go back to Fluorine Binding Sites List in 6phz
Fluorine binding site 2 out of 6 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One


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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F406

b:24.2
occ:1.00
 F16 A:FKS406 0.0 24.2 1.0
C12 A:FKS406 1.3 21.8 1.0
F15 A:FKS406 2.1 27.1 1.0
F17 A:FKS406 2.1 28.4 1.0
C11 A:FKS406 2.4 18.4 1.0
C10 A:FKS406 2.7 17.7 1.0
O A:GLY167 2.8 4.8 1.0
O14 A:FKS406 2.9 12.0 1.0
CD2 A:HIS159 3.3 7.9 1.0
SG A:CYS169 3.4 6.6 1.0
CG A:PRO156 3.4 8.9 1.0
O13 A:FKS406 3.6 13.2 1.0
NE2 A:HIS158 3.7 6.2 1.0
NE2 A:HIS159 3.8 9.0 1.0
CB A:PRO156 3.9 6.6 1.0
CD2 A:HIS158 3.9 7.9 1.0
C A:GLY167 4.1 9.1 1.0
C9 A:FKS406 4.2 18.0 1.0
CB A:TYR168 4.4 3.0 1.0
CD2 A:TYR168 4.4 9.8 1.0
CG A:HIS159 4.5 5.9 1.0
CG A:TYR168 4.8 8.0 1.0
ZN A:ZN403 4.8 13.4 0.4
CD A:PRO156 4.9 3.7 1.0
N A:GLY321 4.9 8.0 1.0
CA A:GLY321 5.0 8.1 1.0
N A:TYR168 5.0 4.2 1.0
CA A:GLY167 5.0 7.2 1.0
C A:TYR168 5.0 5.2 1.0
CA A:TYR168 5.0 5.7 1.0

Fluorine binding site 3 out of 6 in 6phz

Go back to Fluorine Binding Sites List in 6phz
Fluorine binding site 3 out of 6 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One


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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F406

b:28.4
occ:1.00
 F17 A:FKS406 0.0 28.4 1.0
C12 A:FKS406 1.3 21.8 1.0
F16 A:FKS406 2.1 24.2 1.0
F15 A:FKS406 2.2 27.1 1.0
C11 A:FKS406 2.4 18.4 1.0
O14 A:FKS406 2.7 12.0 1.0
N A:GLY321 2.9 8.0 1.0
O13 A:FKS406 2.9 13.2 1.0
CA A:GLY321 3.1 8.1 1.0
C A:GLU320 3.3 9.5 1.0
NE2 A:HIS158 3.3 6.2 1.0
OD2 A:ASP195 3.4 5.0 1.0
CB A:PRO156 3.7 6.6 1.0
C10 A:FKS406 3.7 17.7 1.0
CB A:GLU320 3.7 3.1 1.0
CD2 A:HIS158 3.8 7.9 1.0
ZN A:ZN403 3.8 13.4 0.4
CG A:PRO156 3.8 8.9 1.0
CA A:GLU320 3.8 6.5 1.0
O A:GLU320 4.0 6.8 1.0
CG A:ASP195 4.2 7.9 1.0
CE1 A:HIS158 4.4 7.0 1.0
OE1 A:GLU320 4.5 9.2 1.0
OD1 A:ASP195 4.6 5.8 1.0
C A:GLY321 4.6 9.4 1.0
NE2 A:HIS159 4.6 9.0 1.0
CD2 A:HIS159 4.7 7.9 1.0
SG A:CYS169 4.9 6.6 1.0
O A:GLY167 5.0 4.8 1.0
CG A:HIS158 5.0 6.0 1.0
CG A:GLU320 5.0 5.0 1.0

Fluorine binding site 4 out of 6 in 6phz

Go back to Fluorine Binding Sites List in 6phz
Fluorine binding site 4 out of 6 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One


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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F406

b:28.2
occ:1.00
 F15 B:FKS406 0.0 28.2 1.0
C12 B:FKS406 1.3 25.3 1.0
F16 B:FKS406 2.2 20.9 1.0
F17 B:FKS406 2.2 28.8 1.0
C11 B:FKS406 2.5 19.3 1.0
OH B:TYR323 2.6 15.6 1.0
C10 B:FKS406 2.8 24.6 1.0
O13 B:FKS406 2.9 17.5 1.0
CG B:PRO156 3.1 7.7 1.0
CD2 B:TYR168 3.4 5.8 1.0
O B:GLY167 3.5 5.9 1.0
O14 B:FKS406 3.6 16.7 1.0
CB B:PRO156 3.8 6.7 1.0
CB B:TYR168 3.9 9.0 1.0
CZ B:TYR323 3.9 13.2 1.0
CG B:TYR168 4.1 12.8 1.0
CA B:GLY321 4.2 10.9 1.0
C9 B:FKS406 4.3 13.3 1.0
CD B:PRO156 4.3 11.1 1.0
CE2 B:TYR168 4.3 11.2 1.0
N B:GLY321 4.4 9.8 1.0
SG B:CYS169 4.5 8.1 1.0
C B:GLU320 4.6 9.6 1.0
C B:GLY167 4.6 5.9 1.0
CE1 B:TYR323 4.7 15.5 1.0
O B:GLU320 4.7 7.5 1.0
CG B:GLU28 4.7 12.2 1.0
CD2 B:HIS159 4.7 10.6 1.0
CE2 B:TYR323 4.8 18.4 1.0
NE2 B:HIS158 4.9 9.3 1.0
ZN B:ZN403 4.9 38.3 0.4
CA B:TYR168 5.0 6.2 1.0

Fluorine binding site 5 out of 6 in 6phz

Go back to Fluorine Binding Sites List in 6phz
Fluorine binding site 5 out of 6 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One


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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F406

b:20.9
occ:1.00
 F16 B:FKS406 0.0 20.9 1.0
C12 B:FKS406 1.3 25.3 1.0
F17 B:FKS406 2.1 28.8 1.0
F15 B:FKS406 2.2 28.2 1.0
C11 B:FKS406 2.5 19.3 1.0
O14 B:FKS406 2.8 16.7 1.0
CD2 B:HIS159 2.9 10.6 1.0
C10 B:FKS406 3.0 24.6 1.0
O B:GLY167 3.0 5.9 1.0
SG B:CYS169 3.1 8.1 1.0
NE2 B:HIS158 3.3 9.3 1.0
CD2 B:HIS158 3.3 7.4 1.0
NE2 B:HIS159 3.5 6.2 1.0
CG B:PRO156 3.6 7.7 1.0
O13 B:FKS406 3.6 17.5 1.0
CB B:PRO156 3.9 6.7 1.0
CG B:HIS159 4.0 6.3 1.0
C B:GLY167 4.3 5.9 1.0
C9 B:FKS406 4.3 13.3 1.0
OH B:TYR323 4.5 15.6 1.0
CE1 B:HIS158 4.6 5.3 1.0
CE1 B:HIS159 4.6 9.4 1.0
OE1 B:GLU320 4.6 8.5 1.0
CG B:HIS158 4.6 3.1 1.0
CB B:HIS159 4.8 5.3 1.0
CB B:TYR168 4.8 9.0 1.0
CB B:CYS169 4.8 7.3 1.0
ND1 B:HIS159 4.9 7.4 1.0
ZN B:ZN403 4.9 38.3 0.4
N B:HIS159 4.9 3.8 1.0
CD2 B:TYR168 4.9 5.8 1.0
N B:GLY321 5.0 9.8 1.0
N B:HIS158 5.0 5.1 1.0

Fluorine binding site 6 out of 6 in 6phz

Go back to Fluorine Binding Sites List in 6phz
Fluorine binding site 6 out of 6 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One


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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F406

b:28.8
occ:1.00
 F17 B:FKS406 0.0 28.8 1.0
C12 B:FKS406 1.4 25.3 1.0
F16 B:FKS406 2.1 20.9 1.0
F15 B:FKS406 2.2 28.2 1.0
C11 B:FKS406 2.5 19.3 1.0
N B:GLY321 2.8 9.8 1.0
O13 B:FKS406 2.9 17.5 1.0
O14 B:FKS406 3.0 16.7 1.0
C B:GLU320 3.1 9.6 1.0
CA B:GLY321 3.2 10.9 1.0
CB B:PRO156 3.4 6.7 1.0
NE2 B:HIS158 3.4 9.3 1.0
CB B:GLU320 3.4 5.8 1.0
CA B:GLU320 3.5 5.5 1.0
CG B:PRO156 3.5 7.7 1.0
O B:GLU320 3.7 7.5 1.0
OD1 B:ASP195 3.7 8.2 1.0
CD2 B:HIS158 3.7 7.4 1.0
C10 B:FKS406 3.8 24.6 1.0
OH B:TYR323 3.9 15.6 1.0
ZN B:ZN403 4.2 38.3 0.4
OE1 B:GLU320 4.2 8.5 1.0
CG B:ASP195 4.5 15.4 1.0
CE1 B:HIS158 4.6 5.3 1.0
CG B:GLU320 4.7 8.0 1.0
SG B:CYS169 4.7 8.1 1.0
C B:GLY321 4.7 12.2 1.0
OD2 B:ASP195 4.8 5.7 1.0
CD2 B:HIS159 4.8 10.6 1.0
NE2 B:HIS159 4.8 6.2 1.0
CA B:PRO156 4.9 5.8 1.0
O B:GLY167 4.9 5.9 1.0
CD B:GLU320 4.9 11.8 1.0
N B:GLU320 5.0 8.2 1.0
CG B:HIS158 5.0 3.1 1.0
CD B:PRO156 5.0 11.1 1.0
CZ B:TYR323 5.0 13.2 1.0

Reference:

J.D.Osko, B.W.Roose, S.A.Shinsky, D.W.Christianson. Structure and Function of the Acetylpolyamine Amidohydrolase From the Deep Earth Halophilemarinobacter Subterrani. Biochemistry V. 58 3755 2019.
ISSN: ISSN 0006-2960
PubMed: 31436969
DOI: 10.1021/ACS.BIOCHEM.9B00582
Page generated: Fri Aug 2 00:25:42 2024

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