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Fluorine in PDB 6zde: 17BETA-Hydroxysteroid Dehydrogenase Type 14 Variant S205 in Complex with Pentafluorophenol

Protein crystallography data

The structure of 17BETA-Hydroxysteroid Dehydrogenase Type 14 Variant S205 in Complex with Pentafluorophenol, PDB code: 6zde was solved by M.J.Badran, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.65 / 1.87
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 91.251, 91.251, 133.06, 90, 90, 90
R / Rfree (%) 16.4 / 19.1

Other elements in 6zde:

The structure of 17BETA-Hydroxysteroid Dehydrogenase Type 14 Variant S205 in Complex with Pentafluorophenol also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the 17BETA-Hydroxysteroid Dehydrogenase Type 14 Variant S205 in Complex with Pentafluorophenol (pdb code 6zde). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the 17BETA-Hydroxysteroid Dehydrogenase Type 14 Variant S205 in Complex with Pentafluorophenol, PDB code: 6zde:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 6zde

Go back to Fluorine Binding Sites List in 6zde
Fluorine binding site 1 out of 5 in the 17BETA-Hydroxysteroid Dehydrogenase Type 14 Variant S205 in Complex with Pentafluorophenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 17BETA-Hydroxysteroid Dehydrogenase Type 14 Variant S205 in Complex with Pentafluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:23.5
occ:1.00
 F07 A:QFZ301 0.0 23.5 1.0
C06 A:QFZ301 1.4 22.3 1.0
C05 A:QFZ301 2.3 25.4 1.0
C01 A:QFZ301 2.4 24.6 1.0
F08 A:QFZ301 2.7 26.8 1.0
O12 A:QFZ301 2.8 23.4 1.0
OH A:TYR154 2.9 21.4 1.0
C2N A:NAD302 3.1 18.9 1.0
C3N A:NAD302 3.2 20.1 1.0
N1N A:NAD302 3.4 22.3 1.0
O2D A:NAD302 3.6 20.0 1.0
CZ A:TYR154 3.6 20.9 1.0
C04 A:QFZ301 3.6 29.9 1.0
C02 A:QFZ301 3.6 30.6 1.0
C4N A:NAD302 3.7 20.1 1.0
C2D A:NAD302 3.7 21.1 1.0
CB A:HIS93 3.7 18.5 1.0
C6N A:NAD302 3.8 20.4 1.0
C7N A:NAD302 3.9 21.9 1.0
CD2 A:LEU191 4.0 20.3 1.0
C5N A:NAD302 4.0 21.1 1.0
CD2 A:HIS93 4.0 20.5 1.0
C1D A:NAD302 4.1 19.7 1.0
C03 A:QFZ301 4.1 29.9 1.0
CE1 A:TYR154 4.1 21.8 1.0
CG A:HIS93 4.2 22.5 1.0
N7N A:NAD302 4.3 21.5 1.0
CE2 A:TYR154 4.4 17.7 1.0
O7N A:NAD302 4.5 22.1 1.0
F09 A:QFZ301 4.7 31.8 1.0
F11 A:QFZ301 4.8 32.7 1.0
CA A:HIS93 4.9 18.8 1.0
N A:HIS93 4.9 20.3 1.0

Fluorine binding site 2 out of 5 in 6zde

Go back to Fluorine Binding Sites List in 6zde
Fluorine binding site 2 out of 5 in the 17BETA-Hydroxysteroid Dehydrogenase Type 14 Variant S205 in Complex with Pentafluorophenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 17BETA-Hydroxysteroid Dehydrogenase Type 14 Variant S205 in Complex with Pentafluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:26.8
occ:1.00
 F08 A:QFZ301 0.0 26.8 1.0
C05 A:QFZ301 1.4 25.4 1.0
C06 A:QFZ301 2.3 22.3 1.0
C04 A:QFZ301 2.4 29.9 1.0
F07 A:QFZ301 2.7 23.5 1.0
F09 A:QFZ301 2.8 31.8 1.0
CD2 A:LEU191 3.3 20.3 1.0
C01 A:QFZ301 3.6 24.6 1.0
C03 A:QFZ301 3.6 29.9 1.0
CG A:LEU191 3.7 22.3 1.0
CD1 A:LEU195 3.7 24.4 1.0
CB A:HIS93 3.8 18.5 1.0
C7N A:NAD302 3.9 21.9 1.0
N7N A:NAD302 3.9 21.5 1.0
C02 A:QFZ301 4.1 30.6 1.0
O7N A:NAD302 4.1 22.1 1.0
C3N A:NAD302 4.2 20.1 1.0
CG A:HIS93 4.3 22.5 1.0
CD2 A:HIS93 4.3 20.5 1.0
CD1 A:TRP192 4.5 27.1 1.0
C2N A:NAD302 4.5 18.9 1.0
CB A:LEU191 4.6 22.7 1.0
N A:TRP192 4.7 21.6 1.0
O12 A:QFZ301 4.8 23.4 1.0
O A:HOH501 4.8 33.6 1.0
F10 A:QFZ301 4.8 35.1 1.0
CD1 A:LEU191 4.8 25.2 1.0
CA A:TRP192 4.8 23.1 1.0
O1N A:NAD302 4.9 19.6 1.0
C A:LEU191 4.9 25.4 1.0
C4N A:NAD302 4.9 20.1 1.0

Fluorine binding site 3 out of 5 in 6zde

Go back to Fluorine Binding Sites List in 6zde
Fluorine binding site 3 out of 5 in the 17BETA-Hydroxysteroid Dehydrogenase Type 14 Variant S205 in Complex with Pentafluorophenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 17BETA-Hydroxysteroid Dehydrogenase Type 14 Variant S205 in Complex with Pentafluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:31.8
occ:1.00
 F09 A:QFZ301 0.0 31.8 1.0
C04 A:QFZ301 1.4 29.9 1.0
C05 A:QFZ301 2.4 25.4 1.0
C03 A:QFZ301 2.4 29.9 1.0
F08 A:QFZ301 2.8 26.8 1.0
F10 A:QFZ301 2.8 35.1 1.0
NE1 A:TRP192 3.2 23.9 1.0
O A:HOH501 3.3 33.6 1.0
CD1 A:TRP192 3.3 27.1 1.0
O A:HOH541 3.4 37.1 1.0
C06 A:QFZ301 3.6 22.3 1.0
C02 A:QFZ301 3.6 30.6 1.0
CE2 A:TRP192 3.8 27.4 1.0
CG A:TRP192 3.9 23.9 1.0
CD1 A:LEU195 4.0 24.4 1.0
C01 A:QFZ301 4.1 24.6 1.0
CD2 A:TRP192 4.2 22.0 1.0
O7N A:NAD302 4.3 22.1 1.0
OD1 A:ASN186 4.4 21.2 1.0
O A:HOH462 4.5 31.3 1.0
CZ2 A:TRP192 4.6 27.5 1.0
F07 A:QFZ301 4.7 23.5 1.0
F11 A:QFZ301 4.8 32.7 1.0
CA A:TRP192 4.8 23.1 1.0
C7N A:NAD302 4.8 21.9 1.0
CB A:TRP192 4.8 23.0 1.0
CD2 A:HIS93 4.9 20.5 1.0

Fluorine binding site 4 out of 5 in 6zde

Go back to Fluorine Binding Sites List in 6zde
Fluorine binding site 4 out of 5 in the 17BETA-Hydroxysteroid Dehydrogenase Type 14 Variant S205 in Complex with Pentafluorophenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 17BETA-Hydroxysteroid Dehydrogenase Type 14 Variant S205 in Complex with Pentafluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:35.1
occ:1.00
 F10 A:QFZ301 0.0 35.1 1.0
C03 A:QFZ301 1.4 29.9 1.0
C02 A:QFZ301 2.4 30.6 1.0
C04 A:QFZ301 2.4 29.9 1.0
F11 A:QFZ301 2.7 32.7 1.0
F09 A:QFZ301 2.8 31.8 1.0
O A:HOH462 3.0 31.3 1.0
OD1 A:ASN186 3.1 21.2 1.0
NE2 A:GLN148 3.5 28.0 1.0
O A:HOH501 3.6 33.6 1.0
C01 A:QFZ301 3.6 24.6 1.0
C05 A:QFZ301 3.6 25.4 1.0
C06 A:QFZ301 4.1 22.3 1.0
NE1 A:TRP192 4.1 23.9 1.0
CG A:ASN186 4.2 23.4 1.0
CD A:GLN148 4.5 31.3 1.0
F08 A:QFZ301 4.8 26.8 1.0
O12 A:QFZ301 4.8 23.4 1.0
O A:HOH541 4.8 37.1 1.0
CD1 A:TRP192 4.9 27.1 1.0
CE2 A:TRP192 4.9 27.4 1.0
O7N A:NAD302 4.9 22.1 1.0
ND2 A:ASN186 4.9 26.9 1.0
OE1 A:GLN148 5.0 24.9 1.0

Fluorine binding site 5 out of 5 in 6zde

Go back to Fluorine Binding Sites List in 6zde
Fluorine binding site 5 out of 5 in the 17BETA-Hydroxysteroid Dehydrogenase Type 14 Variant S205 in Complex with Pentafluorophenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of 17BETA-Hydroxysteroid Dehydrogenase Type 14 Variant S205 in Complex with Pentafluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:32.7
occ:1.00
 F11 A:QFZ301 0.0 32.7 1.0
C02 A:QFZ301 1.4 30.6 1.0
C03 A:QFZ301 2.4 29.9 1.0
C01 A:QFZ301 2.4 24.6 1.0
F10 A:QFZ301 2.7 35.1 1.0
O12 A:QFZ301 2.8 23.4 1.0
CG1 A:VAL143 3.2 20.5 1.0
OG A:SER141 3.5 17.3 1.0
C04 A:QFZ301 3.6 29.9 1.0
C06 A:QFZ301 3.6 22.3 1.0
CG2 A:VAL143 4.0 20.6 1.0
C05 A:QFZ301 4.1 25.4 1.0
CB A:VAL143 4.2 17.6 1.0
NE2 A:GLN148 4.3 28.0 1.0
C4N A:NAD302 4.3 20.1 1.0
OE1 A:GLN148 4.4 24.9 1.0
CD A:GLN148 4.5 31.3 1.0
C5N A:NAD302 4.5 21.1 1.0
F09 A:QFZ301 4.8 31.8 1.0
F07 A:QFZ301 4.8 23.5 1.0
CE2 A:TYR154 4.8 17.7 1.0
CD2 A:HIS93 4.8 20.5 1.0
OD1 A:ASN186 4.8 21.2 1.0
N A:VAL143 4.8 19.2 1.0
CB A:SER141 4.8 19.5 1.0
O A:GLY185 4.9 28.2 1.0

Reference:

M.J.Badran, A.Heine, G.Klebe. 17BETA-Hydroxysteroid Dehydrogenase Type 14 Variant S205 in Complex with Pentafluorophenol To Be Published.
Page generated: Fri Aug 2 05:09:01 2024

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