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Fluorine in PDB 5g10: Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide

Protein crystallography data

The structure of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide, PDB code: 5g10 was solved by A.Kraemer, F.J.Meyer-Almes, O.Yildiz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.94 / 1.71
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.740, 81.740, 205.210, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 19.4

Other elements in 5g10:

The structure of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide (pdb code 5g10). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide, PDB code: 5g10:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5g10

Go back to Fluorine Binding Sites List in 5g10
Fluorine binding site 1 out of 6 in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1375

b:21.4
occ:1.00
 F2 A:6DK1375 0.0 21.4 1.0
C A:6DK1375 1.3 20.6 1.0
F A:6DK1375 2.1 21.8 1.0
F1 A:6DK1375 2.1 25.4 1.0
C1 A:6DK1375 2.4 19.5 1.0
C2 A:6DK1375 2.9 20.7 1.0
O2 A:6DK1375 3.0 17.9 1.0
CD2 A:HIS144 3.1 16.9 1.0
SG A:CYS154 3.1 15.1 1.0
O A:GLY152 3.2 16.9 1.0
CD2 A:HIS143 3.3 15.7 1.0
NE2 A:HIS143 3.4 16.6 1.0
O1 A:6DK1375 3.6 17.6 1.0
NE2 A:HIS144 3.6 16.6 1.0
CG A:PRO141 3.9 19.1 1.0
CB A:PRO141 3.9 18.8 1.0
CG A:HIS144 4.2 16.7 1.0
C3 A:6DK1375 4.3 20.9 1.0
C A:GLY152 4.4 18.5 1.0
OE1 A:GLU310 4.4 19.2 1.0
OH A:TYR313 4.5 23.3 1.0
CG A:HIS143 4.6 15.0 1.0
CE1 A:HIS143 4.7 16.7 1.0
CE1 A:HIS144 4.7 17.7 1.0
ZN A:ZN1372 4.7 12.8 0.7
N A:HIS144 4.9 14.9 1.0
CB A:HIS144 4.9 16.7 1.0
CB A:CYS154 4.9 15.2 1.0
N A:HIS143 4.9 13.4 1.0
OD2 A:ASP181 4.9 12.1 1.0

Fluorine binding site 2 out of 6 in 5g10

Go back to Fluorine Binding Sites List in 5g10
Fluorine binding site 2 out of 6 in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1375

b:21.8
occ:1.00
 F A:6DK1375 0.0 21.8 1.0
C A:6DK1375 1.3 20.6 1.0
F2 A:6DK1375 2.1 21.4 1.0
F1 A:6DK1375 2.1 25.4 1.0
C1 A:6DK1375 2.3 19.5 1.0
OH A:TYR313 2.7 23.3 1.0
O1 A:6DK1375 2.8 17.6 1.0
C2 A:6DK1375 2.8 20.7 1.0
CG A:PRO141 3.2 19.1 1.0
O A:HOH2053 3.4 29.7 1.0
O2 A:6DK1375 3.6 17.9 1.0
CB A:PRO141 3.6 18.8 1.0
O A:GLY152 3.9 16.9 1.0
CA A:GLY311 4.0 16.7 1.0
CZ A:TYR313 4.0 23.4 1.0
CD2 A:PHE153 4.1 23.1 1.0
N A:GLY311 4.1 16.2 1.0
C3 A:6DK1375 4.3 20.9 1.0
CB A:PHE153 4.4 20.4 1.0
C A:GLU310 4.4 16.2 1.0
O A:GLU310 4.5 15.8 1.0
CD A:PRO141 4.5 18.6 1.0
SG A:CYS154 4.6 15.1 1.0
ZN A:ZN1372 4.6 12.8 0.7
CG A:PHE153 4.7 22.0 1.0
CE2 A:TYR313 4.8 21.2 1.0
CE1 A:TYR313 4.8 24.2 1.0
OD2 A:ASP181 4.9 12.1 1.0
NE2 A:HIS143 4.9 16.6 1.0
CD2 A:HIS144 4.9 16.9 1.0
CG A:GLU41 5.0 24.5 1.0
CE2 A:PHE153 5.0 25.2 1.0
C A:GLY152 5.0 18.5 1.0

Fluorine binding site 3 out of 6 in 5g10

Go back to Fluorine Binding Sites List in 5g10
Fluorine binding site 3 out of 6 in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1375

b:25.4
occ:1.00
 F1 A:6DK1375 0.0 25.4 1.0
C A:6DK1375 1.3 20.6 1.0
F A:6DK1375 2.1 21.8 1.0
F2 A:6DK1375 2.1 21.4 1.0
C1 A:6DK1375 2.3 19.5 1.0
O1 A:6DK1375 2.8 17.6 1.0
O2 A:6DK1375 2.8 17.9 1.0
N A:GLY311 3.0 16.2 1.0
OD2 A:ASP181 3.1 12.1 1.0
NE2 A:HIS143 3.3 16.6 1.0
CA A:GLY311 3.4 16.7 1.0
C A:GLU310 3.4 16.2 1.0
CD2 A:HIS143 3.4 15.7 1.0
CB A:GLU310 3.6 16.7 1.0
C2 A:6DK1375 3.7 20.7 1.0
ZN A:ZN1372 3.7 12.8 0.7
CB A:PRO141 3.9 18.8 1.0
CG A:ASP181 3.9 12.1 1.0
CA A:GLU310 3.9 15.7 1.0
OE1 A:GLU310 4.0 19.2 1.0
OH A:TYR313 4.0 23.3 1.0
O A:GLU310 4.1 15.8 1.0
CG A:PRO141 4.2 19.1 1.0
OD1 A:ASP181 4.2 13.2 1.0
CE1 A:HIS143 4.4 16.7 1.0
O A:HOH2053 4.4 29.7 1.0
CG A:HIS143 4.7 15.0 1.0
CG A:GLU310 4.7 17.0 1.0
NE2 A:HIS144 4.8 16.6 1.0
CD2 A:HIS144 4.8 16.9 1.0
CD A:GLU310 4.8 18.5 1.0
C A:GLY311 4.9 16.9 1.0
SG A:CYS154 4.9 15.1 1.0
OD2 A:ASP269 4.9 14.2 1.0
C3 A:6DK1375 5.0 20.9 1.0
CB A:ASP181 5.0 11.4 1.0

Fluorine binding site 4 out of 6 in 5g10

Go back to Fluorine Binding Sites List in 5g10
Fluorine binding site 4 out of 6 in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1381

b:22.9
occ:1.00
 F2 B:6DK1381 0.0 22.9 1.0
C B:6DK1381 1.3 21.4 1.0
F B:6DK1381 2.1 23.6 1.0
F1 B:6DK1381 2.1 23.0 1.0
C1 B:6DK1381 2.4 20.4 1.0
C2 B:6DK1381 2.9 20.8 1.0
O2 B:6DK1381 3.0 19.8 1.0
SG B:CYS154 3.1 15.1 1.0
CD2 B:HIS144 3.2 18.8 1.0
O B:GLY152 3.2 17.4 1.0
CD2 B:HIS143 3.4 16.4 1.0
NE2 B:HIS143 3.5 16.4 1.0
O1 B:6DK1381 3.6 19.2 1.0
NE2 B:HIS144 3.7 18.6 1.0
CG B:PRO141 3.8 16.1 1.0
CB B:PRO141 3.9 15.5 1.0
CG B:HIS144 4.2 18.1 1.0
C3 B:6DK1381 4.3 22.5 1.0
C B:GLY152 4.4 18.6 1.0
OE1 B:GLU310 4.5 18.4 1.0
OH B:TYR313 4.5 22.3 1.0
CG B:HIS143 4.7 15.3 1.0
ZN B:ZN1378 4.8 14.0 0.7
CE1 B:HIS144 4.8 19.1 1.0
CE1 B:HIS143 4.8 17.0 1.0
CB B:CYS154 4.9 16.3 1.0
N B:HIS143 4.9 14.3 1.0
N B:HIS144 4.9 15.0 1.0
CB B:HIS144 4.9 16.8 1.0
CB B:PHE153 5.0 20.6 1.0
OD2 B:ASP181 5.0 13.6 1.0

Fluorine binding site 5 out of 6 in 5g10

Go back to Fluorine Binding Sites List in 5g10
Fluorine binding site 5 out of 6 in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1381

b:23.6
occ:1.00
 F B:6DK1381 0.0 23.6 1.0
C B:6DK1381 1.3 21.4 1.0
F1 B:6DK1381 2.1 23.0 1.0
F2 B:6DK1381 2.1 22.9 1.0
C1 B:6DK1381 2.3 20.4 1.0
OH B:TYR313 2.6 22.3 1.0
O1 B:6DK1381 2.8 19.2 1.0
C2 B:6DK1381 2.9 20.8 1.0
CG B:PRO141 3.2 16.1 1.0
O B:HOH2041 3.3 28.4 1.0
O2 B:6DK1381 3.6 19.8 1.0
CB B:PRO141 3.7 15.5 1.0
O B:GLY152 3.9 17.4 1.0
CD2 B:PHE153 4.0 23.6 1.0
CZ B:TYR313 4.0 18.3 1.0
CA B:GLY311 4.0 14.6 1.0
N B:GLY311 4.2 15.1 1.0
C3 B:6DK1381 4.3 22.5 1.0
CB B:PHE153 4.3 20.6 1.0
C B:GLU310 4.4 14.8 1.0
CD B:PRO141 4.5 16.0 1.0
O B:GLU310 4.5 14.8 1.0
CG B:PHE153 4.6 22.3 1.0
ZN B:ZN1378 4.6 14.0 0.7
SG B:CYS154 4.6 15.1 1.0
CE1 B:TYR313 4.8 19.7 1.0
CE2 B:TYR313 4.8 17.2 1.0
CE2 B:PHE153 4.9 24.5 1.0
CG B:GLU41 4.9 24.6 1.0
OD2 B:ASP181 4.9 13.6 1.0
CD2 B:HIS144 5.0 18.8 1.0
NE2 B:HIS143 5.0 16.4 1.0

Fluorine binding site 6 out of 6 in 5g10

Go back to Fluorine Binding Sites List in 5g10
Fluorine binding site 6 out of 6 in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1381

b:23.0
occ:1.00
 F1 B:6DK1381 0.0 23.0 1.0
C B:6DK1381 1.3 21.4 1.0
F B:6DK1381 2.1 23.6 1.0
F2 B:6DK1381 2.1 22.9 1.0
C1 B:6DK1381 2.4 20.4 1.0
O2 B:6DK1381 2.8 19.8 1.0
O1 B:6DK1381 2.8 19.2 1.0
N B:GLY311 3.0 15.1 1.0
OD2 B:ASP181 3.2 13.6 1.0
NE2 B:HIS143 3.3 16.4 1.0
C B:GLU310 3.4 14.8 1.0
CA B:GLY311 3.4 14.6 1.0
CD2 B:HIS143 3.5 16.4 1.0
CB B:GLU310 3.6 14.7 1.0
C2 B:6DK1381 3.7 20.8 1.0
CB B:PRO141 3.8 15.5 1.0
ZN B:ZN1378 3.8 14.0 0.7
CA B:GLU310 3.9 14.2 1.0
OH B:TYR313 4.0 22.3 1.0
OE1 B:GLU310 4.0 18.4 1.0
CG B:ASP181 4.0 12.6 1.0
O B:GLU310 4.1 14.8 1.0
CG B:PRO141 4.1 16.1 1.0
O B:HOH2041 4.3 28.4 1.0
OD1 B:ASP181 4.3 13.2 1.0
CE1 B:HIS143 4.5 17.0 1.0
CG B:GLU310 4.7 15.1 1.0
CG B:HIS143 4.7 15.3 1.0
CD B:GLU310 4.8 17.4 1.0
CD2 B:HIS144 4.8 18.8 1.0
NE2 B:HIS144 4.8 18.6 1.0
SG B:CYS154 4.8 15.1 1.0
C B:GLY311 4.9 15.3 1.0

Reference:

A.Kramer, T.Wagner, O.Yildiz, F.J.Meyer-Almes. Crystal Structure of A Histone Deacetylase Homologue From Pseudomonas Aeruginosa. Biochemistry V. 55 6858 2016.
ISSN: ISSN 1520-4995
PubMed: 27951649
DOI: 10.1021/ACS.BIOCHEM.6B00613
Page generated: Thu Aug 1 09:31:19 2024

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