Atomistry » Fluorine » PDB 5fd2-5g3j » 5g10
Atomistry »
  Fluorine »
    PDB 5fd2-5g3j »
      5g10 »

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: Tue Jul 15 03:37:38 2025

Last articles

Mg in 9F37
Mg in 9EZL
Mg in 9F28
Mg in 9F2R
Mg in 9F12
Mg in 9F11
Mg in 9F10
Mg in 9F0Z
Mg in 9F0Y
Mg in 9F07
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy