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Fluorine in PDB 5m90: Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol

Protein crystallography data

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol, PDB code: 5m90 was solved by C.Kunze, M.Bommer, W.R.Hagen, M.Uksa, H.Dobbek, T.Schubert, G.Diekert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.30 / 1.60
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 73.631, 73.631, 185.137, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 16.7

Other elements in 5m90:

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol also contains other interesting chemical elements:

Cobalt (Co) 2 atoms
Iron (Fe) 16 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol (pdb code 5m90). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol, PDB code: 5m90:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5m90

Go back to Fluorine Binding Sites List in 5m90
Fluorine binding site 1 out of 8 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F509

b:28.6
occ:0.70
 F2 A:JIF509 0.0 28.6 0.7
C3 A:JIF509 1.4 23.2 0.7
C4 A:JIF509 2.3 17.1 0.7
C2 A:JIF509 2.4 23.7 0.7
F1 A:JIF509 2.7 24.5 0.7
CH2 A:TRP56 3.0 24.1 1.0
CZ2 A:TRP56 3.0 28.5 1.0
CB A:TYR102 3.0 18.4 1.0
O A:HOH878 3.3 36.0 1.0
CG A:TYR102 3.3 18.5 1.0
C5 A:JIF509 3.6 18.7 0.7
C1 A:JIF509 3.6 22.2 0.7
CD2 A:TYR102 3.9 20.1 1.0
CD1 A:TYR102 3.9 18.3 1.0
CE1 A:PHE38 4.1 19.6 1.0
C A:JIF509 4.1 25.3 0.7
O A:TYR102 4.3 18.3 1.0
CZ3 A:TRP56 4.3 23.1 1.0
CZ A:PHE38 4.3 19.0 1.0
CE2 A:TRP56 4.4 27.9 1.0
CA A:TYR102 4.4 16.8 1.0
CD1 A:PHE38 4.4 17.0 1.0
O1 A:GOL504 4.5 61.5 1.0
CZ3 A:TRP376 4.6 19.1 1.0
F A:JIF509 4.7 28.7 0.7
O A:JIF509 4.7 24.1 0.7
C A:TYR102 4.8 19.4 1.0
CE2 A:TYR102 4.8 17.9 1.0
CE1 A:TYR102 4.8 20.6 1.0
CE2 A:PHE38 4.9 18.0 1.0
CG A:PHE38 5.0 19.0 1.0

Fluorine binding site 2 out of 8 in 5m90

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Fluorine binding site 2 out of 8 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F509

b:24.5
occ:0.70
 F1 A:JIF509 0.0 24.5 0.7
C4 A:JIF509 1.3 17.1 0.7
C3 A:JIF509 2.4 23.2 0.7
C5 A:JIF509 2.4 18.7 0.7
F2 A:JIF509 2.7 28.6 0.7
F A:JIF509 2.7 28.7 0.7
CE1 A:TYR382 3.0 18.5 1.0
CD1 A:TYR382 3.1 18.6 1.0
C2 A:JIF509 3.6 23.7 0.7
C A:JIF509 3.6 25.3 0.7
CH2 A:TRP56 3.7 24.1 1.0
CZ A:TYR382 3.7 16.3 1.0
CZ2 A:TRP96 3.8 14.3 1.0
CD1 A:TYR102 3.8 18.3 1.0
CZ3 A:TRP376 3.8 19.1 1.0
CG A:TYR382 3.9 17.0 1.0
C1 A:JIF509 4.1 22.2 0.7
CG A:TYR102 4.1 18.5 1.0
CH2 A:TRP96 4.2 16.8 1.0
CE1 A:TYR102 4.2 20.6 1.0
CE2 A:TYR382 4.3 17.1 1.0
OH A:TYR382 4.3 18.7 1.0
CE3 A:TRP376 4.4 22.4 1.0
CD2 A:TYR382 4.4 14.7 1.0
CZ3 A:TRP56 4.4 23.1 1.0
CB A:TYR102 4.5 18.4 1.0
CZ2 A:TRP56 4.6 28.5 1.0
O A:HOH806 4.7 19.8 1.0
O A:HOH965 4.7 32.2 1.0
CE2 A:TRP96 4.7 14.5 1.0
CB A:TYR382 4.8 16.6 1.0
CD2 A:TYR102 4.8 20.1 1.0
CZ A:TYR102 4.9 22.0 1.0
CH2 A:TRP376 4.9 18.1 1.0

Fluorine binding site 3 out of 8 in 5m90

Go back to Fluorine Binding Sites List in 5m90
Fluorine binding site 3 out of 8 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F509

b:28.7
occ:0.70
 F A:JIF509 0.0 28.7 0.7
C5 A:JIF509 1.3 18.7 0.7
C4 A:JIF509 2.3 17.1 0.7
C A:JIF509 2.3 25.3 0.7
F1 A:JIF509 2.7 24.5 0.7
CG A:TYR382 2.9 17.0 1.0
CD2 A:TYR382 3.1 14.7 1.0
CD1 A:TYR382 3.3 18.6 1.0
CZ2 A:TRP96 3.4 14.3 1.0
CB A:TYR382 3.4 16.6 1.0
CE2 A:TYR382 3.6 17.1 1.0
C3 A:JIF509 3.6 23.2 0.7
CG2 A:THR242 3.6 14.6 1.0
C1 A:JIF509 3.6 22.2 0.7
CH2 A:TRP96 3.6 16.8 1.0
CE1 A:TYR382 3.8 18.5 1.0
CZ A:TYR382 3.9 16.3 1.0
CZ3 A:TRP376 4.0 19.1 1.0
C2 A:JIF509 4.1 23.7 0.7
CH2 A:TRP376 4.3 18.1 1.0
CE2 A:TYR246 4.5 18.4 1.0
F2 A:JIF509 4.7 28.6 0.7
CE2 A:TRP96 4.7 14.5 1.0
O A:JIF509 4.7 24.1 0.7
CB A:THR242 4.8 14.4 1.0
CA A:TYR382 4.8 16.8 1.0
OH A:TYR382 4.9 18.7 1.0
N40 A:BVQ503 4.9 17.3 1.0
C38 A:BVQ503 4.9 19.0 1.0
CE3 A:TRP376 5.0 22.4 1.0
O39 A:BVQ503 5.0 18.3 1.0

Fluorine binding site 4 out of 8 in 5m90

Go back to Fluorine Binding Sites List in 5m90
Fluorine binding site 4 out of 8 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F507

b:36.8
occ:0.82
 F2 B:JIF507 0.0 36.8 0.8
C3 B:JIF507 1.4 31.5 0.8
C4 B:JIF507 2.3 27.3 0.8
C2 B:JIF507 2.4 30.9 0.8
F1 B:JIF507 2.7 33.6 0.8
O B:HOH885 2.8 48.7 1.0
CB B:TYR102 3.1 20.0 1.0
CH2 B:TRP56 3.3 31.6 1.0
CZ2 B:TRP56 3.4 30.6 1.0
CG B:TYR102 3.5 20.4 1.0
C5 B:JIF507 3.6 25.9 0.8
C1 B:JIF507 3.6 30.6 0.8
CD2 B:TYR102 3.9 20.4 1.0
C B:JIF507 4.1 30.6 0.8
CD1 B:TYR102 4.1 20.6 1.0
CE1 B:PHE38 4.1 19.3 1.0
CD1 B:PHE38 4.3 21.9 1.0
O B:TYR102 4.4 21.9 1.0
CZ B:PHE38 4.4 23.6 1.0
CA B:TYR102 4.5 18.9 1.0
CZ3 B:TRP56 4.6 30.7 1.0
CG B:PHE38 4.7 24.5 1.0
O B:JIF507 4.7 25.1 0.8
CE2 B:PHE38 4.8 20.5 1.0
CE2 B:TRP56 4.8 26.1 1.0
CZ3 B:TRP376 4.8 23.8 1.0
C B:TYR102 4.9 20.1 1.0
CE2 B:TYR102 4.9 19.2 1.0
CD2 B:PHE38 4.9 19.2 1.0

Fluorine binding site 5 out of 8 in 5m90

Go back to Fluorine Binding Sites List in 5m90
Fluorine binding site 5 out of 8 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F507

b:33.6
occ:0.82
 F1 B:JIF507 0.0 33.6 0.8
C4 B:JIF507 1.3 27.3 0.8
C3 B:JIF507 2.4 31.5 0.8
C5 B:JIF507 2.4 25.9 0.8
F2 B:JIF507 2.7 36.8 0.8
CE1 B:TYR382 3.2 19.1 1.0
CD1 B:TYR382 3.5 20.1 1.0
C2 B:JIF507 3.6 30.9 0.8
CD1 B:TYR102 3.6 20.6 1.0
C B:JIF507 3.6 30.6 0.8
CZ B:TYR382 3.9 20.3 1.0
CG B:TYR102 3.9 20.4 1.0
CZ2 B:TRP96 4.0 17.6 1.0
CH2 B:TRP56 4.0 31.6 1.0
CE1 B:TYR102 4.0 20.3 1.0
CZ3 B:TRP376 4.0 23.8 1.0
C1 B:JIF507 4.1 30.6 0.8
CB B:TYR102 4.3 20.0 1.0
CG B:TYR382 4.3 19.4 1.0
CH2 B:TRP96 4.3 14.8 1.0
OH B:TYR382 4.4 18.6 1.0
CD2 B:TYR102 4.5 20.4 1.0
O B:HOH697 4.5 21.3 1.0
O B:HOH903 4.5 31.6 1.0
CE3 B:TRP376 4.5 22.0 1.0
CZ B:TYR102 4.6 21.2 1.0
CE2 B:TYR382 4.6 18.3 1.0
CZ3 B:TRP56 4.7 30.7 1.0
CD2 B:TYR382 4.8 17.7 1.0
CE2 B:TYR102 4.8 19.2 1.0
CE2 B:TRP96 4.9 15.3 1.0
CZ2 B:TRP56 4.9 30.6 1.0

Fluorine binding site 6 out of 8 in 5m90

Go back to Fluorine Binding Sites List in 5m90
Fluorine binding site 6 out of 8 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F508

b:36.1
occ:0.68
 F2 B:JIF508 0.0 36.1 0.7
C3 B:JIF508 1.4 28.6 0.7
C4 B:JIF508 2.3 28.4 0.7
C2 B:JIF508 2.4 32.1 0.7
O B:HOH872 2.5 39.5 1.0
F1 B:JIF508 2.7 31.8 0.7
O B:HOH857 3.1 32.2 1.0
OE2 B:GLU191 3.2 30.1 0.4
CA B:ILE190 3.3 21.5 1.0
O B:GLU189 3.3 26.4 1.0
CG B:GLU191 3.4 26.9 0.4
N B:GLU191 3.5 22.9 0.6
N B:GLU191 3.5 23.3 0.4
C5 B:JIF508 3.6 25.8 0.7
C B:ILE190 3.6 22.0 1.0
C1 B:JIF508 3.6 33.1 0.7
CD B:GLU191 3.8 27.9 0.4
N B:ILE190 3.9 20.9 1.0
C B:GLU189 3.9 24.9 1.0
CG B:GLU191 4.1 26.8 0.6
C B:JIF508 4.1 21.8 0.7
CB B:GLU191 4.4 26.6 0.4
O B:ILE190 4.4 22.3 1.0
CB B:ILE190 4.5 23.1 1.0
CA B:GLU191 4.5 24.9 0.4
CA B:GLU191 4.6 24.5 0.6
CB B:GLU191 4.6 26.0 0.6
F B:JIF508 4.7 31.8 0.7
O B:JIF508 4.7 46.4 0.7
CG2 B:ILE190 4.9 25.5 1.0
OE2 B:GLU191 4.9 28.9 0.6
OE1 B:GLU191 5.0 29.3 0.4

Fluorine binding site 7 out of 8 in 5m90

Go back to Fluorine Binding Sites List in 5m90
Fluorine binding site 7 out of 8 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F508

b:31.8
occ:0.68
 F1 B:JIF508 0.0 31.8 0.7
C4 B:JIF508 1.3 28.4 0.7
C3 B:JIF508 2.3 28.6 0.7
C5 B:JIF508 2.4 25.8 0.7
F2 B:JIF508 2.7 36.1 0.7
F B:JIF508 2.7 31.8 0.7
C B:ILE190 3.3 22.0 1.0
O B:ILE190 3.3 22.3 1.0
N B:ILE190 3.3 20.9 1.0
C B:GLU189 3.5 24.9 1.0
CA B:ILE190 3.5 21.5 1.0
C2 B:JIF508 3.6 32.1 0.7
C B:JIF508 3.6 21.8 0.7
O B:GLU189 3.6 26.4 1.0
CG1 B:VAL174 3.7 23.5 1.0
N B:GLU191 3.8 22.9 0.6
CG2 B:VAL174 3.8 22.4 1.0
CB B:GLU189 3.8 20.5 1.0
N B:GLU191 3.8 23.3 0.4
CG B:GLU191 3.9 26.9 0.4
C1 B:JIF508 4.1 33.1 0.7
CB B:VAL174 4.2 21.6 1.0
CG B:GLU191 4.2 26.8 0.6
CA B:GLU189 4.3 22.2 1.0
CA B:VAL174 4.4 19.3 1.0
CA B:GLU191 4.5 24.5 0.6
CA B:GLU191 4.5 24.9 0.4
CG2 B:VAL34 4.6 23.3 1.0
O B:HOH872 4.8 39.5 1.0
OE2 B:GLU191 4.8 30.1 0.4
CB B:GLU191 4.8 26.6 0.4
CD B:GLU191 4.9 27.9 0.4
OE1 B:GLU189 4.9 26.9 1.0
CB B:GLU191 5.0 26.0 0.6

Fluorine binding site 8 out of 8 in 5m90

Go back to Fluorine Binding Sites List in 5m90
Fluorine binding site 8 out of 8 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 3,4,5- Trifluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F508

b:31.8
occ:0.68
 F B:JIF508 0.0 31.8 0.7
C5 B:JIF508 1.3 25.8 0.7
C4 B:JIF508 2.3 28.4 0.7
C B:JIF508 2.4 21.8 0.7
F1 B:JIF508 2.7 31.8 0.7
N2 B:BEN506 3.1 33.8 1.0
C B:BEN506 3.4 39.3 1.0
N1 B:BEN506 3.5 35.2 1.0
C3 B:JIF508 3.6 28.6 0.7
C1 B:JIF508 3.6 33.1 0.7
OE1 B:GLU189 3.6 26.9 1.0
CG1 B:VAL174 3.8 23.5 1.0
CG2 B:VAL174 3.8 22.4 1.0
CB B:THR39 3.9 23.5 1.0
CG2 B:VAL34 4.0 23.3 1.0
O B:THR39 4.0 27.1 1.0
C2 B:JIF508 4.1 32.1 0.7
C1 B:BEN506 4.2 39.5 1.0
CB B:GLU189 4.3 20.5 1.0
CG2 B:THR39 4.3 21.3 1.0
CB B:VAL174 4.4 21.6 1.0
C6 B:BEN506 4.5 46.8 1.0
CA B:THR39 4.6 22.5 1.0
CD B:GLU189 4.6 26.3 1.0
C B:THR39 4.6 24.6 1.0
F2 B:JIF508 4.7 36.1 0.7
O B:JIF508 4.7 46.4 0.7
OG1 B:THR39 4.8 22.5 1.0
CB B:VAL34 4.9 22.8 1.0

Reference:

C.Kunze, M.Bommer, W.R.Hagen, M.Uksa, H.Dobbek, T.Schubert, G.Diekert. Cobamide-Mediated Enzymatic Reductive Dehalogenation Via Long-Range Electron Transfer. Nat Commun V. 8 15858 2017.
ISSN: ESSN 2041-1723
PubMed: 28671181
DOI: 10.1038/NCOMMS15858
Page generated: Thu Aug 1 11:39:04 2024

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