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Fluorine in PDB 5m8z: Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol

Protein crystallography data

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol, PDB code: 5m8z 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) 47.26 / 1.66
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 73.579, 73.579, 184.962, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 16.1

Other elements in 5m8z:

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol 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 2,3- Difluorophenol (pdb code 5m8z). 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 2,3- Difluorophenol, PDB code: 5m8z:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5m8z

Go back to Fluorine Binding Sites List in 5m8z
Fluorine binding site 1 out of 8 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol


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 2,3- Difluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F513

b:30.0
occ:0.56
 F1 A:ZTN513 0.0 30.0 0.6
F A:ZTN513 0.1 30.7 0.4
C4 A:ZTN513 1.3 22.9 0.4
C3 A:ZTN513 1.3 22.9 0.6
C3 A:ZTN513 2.2 22.5 0.4
C5 A:ZTN513 2.3 22.5 0.4
C2 A:ZTN513 2.3 20.7 0.6
C4 A:ZTN513 2.4 21.4 0.6
F1 A:ZTN513 2.6 26.6 0.4
F A:ZTN513 2.7 27.6 0.6
O A:ZTN513 2.7 26.4 0.6
O A:HOH674 2.9 36.4 1.0
O A:TYR102 3.0 21.1 1.0
O A:HOH694 3.1 23.2 1.0
CB A:TYR102 3.4 20.6 1.0
CZ A:PHE38 3.4 19.7 1.0
CE2 A:PHE38 3.4 17.9 1.0
C2 A:ZTN513 3.5 25.5 0.4
C A:ZTN513 3.5 24.3 0.4
C1 A:ZTN513 3.6 24.6 0.6
C5 A:ZTN513 3.6 26.8 0.6
C A:TYR102 3.8 20.3 1.0
CE1 A:PHE38 3.9 18.9 1.0
CD2 A:PHE38 3.9 19.6 1.0
C1 A:ZTN513 4.0 25.2 0.4
C A:ZTN513 4.1 24.8 0.6
CA A:TYR102 4.1 18.2 1.0
CD1 A:PHE38 4.3 19.2 1.0
CG A:PHE38 4.4 19.2 1.0
CG A:TYR102 4.4 19.3 1.0
O A:HOH960 4.5 26.8 1.0
CZ2 A:TRP56 4.6 29.2 1.0
O A:ZTN513 4.6 28.6 0.4
CH2 A:TRP56 4.8 26.2 1.0
N A:GLY103 4.9 18.7 1.0
CD1 A:TYR102 5.0 19.6 1.0
ND2 A:ASN272 5.0 17.4 1.0
CH2 A:TRP96 5.0 17.0 1.0
O A:HOH612 5.0 33.7 0.9

Fluorine binding site 2 out of 8 in 5m8z

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


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 2,3- Difluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F513

b:26.6
occ:0.44
 F1 A:ZTN513 0.0 26.6 0.4
F A:ZTN513 0.1 27.6 0.6
C4 A:ZTN513 1.3 21.4 0.6
C3 A:ZTN513 1.3 22.5 0.4
C3 A:ZTN513 2.3 22.9 0.6
C5 A:ZTN513 2.3 26.8 0.6
C2 A:ZTN513 2.3 25.5 0.4
C4 A:ZTN513 2.4 22.9 0.4
F1 A:ZTN513 2.6 30.0 0.6
F A:ZTN513 2.7 30.7 0.4
O A:HOH612 2.7 33.7 0.9
O A:ZTN513 2.7 28.6 0.4
OH A:TYR246 2.8 17.3 1.0
O A:HOH694 3.1 23.2 1.0
ND2 A:ASN272 3.3 17.4 1.0
CE2 A:PHE38 3.4 17.9 1.0
C2 A:ZTN513 3.5 20.7 0.6
C A:ZTN513 3.6 24.8 0.6
CZ A:PHE38 3.6 19.7 1.0
C1 A:ZTN513 3.6 25.2 0.4
C5 A:ZTN513 3.6 22.5 0.4
CZ A:TYR246 3.6 16.6 1.0
C1 A:ZTN513 4.0 24.6 0.6
C A:ZTN513 4.1 24.3 0.4
CE2 A:TYR246 4.2 16.4 1.0
CD2 A:PHE38 4.4 19.6 1.0
CE1 A:TYR246 4.4 17.6 1.0
O A:TYR102 4.5 21.1 1.0
CG A:ASN272 4.6 18.5 1.0
O A:ZTN513 4.6 26.4 0.6
C54 A:BVQ503 4.8 15.7 1.0
NH2 A:ARG305 4.8 16.0 1.0
CE1 A:PHE38 4.8 18.9 1.0
N24 A:BVQ503 4.8 17.2 1.0
CO A:BVQ503 4.9 17.3 1.0
C19 A:BVQ503 5.0 15.3 1.0

Fluorine binding site 3 out of 8 in 5m8z

Go back to Fluorine Binding Sites List in 5m8z
Fluorine binding site 3 out of 8 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol


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 2,3- Difluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F513

b:27.6
occ:0.56
 F A:ZTN513 0.0 27.6 0.6
F1 A:ZTN513 0.1 26.6 0.4
C4 A:ZTN513 1.3 21.4 0.6
C3 A:ZTN513 1.4 22.5 0.4
C3 A:ZTN513 2.3 22.9 0.6
C5 A:ZTN513 2.4 26.8 0.6
C2 A:ZTN513 2.4 25.5 0.4
C4 A:ZTN513 2.4 22.9 0.4
OH A:TYR246 2.7 17.3 1.0
F1 A:ZTN513 2.7 30.0 0.6
O A:ZTN513 2.7 28.6 0.4
F A:ZTN513 2.8 30.7 0.4
O A:HOH612 2.8 33.7 0.9
O A:HOH694 3.1 23.2 1.0
ND2 A:ASN272 3.2 17.4 1.0
CE2 A:PHE38 3.5 17.9 1.0
CZ A:TYR246 3.5 16.6 1.0
C2 A:ZTN513 3.6 20.7 0.6
C A:ZTN513 3.6 24.8 0.6
C1 A:ZTN513 3.7 25.2 0.4
C5 A:ZTN513 3.7 22.5 0.4
CZ A:PHE38 3.7 19.7 1.0
C1 A:ZTN513 4.1 24.6 0.6
CE2 A:TYR246 4.1 16.4 1.0
C A:ZTN513 4.2 24.3 0.4
CE1 A:TYR246 4.3 17.6 1.0
O A:TYR102 4.4 21.1 1.0
CG A:ASN272 4.5 18.5 1.0
CD2 A:PHE38 4.5 19.6 1.0
NH2 A:ARG305 4.7 16.0 1.0
O A:ZTN513 4.7 26.4 0.6
C54 A:BVQ503 4.7 15.7 1.0
N24 A:BVQ503 4.8 17.2 1.0
CE1 A:PHE38 4.9 18.9 1.0
C19 A:BVQ503 4.9 15.3 1.0
CO A:BVQ503 5.0 17.3 1.0

Fluorine binding site 4 out of 8 in 5m8z

Go back to Fluorine Binding Sites List in 5m8z
Fluorine binding site 4 out of 8 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol


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 2,3- Difluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F513

b:30.7
occ:0.44
 F A:ZTN513 0.0 30.7 0.4
F1 A:ZTN513 0.1 30.0 0.6
C4 A:ZTN513 1.3 22.9 0.4
C3 A:ZTN513 1.4 22.9 0.6
C3 A:ZTN513 2.3 22.5 0.4
C5 A:ZTN513 2.4 22.5 0.4
C2 A:ZTN513 2.4 20.7 0.6
C4 A:ZTN513 2.4 21.4 0.6
F1 A:ZTN513 2.7 26.6 0.4
O A:ZTN513 2.7 26.4 0.6
F A:ZTN513 2.8 27.6 0.6
O A:HOH674 2.8 36.4 1.0
O A:TYR102 2.9 21.1 1.0
O A:HOH694 3.1 23.2 1.0
CB A:TYR102 3.4 20.6 1.0
CZ A:PHE38 3.4 19.7 1.0
CE2 A:PHE38 3.4 17.9 1.0
C A:ZTN513 3.6 24.3 0.4
C2 A:ZTN513 3.6 25.5 0.4
C1 A:ZTN513 3.7 24.6 0.6
C5 A:ZTN513 3.7 26.8 0.6
C A:TYR102 3.8 20.3 1.0
CE1 A:PHE38 3.9 18.9 1.0
CD2 A:PHE38 3.9 19.6 1.0
C1 A:ZTN513 4.1 25.2 0.4
CA A:TYR102 4.1 18.2 1.0
C A:ZTN513 4.2 24.8 0.6
CD1 A:PHE38 4.3 19.2 1.0
CG A:PHE38 4.3 19.2 1.0
CG A:TYR102 4.4 19.3 1.0
O A:HOH960 4.4 26.8 1.0
CZ2 A:TRP56 4.6 29.2 1.0
O A:ZTN513 4.7 28.6 0.4
CH2 A:TRP56 4.8 26.2 1.0
N A:GLY103 4.8 18.7 1.0
CD1 A:TYR102 5.0 19.6 1.0
O1 A:GOL505 5.0 59.7 1.0
ND2 A:ASN272 5.0 17.4 1.0

Fluorine binding site 5 out of 8 in 5m8z

Go back to Fluorine Binding Sites List in 5m8z
Fluorine binding site 5 out of 8 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol


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 2,3- Difluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F507

b:22.7
occ:0.46
 F1 B:ZTN507 0.0 22.7 0.5
F B:ZTN507 0.2 24.7 0.5
C4 B:ZTN507 1.3 23.3 0.5
C3 B:ZTN507 1.3 23.2 0.5
C3 B:ZTN507 2.2 23.9 0.5
C2 B:ZTN507 2.3 25.3 0.5
C4 B:ZTN507 2.4 23.9 0.5
C5 B:ZTN507 2.4 25.9 0.5
F1 B:ZTN507 2.5 26.2 0.5
F B:ZTN507 2.7 25.9 0.5
O B:ZTN507 2.7 28.8 0.5
OH B:TYR246 2.8 20.3 1.0
O B:HOH713 3.1 23.8 1.0
CE2 B:PHE38 3.3 22.6 1.0
ND2 B:ASN272 3.3 17.8 1.0
C2 B:ZTN507 3.5 23.2 0.5
CZ B:PHE38 3.5 24.5 1.0
C1 B:ZTN507 3.6 24.2 0.5
C5 B:ZTN507 3.6 23.9 0.5
C B:ZTN507 3.6 24.4 0.5
CZ B:TYR246 3.7 16.9 1.0
C1 B:ZTN507 4.0 25.2 0.5
C B:ZTN507 4.1 25.1 0.5
CE2 B:TYR246 4.2 18.5 1.0
CD2 B:PHE38 4.3 21.4 1.0
O B:TYR102 4.4 22.0 1.0
CE1 B:TYR246 4.4 17.8 1.0
O B:ZTN507 4.6 29.6 0.5
CG B:ASN272 4.7 19.1 1.0
CE1 B:PHE38 4.7 21.2 1.0
C54 B:BVQ503 4.7 17.2 1.0
NH2 B:ARG305 4.8 18.8 1.0
N24 B:BVQ503 4.8 20.9 1.0
O B:HOH610 5.0 34.2 1.0
CO B:BVQ503 5.0 19.7 1.0

Fluorine binding site 6 out of 8 in 5m8z

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Fluorine binding site 6 out of 8 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol


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 2,3- Difluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F507

b:26.2
occ:0.46
 F1 B:ZTN507 0.0 26.2 0.5
F B:ZTN507 0.3 25.9 0.5
C4 B:ZTN507 1.3 23.9 0.5
C3 B:ZTN507 1.3 23.9 0.5
C3 B:ZTN507 2.2 23.2 0.5
C2 B:ZTN507 2.4 23.2 0.5
C4 B:ZTN507 2.4 23.3 0.5
C5 B:ZTN507 2.4 23.9 0.5
F1 B:ZTN507 2.5 22.7 0.5
F B:ZTN507 2.7 24.7 0.5
O B:ZTN507 2.8 29.6 0.5
O B:HOH610 2.8 34.2 1.0
O B:HOH713 3.1 23.8 1.0
O B:TYR102 3.2 22.0 1.0
CZ B:PHE38 3.2 24.5 1.0
CE2 B:PHE38 3.3 22.6 1.0
C2 B:ZTN507 3.5 25.3 0.5
CB B:TYR102 3.5 20.0 1.0
C B:ZTN507 3.6 25.1 0.5
C1 B:ZTN507 3.6 25.2 0.5
C5 B:ZTN507 3.6 25.9 0.5
CE1 B:PHE38 3.7 21.2 1.0
CD2 B:PHE38 3.7 21.4 1.0
C B:TYR102 3.9 18.4 1.0
C1 B:ZTN507 4.0 24.2 0.5
C B:ZTN507 4.1 24.4 0.5
CD1 B:PHE38 4.1 22.7 1.0
CG B:PHE38 4.2 21.9 1.0
CA B:TYR102 4.3 19.4 1.0
O B:HOH890 4.4 27.6 1.0
O B:ZTN507 4.5 28.8 0.5
CG B:TYR102 4.6 22.7 1.0
CZ2 B:TRP56 4.7 39.8 1.0
CH2 B:TRP56 4.7 32.7 1.0
ND2 B:ASN272 5.0 17.8 1.0
N B:GLY103 5.0 18.8 1.0

Fluorine binding site 7 out of 8 in 5m8z

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Fluorine binding site 7 out of 8 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 2,3- Difluorophenol


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 2,3- Difluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F507

b:25.9
occ:0.46
 F B:ZTN507 0.0 25.9 0.5
F1 B:ZTN507 0.3 26.2 0.5
C4 B:ZTN507 1.3 23.9 0.5
C3 B:ZTN507 1.4 23.9 0.5
C2 B:ZTN507 2.3 23.2 0.5
C3 B:ZTN507 2.3 23.2 0.5
C5 B:ZTN507 2.4 23.9 0.5
C4 B:ZTN507 2.5 23.3 0.5
O B:ZTN507 2.6 29.6 0.5
F1 B:ZTN507 2.7 22.7 0.5
O B:HOH610 2.7 34.2 1.0
F B:ZTN507 2.9 24.7 0.5
O B:TYR102 3.0 22.0 1.0
O B:HOH713 3.2 23.8 1.0
CB B:TYR102 3.2 20.0 1.0
CZ B:PHE38 3.5 24.5 1.0
CE2 B:PHE38 3.6 22.6 1.0
C2 B:ZTN507 3.6 25.3 0.5
C B:ZTN507 3.6 25.1 0.5
C1 B:ZTN507 3.6 25.2 0.5
C B:TYR102 3.7 18.4 1.0
C5 B:ZTN507 3.7 25.9 0.5
CE1 B:PHE38 3.9 21.2 1.0
CD2 B:PHE38 4.0 21.4 1.0
CA B:TYR102 4.0 19.4 1.0
C1 B:ZTN507 4.1 24.2 0.5
C B:ZTN507 4.2 24.4 0.5
CG B:TYR102 4.3 22.7 1.0
CD1 B:PHE38 4.3 22.7 1.0
CG B:PHE38 4.3 21.9 1.0
O B:HOH890 4.4 27.6 1.0
CZ2 B:TRP56 4.7 39.8 1.0
O B:ZTN507 4.7 28.8 0.5
CH2 B:TRP56 4.7 32.7 1.0
N B:GLY103 4.8 18.8 1.0
CD1 B:TYR102 4.8 20.4 1.0
O1 B:GOL504 5.0 60.6 1.0

Fluorine binding site 8 out of 8 in 5m8z

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


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 2,3- Difluorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F507

b:24.7
occ:0.46
 F B:ZTN507 0.0 24.7 0.5
F1 B:ZTN507 0.2 22.7 0.5
C4 B:ZTN507 1.4 23.3 0.5
C3 B:ZTN507 1.4 23.2 0.5
C2 B:ZTN507 2.3 25.3 0.5
C3 B:ZTN507 2.3 23.9 0.5
C5 B:ZTN507 2.4 25.9 0.5
C4 B:ZTN507 2.5 23.9 0.5
O B:ZTN507 2.6 28.8 0.5
OH B:TYR246 2.6 20.3 1.0
F1 B:ZTN507 2.7 26.2 0.5
F B:ZTN507 2.9 25.9 0.5
O B:HOH713 3.2 23.8 1.0
ND2 B:ASN272 3.3 17.8 1.0
CE2 B:PHE38 3.5 22.6 1.0
CZ B:TYR246 3.5 16.9 1.0
C1 B:ZTN507 3.6 24.2 0.5
C B:ZTN507 3.6 24.4 0.5
C2 B:ZTN507 3.6 23.2 0.5
CZ B:PHE38 3.7 24.5 1.0
C5 B:ZTN507 3.7 23.9 0.5
CE2 B:TYR246 4.1 18.5 1.0
C1 B:ZTN507 4.1 25.2 0.5
C B:ZTN507 4.1 25.1 0.5
CE1 B:TYR246 4.3 17.8 1.0
CD2 B:PHE38 4.5 21.4 1.0
O B:TYR102 4.6 22.0 1.0
CG B:ASN272 4.6 19.1 1.0
NH2 B:ARG305 4.6 18.8 1.0
O B:ZTN507 4.7 29.6 0.5
C54 B:BVQ503 4.8 17.2 1.0
N24 B:BVQ503 4.8 20.9 1.0
CE1 B:PHE38 4.8 21.2 1.0
CO B:BVQ503 4.9 19.7 1.0
C19 B:BVQ503 4.9 19.1 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 11:38:37 2024

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